link.springer.com1… · XLS file · Web view · 2014-03-18Wright SI, Charlesworth B. The HKA...

Year count Live Dead Other %live % unavailab1998 8 3 4 1 0.38 63%1999 6 5 1 0 0.83 17%2000 9 4 4 1 0.44 56%2001 28 20 8 0 0.71 29%2002 78 71 6 0 0.91 9%2003 86 69 17 0 0.80 20%2004 172 158 13 1 0.92 8%2005 240 215 24 1 0.90 10%

2006 (1/31) 28 27 1 0 0.96 4%

Totals 655 572 78 4 0.76 24%

Year Journal Non-Journal1998 0 41999 0 12000 1 32001 0 82002 0 62003 0 172004 0 132005 4 21

Totals 5 73

1 2 3 4 5 6 7 80

50

100

150

200

250

Supplementary Data Availability

Accessible Inaccessible

Year

# o

f M

anus

crip

ts

1 2 3 4 5 6 7 80

50

100

150

200

250

300

0%

10%

20%

30%

40%

50%

60%

70%

8 6 928

78 86

172

240

63%

17%

56%

29%

9%

20%

8%10%

# of Manuscripts with Supplementary Links vs % Un-available

# Manuscripts% Unavailable

Year

# of

Man

uscr

ipts

% U

nava

ilabl

e

1 2 3 4 5 6 7 80

5

10

15

20

25

Location of Inaccessible Supplementary Data

Non-Journal website Journal web-site

Year

# o

f Man

uscr

ipts

1 2 3 4 5 6 7 80

50

100

150

200

250



Year

# o

f M

anus

crip

ts

1 2 3 4 5 6 7 80

50

100

150

200

250

300

0%

10%

20%

30%

40%

50%

60%

70%

8 6 928

78 86

172

240

63%

17%

56%

29%

9%

20%

8%10%

# of Manuscripts with Supplementary Links vs % Un-available

# Manuscripts% Unavailable

Year

# of

Man

uscr

ipts

% U

nava

ilabl

e

Dead JournaDead Non-journal0 4 00 1 01 3 -10 8 00 6 00 17 00 13 04 21 -3

-1

5

1 2 3 4 5 6 7 80

50

100

150

200

250



Year

# o

f M

anus

crip

ts

1 2 3 4 5 6 7 80

50

100

150

200

250



Year

# o

f M

anus

crip

ts

Bioinformatics 71 3 2 52Nucleic Acids Researc 61 59 0 0Genetics 30 14 10 6

Total 162 76 12 58

% TotalBioinformatics 99% 4% 3% 73%Nucleic Acids Researc 100% 97% 0% 0%Genetics 100% 47% 33% 20%

Total Unique (9/1/04-12/31/04

Accessible Journal

inaccessible Journal

Accessible Non- Journal

% Accessible @ Journal

% Inaccesible @ Journal

% Accesible Non-Journal

1 2 30%

20%

40%

60%

80%

100%

120%

4%

97%

47%

3% 0%

33%

73%

0%

20%18%

3% 0%

Accessiblity by Location of Supplementary Resources

Accessible at journal Inaccessible at journalAccessible at other location Inaccessible at other location

13 21% 79% 18%2 3% 97% 3%0 33% 67% 0%

15

18%3%0%

Inaccessible non-journal

Total Inaccessible %

Total Accessible %

Total inaccessible Non- Journal

% Accessible non-journal

3%0%

33%

Total Inaccessible Journal

submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). SUPPLEMENTARY INFORMATION: Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html CONTACT: (kworley,culpep)@bcm.tmc.edu PMver architecture of the asthma and allergy gene database. AVAILABILITY: Database and server templates are available on request from the first author. Supplementary Information : The URL of the asthma and allergy gene database is http://cooke.gsf.de PMID: 9918958 [PubMed - indexed for MEDLINE]evaluated (optimally, the result of a MEDLINE search by keyword) and the results are returned in the form of Web pages for keywords, sentences and s. SUPPLEMENTARY INFORMATION: Web pages containing full information on the examples mentioned in the text are available at: http://www.cnb.uam.es/ approx it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? SUPPLEMENTARY INFORMATION: A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de CONTuam.es/EUCLID, with the corresponding dictionaries for the generation of three, eight and 14 functional classes. Contact: E-mail: [email protected] SUPPLEMENTARY INFORMATION: The results of the EUCLID classification of different genomes are available at http://www.sander.ebi.ac. uk/genequiz/. A dective interface for ease of querying the database and displaying maps. AVAILABILITY: The extensions can be obtained via ftp.sanger.ac.uk/pub/zmapper. Supplementary information: The User's Manual can be viewed from http:/www.sanger.ac.uk/Users/cari/Z.shtml. CONTACT: [email protected] PMID: 9694993 [Pecular modelling and 3D survey. AVAILABILITY: TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito CONTACT: [email protected] Supplementary information: http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html PMID: 9545453 [PubMed - indexed for MEDLINE] (when possible) relative atomic or formula masses, and mass/amount and amount/mass concentration conversion factors. This paper gives background and supplementary information which should be borne in mind when providing interpretation or using the Web table. Supplementary tables listing (i) common

Live? Journal? Reference

No no 1: Bioinformatics. 1998;14(10):890-1.

Yes no 2: Bioinformatics. 1998;14(9):827-8.

yes no 3: Bioinformatics. 1998;14(7):600-7.


yes no 5: Bioinformatics. 1998;14(6):542-3.



No Link no 8: Ann Clin Biochem. 1998 Mar;35 ( Pt 2):261-7.

BEAUTY-X: enhanced BLAST searches for DNA queries.

An Internet linkage and mutation database for the complex phenotype asthma.

Automatic extraction of keywords from scientific text: application to the

Comprehensive, comprehensible, distributed and intelligent databases: current

EUCLID: automatic classification of proteins in functional classes by their

Z extensions to the RHMAPPER package.

Incremental threading optimization (TITO) to help alignment and modelling of

Guidelines for the interpretation of analytical toxicology results and unit of

Worley KC, Culpepper P, Wiese BA, Smith RF.

Wjst M, Immervoll T.

knowledge domain of protein families.

status.

database annotations.

Soderlund C, Lau T, Deloukas P.

remote homologues.

measurement conversion factors.

PMID: 9927720 [PubMed - indexed for MEDLINE]








Reference

genome.org

rated by an example taken from sugar metabolism. AVAILABILITY: METATOOL is available from ftp://bmsdarwin.brookes.ac. uk/pub/software/ibmpc/metatool. SUPPLEMENTARY INFORMATION: http://www. biologie.hu-berlin.de/biophysics/Theory/tpfeiffer/metatoo l.html PMID: 10222413 [PubMed - indexed for MEDLINE]WEET is accessible via the Internet at http://www.dkfz-heidelberg.de/spec/. CONTACT: a. [email protected] or w.vonderlieth@ dkfz-heidelberg.de SUPPLEMENTARY INFORMATION: The current version of SWEET generates only one conformation out of a manifold. Several authors have analysed possible confITY: http://www.icgeb.trieste.it/domain. Mirror site is available at http://sbase.abc.hu/domain. A standalone programme will be available on request. SUPPLEMENTARY INFORMATION: A series of help files is available at the above addresses. PMID: 10320404 [PubMed - indexed for MEDLINE]uss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies. [This paper contains supplementary data that can be found at http://www.genome.org [corrected]]. PMID: 10508839 [PubMed - indexed for MEDLINE]

Live?

No no 4: Bioinforma

yes no 2: Bioinforma



yes yes 1: Genome Reyes yes 1: Genome Res

Journal?

METATOOL: for studying metabolic networks.

SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.

The domain-server: direct prediction of protein domain-homologies from BLAST

E-CELL: software environment for whole-cell simulation.

Erratum in:A 3-Mb high-resolution BAC/PAC contig of 12q22 encompassing the 830-kb conseminimal deletion in male germ cell tumors.

Pfeiffer T, Sanchez-Valdenebro I, Nuno JC, Montero F, Schuster S.

Bohne A, Lang E, von der Lieth CW.

search.

Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K,

Genome Res 1999 Nov;9(11):1156.Murty VV, Montgomery K, Dutta S, Bala S, Renault B, Bosl GJ, Kucherlapati R,Chaganti RS.

Reference

tp from snipe.pharmacy. ualberta.ca/pub. The training

methods may be extended to characterize the evolution of any phylogenetically

VAILABILITY: Secondary structure alignment homepage at http://lutece.rutgers.edu/ssas CONTACT: [email protected]; [email protected] Supplementary Information: Genome sequence/structure alignment results at http://lutece.rutgers.edu/ss_fold_predictions. PMID: 11159310 [PubMed - inde

red for AZ expression. However, no homolog was detected in the completed genome of the budding yeast Saccharomyces cerevisiae. Procedural details and supplementary information can be found at http://itsa.ucsf.edu/ approximately czhu/AZ. PMID: 10871270 [PubMed - indexed for MEDLINE]erimental crosses of plants or animals. AVAILABILITY: The add-on packages are freely available at http://www.mathsource.com/cgi-bin/msitem?0209-30 4. SUPPLEMENTARY INFORMATION: A tutorial notebook file is included with the packages at the mathsource site. PMID: 10869043 [PubMed - indexed for MEDLINE

ts; for N(2)H(4), assignments have been found for 14 new FIRL transition systems and verified for five others. Lists have been produced (deposited as supplementary data with the JMS archive reached at www.idealibrary.com or available on request from the authors) of CH(3)OH and N(2)H(4) FIRL lines poAVAILABILITY: The model.it server is freely available at http://www.icgeb.trieste.it/dna/ CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: a series of help files is available at the above address. PMID: 11269231 [PubMed - indexed for MEDLINE]ures used, and major features of the revised charts. METHODS: Data from five national health examination surveys collected from 1963 to 1994 and five supplementary data sources were combined to establish an analytic growth chart data set. A variety of statistical procedures were used to produce smoovarious origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. SUPPLEMENTARY INFORMATION: The additional bibliography and list of Internet resources on bioinorganic chemistry are available at http://www.ebi.ac.uk/

Live? Journal?

No no 3: Bioinformatics. 2000 Nov;16(11):988-1002.

no no 6: Bioinformatics. 2000 May;16(5):478-81.

No No 7: Bioinformatics. 2000 Apr;16(4):408-10.No yes 1 : Bioinformatics. 2000 May;16(5):425-38.

no link no 5: J Mol Spectrosc. 2000 Nov;204(1):48-54.

yes no 1: Bioinformatics. 2000 Nov;16(11):1044-5.

yes no 2: Adv Data. 2000 Jun 8;(314):1-27.

yes no 4: Bioinformatics. 2000 Oct;16(10):851-64.yes no 2: Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):

Iterative sequence/secondary structure search for protein homologs: comparison

A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces

Mathematica packages for simulation of experimental genetics.Prediction of genetic structure in eukaryotic DNA using reference point logistic

LaseRitz: Far-Infrared Laser Line Assignment and Prediction by the Ritz

Model.it: building three dimensional DNA models from sequence data.

CDC growth charts: United States.

Bioinorganic motifs: towards functional classification of metalloproteins.An archaeal genomic signature.

with amino acid sequence alignments and application to fold recognition in

pombe but not detected in budding yeast Saccharomyces cerevisiae.

Manly KF.Hooper PM, Zhang H, Wishart DS.

Combination Principle, with Application to Methanol and Hydrazine.

Vlahovicek K, Pongor S.

Kuczmarski RJ, Ogden CL, Grummer-Strawn LM, Flegal KM, Guo SS, Wei R, Mei Z,

Degtyarenko K.Graham DE, Overbeek R, Olsen GJ, Woese CR.



PMID: 10869043 [PubMed - indexed for MEDLINE]PMID: 10871265 [PubMed - indexed for MEDLINE]

PMID: 11034841 [PubMed - as supplied by publisher]




Referencethe command-line and for the www-version are available on request. CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html. PMID: 117512vailable at http://www.stat.washington.edu/fraley/mclust. The software for the diagonal model is under development. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: http://www.cs.washington.edu/homes/kayee/model. PMID: 11673243 [PubMed - indexed for MEDLINE]h a common threading tool making their comparisons easier. AVAILABILITY: The meta-server is available free at http://www.infobiosud.cnrs.fr/bioserver SUPPLEMENTARY INFORMATION: http://www.infobiosud.cnrs.fr/bioserver/hah1.html Publication Types: Validation Studies PMID: 11524382 [PubMed - indexed fo

lts in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Arlequin is available at:equence to structure threading. AVAILABILITY: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html. SUPPLEMENTARY INFORMATION: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary matequence to structure threading. AVAILABILITY: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html. SUPPLEMENTARY INFORMATION: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary matcan bind to several HLA-DR alleles. AVAILABILITY: The server is available at http://www.imtech.res.in/raghava/propred/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.imtech.res.in/raghava/propred/page3.html PMID: 11751237 [PubMed - indexed for MEDLINE]b-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc. PMID: 11751236 [PubMedat http://BioInfo.PL/ToolShop/. The administrator should be contacted to couple the tested server to the evaluation suite. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The evaluation procedures are similar to those implemented in the continuous online server evaluation program, LiveBench. Awww.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html. CONTACT: [email protected]; [email protected]; [email protected] Supplementary information: Additional data from the cross-genomic comparisons examined in the discussion section are linked from http://www.biosci.ohi gene products were 0-6% different in amino acid sequence, but the differences did not alter residues thought to be involved in protein function (see supplementary data at http://mic.sgmjournals.org or http://www.uic.edu/depts/mcmi/individual/gupta/index.htm). For representative IncH plasmid R476b ahydrogen. AVAILABILITY: Programs available from http://geometry.molmovdb.org. CONTACT: [email protected]; [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Available at http://geometry.molmovdb.org. PMID: 11673240 [PubMed - indexed for MEDLINE]TACT: [email protected]; [email protected]; [email protected]; [email protected]; [email protected]. SUPPLEMENTARY INFORMATION: http://www.zaik.uni-koeln.de/~schliep/ProtClust.html. PMID: 11673238 [PubMed - indexed for MEDLINE]

e apex may be proportional to stress on the cell wall. We propose that turgor-pressure wall stress modulates local apical cell wall growth rates. A supplementary model, relating cell wall curvature and growth rate in the cut-interwhorl, characterizes how the stalk's final dimensions and nearly cylure, but we suggest that secondary structure profiles may also be useful in the future. The classification forms a framework around which a wealth of supplementary information about the peptidases is organized. This includes images of three-dimensional structures, alignments of matching human and moent tissues, 13 genes appeared differentially expressed among tissues. AVAILABILITY: The expression data of the ribosomal protein genes together with supplementary material (complete transcriptional profiles of the considered human tissues) are freely available at the site GETProfiles (http://telethfrom our model is an estimation of the fold composition of the initial genome, which potentially relates to the common ancestor for modern organisms. Supplementary material pertaining to this work is available from www.partslist.org/powerlaw. Copyright 2001 Academic Press. MeSH Terms: Animals Computy available at http://BioInfo.PL/meta/, some remote servers have however restrictions for non-academic users, which are respected by the meta server. SUPPLEMENTARY INFORMATION: Results of several sessions of the CAFASP and LiveBench programs for assessment of performance of fold-recognition servers s based on sorting signals. AVAILABILITY: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. PMID: 11524373 [PubMed - indexed for MEDs based on sorting signals. AVAILABILITY: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. MeSH Terms: Amino Acid Sequence Amino Ac[VO(naph-tris)](2)] [where naph-tris is the Schiff base formed between o-hydroxynaphthaldehyde and tris(hydroxymethyl)amine] are reported. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0311-5. MeSH Tetative performance with semi-quantitative results in the concentration predictions of both the standard mixture and the real-world sample. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00216-001-1125-6. PMID: 1meotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8. MeSH Tetion to these data, we present a few examples of the many possible applications of this transgenic line for developmental studies in vivo. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-001-0196-x MeSH Tertween amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z. MeSH Tee would provide a rationale why during exercising or physical stress radicals are formed without necessarily being deleterious. This article contains supplementary material that may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/23/v23_11.1064.html.

fect on cell cycle progression and apoptosis, whereas in signal transduction they may act as stimulatory or inhibitory factors. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/Suppmat/23/v23_10.936. Copyrhat CtBP proteins might regulate gene expression directly by means of their enzymatic activities, in addition to serving as simple bridging proteins. Supplementary material for this article can be found on the BioEssays homepage at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/v23_8.684

Live? Journal?

no n

no n

No n

no n

no n

no n

no no

no no

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes no

yes no

yes no

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

4: Bioinformatics. 2001 Dec;17(12):1179-82.

7: Bioinformatics. 2001 Oct;17(10):977-87.

12: Bioinformatics. 2001 Aug;17(8):752-3.








6: Microbiology. 2001 Dec;147(Pt 12):3393-402.



10: Planta. 2001 Aug;213(4):659-66.

11: J Struct Biol. 2001 May-Jun;134(2-3):95-102.


8: J Mol Biol. 2001 Nov 2;313(4):673-81.




1: J Biol Inorg Chem. 2002 Apr;7(4-5):384-96. Epu

2: Anal Bioanal Chem. 2002 Jan;372(1):205-15. Ep

3: Mol Genet Genomics. 2002 Feb;266(6):942-50.

4: Dev Genes Evol. 2001 Dec;211(12):603-10. Epu

5: Arch Microbiol. 2002 Feb;177(2):139-49. Epub 2

7: Bioessays. 2001 Nov;23(11):1064-9.

9: Bioessays. 2001 Oct;23(10):936-46.

12: Bioessays. 2001 Aug;23(8):683-90.

Taxonomy workbench.

Model-based clustering and data transformations for gene expression data.

Easier threading through web-based comparisons and cross-validations.

Genotype transposer: automated genotype manipulation for linkage disequilibrium

Amino acid similarity matrices based on force fields.

Amino acid similarity matrices based on force fields.

ProPred: prediction of HLA-DR binding sites.

mmsearch: a motif arrangement language and search program.

ToolShop: prerelease inspections for protein structure prediction servers.

Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic

Diversity of silver resistance genes in IncH incompatibility group plasmids.

Determining the minimum number of types necessary to represent the sizes of

Clustering protein sequences--structure prediction by transitive homology.

Relationships between growth, morphology and wall stress in the stalk of

The MEROPS database as a protease information system.

Differential expression of genes coding for ribosomal proteins in different

Protein family and fold occurrence in genomes: power-law behaviour and

Structure prediction meta server.

Support vector machine approach for protein subcellular localization prediction.

Support vector machine approach for protein subcellular localization prediction.

Erratum in:

A laser-induced fluorescence dual-fiber optic array detector applied to the

A novel MADS-box gene subfamily with a sister-group relationship to class B

A zebrafish histone variant H2A.F/Z and a transgenic H2A.F/Z:GFP fusion protein

Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing

Plectin repeats and modules: strategic cysteines and their presumed impact on

14-3-3 proteins: key regulators of cell division, signalling and apoptosis.

The CtBP family: enigmatic and enzymatic transcriptional co-repressors.

Wildpaner M, Schneider G, Schleiffer A, Eisenhaber F.

Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL.

Douguet D, Labesse G.

analysis.

Dosztanyi Z, Torda AE.

Dosztanyi Z, Torda AE.

Singh H, Raghava GP.

Junier T, Pagni M, Bucher P.

Rychlewski L.

features.

Gupta A, Phung LT, Taylor DE, Silver S.

protein atoms.

Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R.

Acetabularia acetabulum.

Barrett AJ, Rawlings ND, O'Brien EA.

human tissues.

evolutionary model.

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L.

Hua S, Sun Z.

Hua S, Sun Z.

J Biol Inorg Chem 2002 Jun;7(6):675.

rapid HPLC separation of polycyclic aromatic hydrocarbons.

floral homeotic genes.

for in vivo studies of embryonic development.

bacteria.

cytolinker functions.

van Hemert MJ, Steensma HY, van Heusden GP.

Turner J, Crossley M.






PMID: 11524370 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid SuChemistry, Ph










PMID: 11751223 [PubMed - indexed for MEDLINE] MeSH Terms: Adult Data Interpret

PMID: 11697896 [PubMed - indexed for MEDLINE] MeSH Terms: Animals Computational



PMID: 11524373 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid S Amino Acids/a

PMID: 11941496 [PubMed - indexed for MEDLINE] MeSH Terms: 3T3 Cells Animals

PMID: 11939196 [PubMed]

PMID: 11862488 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid S Angiosperms/c

PMID: 11819118 [PubMed - indexed for MEDLINE] MeSH Terms: Animals Animals, Gene

PMID: 11807563 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid S Ammonia/met

PMID: 11746222 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid S Animals

PMID: 11598960 [PubMed - indexed for MEDLINE] MeSH Terms: 14-3-3 Protei Animals

PMID: 11494316 [PubMed - indexed for MEDLINE] MeSH Terms: Amino Acid MoAmino Acid S

Comparative ComputationalMutation Proteins/chemProteins/genetSequence Alig

Databases, NuExpressed Se Gene ExpressiGene ExpressiHumans Research Supp

Computer SimEvolution, MolGenes, DuplicGenome* Humans Models, Genet

Comparative ComputationalComputer SimDatabases, PrInternet Models, Biolog

Cells, Culture Fibroblasts Glucose/pharmHumans Insulin/pharm Mice

Angiosperms/ Arabidopsis/g Cloning, Mole DNA, ComplemDNA, ComplemGene Expressi

Animals, GeneAnimals, GeneGenes, ReportGreen FluoresHistones/geneHistones/phys

BetaproteobactBetaproteoba BetaproteobacChromatiaceaeChromatiaceaChromatiacea

Ankyrins/chemAnkyrins/physCysteine/chemCysteine/physHumans Intermediate

Apoptosis* Cell Cycle Cell Division Humans Signal Transd Tyrosine 3-M

Animals Binding Sites DNA-Binding PDNA-Binding PDNA-Binding PHistone Deace

ThermodynamSubstances: Proteins

Ribosomal ProSubstances: Ribosomal Proteins

Multigene FamProtein FoldinProteins/chemProteins/classiProteins/genetProteins/meta

Proteins/chemProteins/metaResearch SuppSoftware Subcellular F Substances:

Molecular MimReproducibilitResearch SuppToxicity TestsVanadium ComVanadium Com

Genes, Plant/ In Situ Hybrid MADS Domain Molecular Se Phylogeny Research Supp

Luminescent PMolecular Se Recombinant FResearch SuppZebrafish/embZebrafish/gen

Comparative EnvironmentalGammaproteobaGammaproteobGammaproteobGene Dosage

Intermediate Models, MolecMolecular Se Oxidants/physPlectin Protein Struct

Tyrosine 3-M Substances: 14-3-3 Protei Tyrosine 3-Monooxygenase

PhosphoproteRepressor ProSubstances: C-terminal binDNA-Binding PPhosphoprote

Proteome Research SuppSubstances: Proteins Proteome

Amino Acids Proteins

Vanadium Co Substances: Vanadium Co Insulin Glucose

Sequence Ali Sequence AnaSequence HomZea mays/genSubstances: DNA, Comple

Substances: Histones Luminescent PRecombinant FGreen FluoresSecondary Sou

Molecular Se Nitrosomonas/cNitrosomonasNitrosomonas/Operon Oxidoreductas

Repetitive Se Research SuppSubstances: Ankyrins Intermediate Oxidants

Repressor ProHistone Deacetylases

MADS Domain Secondary SouGENBANK/AJ2GENBANK/AJ3GENBANK/AJ318098

GENBANK/AF414110

Protein Struc Research SuppResearch SuppSequence HomVariation (GenSubstances:

PLEC1 protei Plectin Cysteine

Ammonia Oxidoreducta ammonia monooxygenase

Referenceesults clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset. Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/ Publication Types: Evaluation Studies PMID: 12385990 [PubMed - indexed for MEDLINE]n functional genomics. AVAILABILITY: Java class files are freely available at http://mendel.mc.duke.edu/bioinformatics/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: For more information on TreeMapClusterView (see http://mendel.mc.duke.edu/bioinformatics/software/boxclusterview/), and httools/mpicode. The 'message passing interface' package (MPICH) is available from http:/www.unix.mcs.anl.gov/mpi/mpich. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline. PMID: 12217922 [PubMed - indexed for MEDLINE]ring the effect of the amount of among-site-rate-variation, and the degree of sequence divergence on the resulting ancestral states. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://evolu3.ism.ac.jp/~tal/ Contact: [email protected] PMID: 12176835 [PubMed - indexed for MEDLINE]epository of sequences and population information that is usually dispersed in a variety of other sources. AVAILABILITY: http://www.gen-epi.de/mouse. SUPPLEMENTARY INFORMATION: Documentation and detailed information on population subgroups is available on the homepage: http://www.gen-epi.de/mouse PMia coli growth on two carbon sources (acetate and glucose) at all levels of oxygenation, and the resulting optimal metabolic phenotypes were studied. Supplementary information can be downloaded from our website (http://epicurus.che.udel.edu). Copyright 2002 John Wiley & Sons, Inc. PMID: 11745171 [Putains some weakly predictive information with respect to protein complexes, but we show how this prediction can be improved by combining all of them. Supplementary information is available at http:// bioinfo.mbb.yale.edu/integrate/interactions/. PMID: 12836664 [PubMed - indexed for MEDLINE] supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site. Publication Types: Evaluation Studies PMID: 12s that may play a role in determining the protein's structure and function. AVAILABILITY: http://bioinformatics.org/pecop Contact: [email protected] SUPPLEMENTARY INFORMATION: http://bioinformatics.org/pecop/about_pecop PMID: 12217925 [PubMed - indexed for MEDLINE]ta may improve the quality of multiple sequence alignments, this does not add to the ability of the derived profile HMMs to find sequence homologues. SUPPLEMENTARY INFORMATION: A list of HOMSTRAD families used in this study and the corresponding Pfam families is available at http://www.sanger.ac.uk/ILITY: Use of the XEMBL service is free of charge at http://www.ebi.ac.uk/xembl/, and can be accessed via web forms, CGI, and a SOAP-enabled service. SUPPLEMENTARY INFORMATION: Information on the EMBL Nucleotide Sequence Database is available at http://www.ebi.ac.uk/embl/. The EMBL Object Model is aets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system. AVAILABILITY AND SUPPLEMENTARY INFORMATION: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/ PMID: 12176838 [ers may also encode transframe products. AVAILABILITY: The program is available for download from http://www.gesteland.genetics.utah.edu/freqAnalysis SUPPLEMENTARY INFORMATION: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis PM

applicable to the rapid identification of unique sequences in other DNA sequence sets. AVAILABILITY: Freely available upon request from the authors. Supplementary information: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper PMID: 12117799 [PubMed - indexed for MEDLINE]

adeh et al. (2000; Nature, 403, 503-511), our analyses only partially support the conclusions of the original authors. AVAILABILITY: The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public PMID: 12117794f raw cDNA microarray data. AVAILABILITY: MS-Windows binaries are freely available for non-profit use at http://www.biologie.ens.fr/yeast-publi.html. SUPPLEMENTARY INFORMATION: Scripts for online creation of Arrayplot files are available at http://transcriptome.ens.fr/lgm_bioinfo/ PMID: 12075027 [Pusers in a multi-user/multi-group environment. AVAILABILITY: An AiO specific website, with the possibility to download is at: http://134.99.88.55/aio/ SUPPLEMENTARY INFORMATION: Examples with screen shots- http://134.99.88.55/aio/ : Manual (in PDF format)-http://134.99.88.55/aio/manual.pdf PMID: 1207 as well as in windows containing several tyrosine residues. AVAILABILITY: The Sulfinator is accessible at (http://www.expasy.org/tools/sulfinator/). Supplementary information: Sulfinator documentation is accessible at (http://www.expasy.org/tools/sulfinator/sulfinator-doc.html). PMID: 12050077 [Pubotein/peptide mass spectra simulations. AVAILABILITY: The massXpert program is free for academic and commercial use at http://frl.lptc.u-bordeaux.fr. SUPPLEMENTARY INFORMATION: The http://frl.lptc.u-bordeaux.frsite contains a tutorial for online perusal or download. PMID: 12016065 [PubMed - indexed mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand. AVAILABILITY: http://pbil.univ-lyon1.fr/software/cpgprod.html SUPPLEMENTARY INFORMATION: http://pbil.univ-lyon1.fr/software/cpgprod.html PMID: 12016061 [PubMed - indexed for MEDLINE]ils; (iv) cytoplasmic proteins relative to nuclear ones; and (v) proteins involved in 'protein synthesis,' 'cell structure,' and 'energy production.' SUPPLEMENTARY INFORMATION: http://genecensus.org/expression/translatome PMID: 12016056 [PubMed - indexed for MEDLINE]es and the numbers of molecules involved. AVAILABILITY: The software is available at ftp://ibbrain.ibb.waw.pl/stocksand http://www.ibb.waw.pl/stocks. Supplementary information: Parameters of the model of prokaryotic gene expression are available in example files of software distribution. PMID: 11934ogy-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz.de/tbi/services/mchips PMID: 11934741 [PubMed - indexed for MEDLINE]terial LipOProteins (DOLOP) is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop along with additional information on the biosynthetic pathway, supplementary material and other related figures. MeSH Terms: Algorithms Bacteria/chemistry Bacteria/genetics Database Management Systems* Databases, ination chemistry and stability of the native clusters has been investigated through site-directed mutagenesis and spectroscopic analysis. Electronic supplementary material to this paper, containing Mossbauer and UV-visible spectra for mutant Isa1 proteins, can be obtained by using the Springer Linkts. The tool is written in Microsoft Excel 2000 and is available free of charge for use in teaching and research from www.aob.oupjournals.org article supplementary data. PMID: 12324272 [PubMed - indexed for MEDLINE]et allows a safe diagnostic FOB with BAL in patients with hypoxemic ARF, avoiding gas exchange deterioration, and endotracheal intubation. Electronic supplementary material: is available if you access this article at http://dx.doi.org/10.1007/s00134-002-1554-5. On that page (frame on the left side),

fter cardiothoracic surgery alters nursing activity; it reduces the time for documentation and increases the time devoted to patient care. Electronic supplementary material: is available if you access this article at http://dx.org/10.1007/s00134-002-1542-9. On that page (frame on the left side), a l

le if you access this article at http://dx.doi.org/10.1007/s00216-002-1595-1. On that page (frame on the left side), a link takes you directly to the supplementary material. PMID: 12474092 [PubMed]le if you access this article at http://dx.doi.org/10.1007/s00114-002-0353-8. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: Animals Birds/anatomy & histology* China Environment Fossils* Research Support, Non-U.S. Gov't Trees Vertebrates/aling behavior suggests the presence of two pairs of vocal sacs that may contribute to the remarkable call-note complexity in this species. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0335-x. MeSH Te

grees C, 72 h) and in coffee beans after different amounts of roasting. The origin of formation of volatile acidity was also investigated. Electronic supplementary material is available if you access this article at http://dx.doi.org/10.1007/s00216-002-1561-y On that page (frame on the left side) a libration is a useful tool to characterise the performance of pH electrodes. This is demonstrated with different commercial pH electrodes. ELECTRONIC SUPPLEMENTARY MATERIAL is available if you access this article at http://dx.doi.org/10.1007/s00216-002-1506-5. On that page (frame on the left side), nsitivity and specificity of MPSS allowed us to identify a large number of ABA-responsive genes in WT Arabidopsis thaliana. The database given in our supplementary material (http://jcs.biologists.org/supplemental) provides researchers with the opportunity to rapidly assess whether genes of interest le if you access this article at http://dx.doi.org/10.1007/s00425-002-0889-z. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: 2,4-Dichlorophenoxyacetic Acid/pharmacology ATP-Binding Cassette Transporters/genetics* Abscisic Acid/pharmacology functions as well as diffusion coefficients and are compared with the corresponding findings on clusters of alkanes and perfluoroalkanes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s008940020092y. MeSH Terms

the participants was the batch-to-batch variability of commercial Cot1 preparations in their ability to suppress hybridization to repeat sequences. (Supplementary material for this article can be found in the online issue, which is available at http://www.interscience.wiley.com/jpages/0196-4763/sup lignans. Furthermore, it appears that, in this species, the hydroxylation of DOP is a rate-limiting point in the pathway leading to PTOX. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/wo.1007/s00425-002-0834-1. MeSH Teity and cell death. In all, our data suggest that NO induces the AOX1a gene and that AOX may participate to counteract the toxicity of NO. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00425-002-0828-z. MeSH Tequeous solution has been evaluated from the corresponding AM1 thermodynamic parameters. The results agree well with the experimental data. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-002-0094-9 Publicat

the genes for this large family. [The sequence data from this study have been submitted to FlyBase. Annotations for these sequences are available as supplementary material at http://www.genome.org.] MeSH Terms: Amino Acid Sequence Animals Chromosome Mapping Comparative Study Conserved Sequence/genewhen they occur simultaneously as complications of breast cancer treatment. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0024-7. MeSH Terms: Breas

ppears to be that which theoretically leads to the least devascularization. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00276-002-0029-2. MeSH Terms: Artern the development of the IJV and the lateral branch of the accessory nerve. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0020-y. Publication Typespal artery and an early bifurcation of the second palmar metacarpal artery. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0011. Publication Types: localization of the meniscofemoral ligaments should be taken into account. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0023-8. Publication Typesapment and tension from the temporalis muscle and/or the narrow bony canal. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0027-4. MeSH Terms: Cadavatomical results observed on a small sample of subjects of European origin. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0026-5. MeSH Terms: Arterstocene probably contributed to the isolation of the two taxa described. Aspects of ecology and conservation status are briefly discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0320-4. Publicasional protrusions enriched in GM1 occur, which may represent a precursor for the formation of micelles budding into the aqueous subphase. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00249-002-0232-4. MeSH Te Finally, we present results from large-scale simulation of the Rayleigh-Taylor instability and dispersion of colloidal slab in 2D and 3D. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00894-001-0068-3. MeSH Te (5 min). In validation experiments, both methods gave identical results and the measured sulfhydryls/protein matched the expected values. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00216-002-1347-2. Publica

t-day paternal lineages within Poland and their distinctiveness from other parts of Europe, at least in respect to their Y-STR haplotypes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00439-002-0728-0. MeSH Te

ter/coding sequence combinations, as well as to the existence of distinct active-site variants that ultimately influence protein activity. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00438-002-0667-4. MeSH Teterial community as assessed by denaturing gradient gel electrophoresis fingerprinting of PCR amplicons of a portion of the 16S rDNA gene. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-002-0427-1. MeSH Teremendous experimental progress of the past few years is outlined and a number of recent experiments show the current status of the field. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-001-0277-8. PMID: 1cord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-001-0071-8. MeSH Te explained by the implementation of several quality assurance procedures in the NICE registry, such as training and automatic data checks. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00134-002-1272-z MeSH Teralculated. To visualize the motion of protein domains, movies were generated by similarity ranking of the observed protein configurations. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00249-001-0197-8 MeSH Terll the species. This suggests a selective pressure for maintaining the structural and functional configuration of this haplotype in wheat. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0051-9. MeSH Te. Genes of unknown function may by assigned a hypothetical role based on their patterns of expression resembling well characterized genes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0046-6. MeSH Tell correspond to the ancestral function of these genes. The results are discussed in the light of the evolutionary origin of the mesoderm. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-002-0228-1. MeSH Tecapability and further suggest that by the Early Cretaceous ecological diversification of early birds was greater than previously assumed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-001-0276-9. MeSH Ted in muscle lineages in the ecdysozoan representatives Caenorhabditis elegans or Drosophila; the C. elegansgenome has lost Mox altogether. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00427-002-0223-6. MeSH Tel F-box proteins. We conclude that patterning of ppa mRNA could reflect a constraint on ppa function that is not common among F-box genes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-002-0222-7. MeSH Ten-containing protrusions and thereby cell adhesive and migratory behaviour could have potential for therapeutic intervention in these conditions. The supplementary material referred to in this section can be found at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2002/v24.350.html Copyri

ffinity is reduced only 10-fold. The mechanism of Bi(III)-responsive metalloregulation is discussed, based on the findings presented here. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0336-9. MeSH Te

at under physiological condition there is the availability of LIP for catalyzing Fenton-type reactions in close proximity to cellular DNA. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0335-x. MeSH Tediscussed and a comprehensive study of the electronic structure of ligand-cytochrome c complexes and the native protein is also described. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0334-y. MeSH Ted structure of the catalytic subunit of a carbon monoxide dehydrogenase from Carboxydothermus hydrogenoformans and related dehydrogenases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0326-y. MeSH Te the nickel oxidation states in MCR-ox1, MCR-ox2 and MCR-ox3 and to a possible presence of a second redox active group in the active site. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00775-001-0325-z. MeSH Teare highly relevant for unraveling the stepwise assembly process of the stromal PsaC, PsaD and PsaE subunits to the PS I core heterodimer. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0321-3. MeSH Teied. These results suggest that de novo designed peptides may serve as scaffolds for the construction of native bridged sites in proteins. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0320-4. MeSH Te[VO(naph-tris)](2)] [where naph-tris is the Schiff base formed between o-hydroxynaphthaldehyde and tris(hydroxymethyl)amine] are reported. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0311-5. MeSH Tetative performance with semi-quantitative results in the concentration predictions of both the standard mixture and the real-world sample. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00216-001-1125-6. PMID: 1meotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8. MeSH Tetween amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z. MeSH Teransformation and strengthens the role of Src in the development and progression of human colon cancer. Supportive Supplemental Data can be viewed at http://pga.tigr.org/PGApubs.shtml. MeSH Terms: Animals Cell Line, Transformed Cell Transformation, Neoplastic* Cluster Analysis Colonic Neoplasms/gene

Live? Journal?

No n

no n

no n

no n

no n

no n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes n

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes y

yes n

3: Bioinformatics. 2002;18 Suppl 2:S92-9.

5: Bioinformatics. 2002 Sep;18(9):1278-9.



15: Bioinformatics. 2002 Jun;18(6):890-1.

24: Biotechnol Bioeng. 2002 Jan 5;77(1):27-36.

1: J Struct Funct Genomics. 2002;2(2):71-81.

2: Bioinformatics. 2002;18 Suppl 2:S219-30.






13: Bioinformatics. 2002 Jul;18(7):1004-10.

14: Bioinformatics. 2002 Jul;18(7):961-70.



18: Bioinformatics. 2002 May;18(5):769-70.

19: Bioinformatics. 2002 Apr;18(4):644-5.



22: Bioinformatics. 2002 Mar;18(3):470-81.

23: Bioinformatics. 2002 Mar;18(3):423-33.


45: J Biol Inorg Chem. 2002 Apr;7(4-5):526-32. Epub 2002 Feb 13.

4: Ann Bot (Lond). 2002 Oct;90(4):485-8.

1: Intensive Care Med. 2003 Jan;29(1):126-9. Epub 2002 Nov 29.

2: Intensive Care Med. 2003 Jan;29(1):83-90. Epub 2002 Nov 22.

3: Anal Bioanal Chem. 2002 Dec;374(7-8):1242-9. Epub 2002 Nov 6.

4: Naturwissenschaften. 2002 Sep;89(9):394-8. Epub 2002 Aug 21.

5: Naturwissenschaften. 2002 Aug;89(8):352-6. Epub 2002 Jun 22.

6: Anal Bioanal Chem. 2002 Nov;374(5):879-85. Epub 2002 Oct 10.

7: Anal Bioanal Chem. 2002 Nov;374(5):778-86. Epub 2002 Sep 20.

8: J Cell Sci. 2002 Dec 15;115(Pt 24):4891-900.

9: Planta. 2002 Nov;216(1):95-106. Epub 2002 Nov 12.

10: J Mol Model (Online). 2002 Sep;8(9):266-71. Epub 2002 Sep 4.

11: Cytometry. 2002 Oct 1;49(2):43-8.

12: Planta. 2002 Oct;215(6):1031-9. Epub 2002 Jul 25.

13: Planta. 2002 Oct;215(6):914-23. Epub 2002 Jul 25.

14: J Mol Model (Online). 2002 Aug;8(8):246-52.

15: Genome Res. 2002 Sep;12(9):1357-69.

16: Surg Radiol Anat. 2002 May;24(2):87-90.







23: Naturwissenschaften. 2002 May;89(5):201-13.

24: Eur Biophys J. 2002 Jul;31(4):317-22. Epub 2002 Jun 14.

25: J Mol Model (Online). 2002 Jan;8(1):33-43.

26: Anal Bioanal Chem. 2002 Jul;373(4-5):266-76. Epub 2002 Jun 6.

27: Hum Genet. 2002 Jun;110(6):592-600. Epub 2002 May 22.

28: Mol Genet Genomics. 2002 May;267(3):359-69. Epub 2002 Apr 26.

29: Arch Microbiol. 2002 Jul;178(1):65-70. Epub 2002 Apr 30.

30: Naturwissenschaften. 2002 Feb;89(2):47-56.

31: J Mol Model (Online). 2002 Feb;8(2):58-64.

32: Intensive Care Med. 2002 May;28(5):656-9. Epub 2002 Apr 13.

33: Eur Biophys J. 2002 Jun;31(3):172-8. Epub 2002 Jan 29.

35: Funct Integr Genomics. 2002 May;2(1-2):40-50. Epub 2002 Apr 9.

36: Funct Integr Genomics. 2002 May;2(1-2):13-27. Epub 2002 Feb 19.

37: Dev Genes Evol. 2002 May;212(4):186-95. Epub 2002 Apr 18.

38: Naturwissenschaften. 2002 Jan;89(1):34-8.

39: Dev Genes Evol. 2002 Apr;212(3):141-4. Epub 2002 Mar 13.

40: Dev Genes Evol. 2002 Apr;212(3):134-40. Epub 2002 Mar 7.

41: Bioessays. 2002 Apr;24(4):350-61.


43: J Biol Inorg Chem. 2002 Apr;7(4-5):548-50. Epub 2002 Jan 30.






50: J Biol Inorg Chem. 2002 Apr;7(4-5):384-96. Epub 2001 Dec 19.

51: Anal Bioanal Chem. 2002 Jan;372(1):205-15. Epub 2001 Dec 12.

52: Mol Genet Genomics. 2002 Feb;266(6):942-50. Epub 2001 Dec 15.

53: Arch Microbiol. 2002 Feb;177(2):139-49. Epub 2001 Dec 6.

1: Oncogene. 2002 Oct 17;21(47):7256-65.

An efficient and accurate distance based algorithm duplication trePMID: 12385990 [PubMed - indexed for MEDLINE]

Applications of Tree-Maps to hierarchical biological McConnell P, J PMID: 12217926 [PubMed - indexed for MEDLINE]

Parallelized multiple alignment. Kleinjung J, DoPMID: 12217922 [PubMed - indexed for MEDLINE]

A branch-and-bound algorithm for the inference of when the replaPMID: 12176835 [PubMed - indexed for MEDLINE]

MOUSE (Mitochondrial and Other Useful SEquences) genetic markerPMID: 12075028 [PubMed - indexed for MEDLINE]

Characterizing the metabolic phenotype: a phenoty Edwards JS, RaPMID: 11745171 [PubMed - indexed for MEDLINE]

Integration of genomic datasets to predict protein Jansen R, Lan NPMID: 12836664 [PubMed - indexed for MEDLINE]

BioMiner--modeling, analyzing, and visualizing bio networks. PMID: 12386006 [PubMed - indexed for MEDLINE]

PeCoP: automatic determination of persistently consfamilies. PMID: 12217925 [PubMed - indexed for MEDLINE]

The use of structure information to increase alignm homologue detePMID: 12217916 [PubMed - indexed for MEDLINE]

XEMBL: distributing EMBL data in XML format. Wang L, RiethoPMID: 12176844 [PubMed - indexed for MEDLINE]

TFBS: Computational framework for transcription factLenhard B, W PMID: 12176838 [PubMed - indexed for MEDLINE]

Computational identification of putative programmedsites. PMID: 12176827 [PubMed - indexed for MEDLINE]

Determining a unique defining DNA sequence for yetechniques. PMID: 12117799 [PubMed - indexed for MEDLINE]

Deriving quantitative conclusions from microarray eOlshen AB, Jai PMID: 12117794 [PubMed - indexed for MEDLINE]

Arrayplot for visualization and normalization of cD Marc P, Jacq C.PMID: 12075027 [PubMed - indexed for MEDLINE]

AiO, combining DNA/protein programs and oligo-m Karreman C. PMID: 12075025 [PubMed - indexed for MEDLINE]

The Sulfinator: predicting tyrosine sulfation sites i Monigatti F, GaPMID: 12050077 [PubMed - indexed for MEDLINE]

Desktop prediction/analysis of mass spectrometric dusing massXpePMID: 12016065 [PubMed - indexed for MEDLINE]

CpGProD: identifying CpG islands associated with tralarge genomic PMID: 12016061 [PubMed - indexed for MEDLINE]

Analysis of mRNA expression and protein abundancecomparison of PMID: 12016056 [PubMed - indexed for MEDLINE]

STOCKS: STOChastic Kinetic Simulations of biochemialgorithm. PMID: 11934747 [PubMed - indexed for MEDLINE]

Microarray data warehouse allowing for inclusion of statistical analPMID: 11934741 [PubMed - indexed for MEDLINE]

DOLOP--database of bacterial lipoproteins. Madan Babu M,PMID: 12

Iron-sulfur cluster biosynthesis: characterization Isa1. PMID: 11

A modern tool for classical plant growth analysis. Hunt R, CaustoPMID: 12324272 [PubMed - indexed for MEDLINE]

Fiberoptic bronchoscopy during noninvasive positivedelivered by h PMID: 12

Intensive care information system reduces documentcardiothoracic PMID: 12

Comparison of spark OES methods for analysis of incKuss HM, LungPMID: 12474092 [PubMed]

A juvenile coelurosaurian theropod from China indicZhang F, ZhouPMID: 12

Vocal acrobatics in a Chinese frog, Amolops tormotuFeng AS, NarinPMID: 12

New procedures for determination of acids in coffeeon the developPMID: 12434245 [PubMed]

Traceability of pH measurements by glass electrodecharacteristic PMID: 12434231 [PubMed]

Genome-wide gene expression profiling in Arabidopstargets of abscPMID: 12

The plant PDR family of ABC transporters. van den Brule PMID: 12

Molecular dynamics studies on the aggregation of YFriedemann R,PMID: 12

Comparative analysis of comparative genomic hybritechnologies: PMID: 12

Biosynthesis of podophyllotoxin in Linum album cellSeidel V, WindPMID: 12

Nitric oxide induces transcriptional activation of thealternative oxiPMID: 12

Theoretical investigation of the structure and acid-b2-thiolumazinePMID: 12

Genome-wide analysis of the odorant-binding proteimelanogaster.PMID: 12

The cutaneo-lymph node flap of the superficial circuAssouad J, BecPMID: 12

Anatomical study of the blood supply of the coxal b clinical applicaPMID: 12

High duplication of the internal jugular vein: clinica and surgical coPMID: 12

Multiple arterial variation of the human upper limb. Durgun B, YucePMID: 12

An MRI study of the meniscofemoral and transverse Erbagci H, Yil PMID: 12

Nervous branch passing through an accessory canalthe temporal bPMID: 12

Study of the relationship between the suprascapularplexus. PMID: 12

Review of the reticulated python (Python reticulatu description of PMID: 12

Lateral organization of GM1 in phase-separated monforce microscoPMID: 12

Mesoscopic dynamics of colloids simulated with dissfluid particle PMID: 12

Quick measurement of protein sulfhydryls with Ellm4,4'-dithiodipy PMID: 12

Homogeneity and distinctiveness of Polish paternal chromosome micPMID: 12

Combinatorial variation in coding and promoter seq locus in Pisum PMID: 12

Aciduric Proteobacteria isolated from pH 2.9 soil. Curtis P, Naka PMID: 12

Bose-Einstein condensation in dilute atomic gases. Arlt JJ, Bongs PMID: 12046620 [PubMed]

Homology modeling reveals the structural backgroundin thermal sta PMID: 12

Quality of data collected for severity of illness scor Intensive Care PMID: 12

Sampling the conformational space of membrane proScheuring S, MPMID: 12

Two haplotypes of resistance gene analogs have beat the leaf rus PMID: 12

DNA array profiling of gene expression changes du Lee JM, WilliamPMID: 12

Characterisation of two snail genes in the gastropodImplications f PMID: 12

Largest bird from the Early Cretaceous and its implicavian ecologicaPMID: 12

Mox homeobox expression in muscle lineage of the gevidence for a PMID: 11

A conserved F-box gene with unusual transcript locaDas T, PurkayaPMID: 11

Fascins, and their roles in cell structure and functio Kureishy N, SaPMID: 11

Characterization of a metalloregulatory bismuth(III) aureus pI258 CPMID: 11

The level of 8-oxo-7,8-dihydro-2'-deoxyguanosine is the size of th PMID: 11

Solution structure of cyanoferricytochrome c: ligan flexibility and PMID: 11

Hybrid cluster proteins (HCPs) from Desulfovibrio Desulfovibrio PMID: 11

The nickel enzyme methyl-coenzyme M reductase f vitro inductio PMID: 11

Solution structure of the unbound, oxidized Photosycontaining [4F PMID: 11

Stability and nickel binding properties of peptides d the stabilizati PMID: 11

Erratum in: J Biol Inorg C PMID: 11

A laser-induced fluorescence dual-fiber optic array rapid HPLC sepPMID: 11939196 [PubMed]

A novel MADS-box gene subfamily with a sister-groupfloral homeoti PMID: 11

Diversity of ammonia monooxygenase operon in autbacteria. PMID: 11

Malek RL, Irby PMID: 12Identification of Src transformation fingerprint in human colon cancer.











MeSH Terms: Algorithms Bacteria/chemist

MeSH Terms: Alanine Amino Acid Sequ


MeSH Terms: Adult Aged



MeSH Terms: Animals Birds/anatomy &

MeSH Terms: Animals Ranidae/physiolo



MeSH Terms: Abscisic Acid/pharmacology* Arabidopsis/gene

MeSH Terms: 2,4-Dichlorophenoxyacetic Acid/ ATP-Binding Cass

MeSH Terms: Alkanes/chemistry* Computer Simula

MeSH Terms: Animals Comparative Stu

MeSH Terms: Alcohol Oxidoreductases/metabolAldehyde Oxidor

MeSH Terms: Adaptation, Physiological/drug effArabidopsis/cyto

MeSH Terms: Empirical Research Gases/chemistry

MeSH Terms: Amino Acid Sequence Animals

MeSH Terms: Breast/surgery Breast Neoplasms

MeSH Terms: Arteries/anatomy & histology* Cadaver

MeSH Terms: Aged Carcinoma, Squa

MeSH Terms: Axillary Artery/anatomy & histolo Brachial Artery/

MeSH Terms: Adolescent Adult

MeSH Terms: Cadaver Cranial Sutures/

MeSH Terms: Arteries/anatomy & histology Brachial Plexus/

MeSH Terms: Animals Boidae/anatomy &

MeSH Terms: Brain/metabolism Cholesterol/chem

MeSH Terms: Colloids/chemistry* Computer Simula

MeSH Terms: Animals Calibration

MeSH Terms: Alleles Analysis of Varia

MeSH Terms: Genetic Markers Peas/genetics*

MeSH Terms: Culture Media/chemistry Electrophoresis,


MeSH Terms: Amino Acids/analysis Comparative Stu

MeSH Terms: APACHE Comparative Stu

MeSH Terms: Aquaporins/chemistry Bacteriorhodopsi

MeSH Terms: Amino Acid Sequence Blotting, Souther

MeSH Terms: Blotting, Northern Carbocyanines


MeSH Terms: Animals Birds/anatomy &

MeSH Terms: Animals Cell Lineage


MeSH Terms: Actins/physiology* Animals

MeSH Terms: Bacterial Proteins/chemistry* Bacterial Protein


MeSH Terms: Amino Acid Sequence Comparative Stu

MeSH Terms: Aldehyde Oxidoreductases/chemisAmino Acid Sequ

MeSH Terms: Chloroform/chemistry Citric Acid/chemi

MeSH Terms: Amino Acid Sequence Iron-Sulfur Prote

MeSH Terms: Amino Acid Sequence Binding Sites

MeSH Terms: 3T3 Cells Animals


MeSH Terms: Amino Acid Sequence Angiosperms/class

MeSH Terms: Amino Acid Sequence Ammonia/metabo

MeSH Terms: Animals Cell Line, Trans

Bacteria/genetics Database Management Sy

Cloning, Molecular Cross-Linking Reagents/ch

Anoxemia/diagnosis Bronchoalveolar Lavage/m

Cardiac Surgical Procedures/nuEfficiency, Organizational*

China Environment

Research Support, Non-U.S. GoResearch Support, U.S. Gov'

Base Sequence DNA Primers

Abscisic Acid/pharmacology Amino Acid Sequence

Diffusion Fluorocarbons/chemistry*

Drosophila/genetics Education

Carbon Isotopes Cell Division/drug effects

Arabidopsis/enzymology Arabidopsis/genetics*

Hydrogen-Ion Concentration Isomerism

Chromosome Mapping Comparative Study

Breast Neoplasms/surgery Cadaver

Female Fractures, Bone/classificat

Humans Jugular Veins/anatomy & hi

Cadaver Dissection

Aged Aged, 80 and over

Dissection Facial Pain/etiology

Cadaver Europe

Boidae/classification Indonesia

G(M1) Ganglioside/chemistry* Lipid Bilayers/chemistry

Crystallization Hydrophobicity

Comparative Study Disulfides

Databases, Nucleic Acid Europe

Peas/metabolism Promoter Regions (Genetic

Glucose/metabolism Hydrogen-Ion Concentratio

Electrostatics Enzyme Stability

Documentation/standards* Health Services Research

Escherichia coli Proteins* Image Enhancement/meth

Chromosomes Evolution, Molecular

Citric Acid Cycle/genetics DNA Probes

Cell Differentiation/genetics DNA-Binding Proteins/gene

Birds/classification* China

Gene Expression Regulation, Homeodomain Proteins/gen

Carrier Proteins/chemistry* Carrier Proteins/genetics*

Carrier Proteins/chemistry Carrier Proteins/genetics

Bacterial Proteins/metabolism Binding Sites

Aged, 80 and over Ascorbic Acid/blood

Cytochrome c Group/chemistryCytochrome c Group/meta

Bacterial Proteins/chemistry* Bacterial Proteins/isolation

Electron Spin Resonance Spec Euryarchaeota/enzymology

Iron-Sulfur Proteins/metabolis Magnetic Resonance Spect

Cysteine/chemistry Dimerization

Cells, Cultured Fibroblasts

Angiosperms/genetics* Arabidopsis/genetics

Betaproteobacteria/classificati Betaproteobacteria/enzym

Cell Transformation, Neoplasti Cluster Analysis

Databases, Protein* Genome, BactInformati Lipoproteins/chemistry

Cysteine DNA-Binding DNA-BindiDNA-Binding Proteins/met

Bronchoscopy/methods* Female Fiber OptHead Protective Devices*

Female Hospital Inf Humans Intensive Care Units*

Fossils* Research SupTrees Vertebrates/anatomy & histology*

Time Factors Vocalization, Grant SupR01DC00222/DC/NIDCD

Gene Expression Profiling* Gene ExpressGenome, Mutation*

Angiosperms/drug effects Angiosperms/Angiospe Arabidopsis/drug effects

Models, Molecular* Molecular St Research Software

Female Genetics, MeGenomicsHumans

Cells, Cultured ChromatograpCinnamateCinnamates/pharmacolog

Blotting, Northern Cells, Cultur CytochromCytochrome c Group/meta

Models, Chemical* Molecular St Pteridine Research Support, Non-U.S

Conserved Sequence/genetics Databases, GDrosophilDrosophila Proteins/genet

Feasibility Studies Female Humans Iliac Artery*

Fractures, Bone/surgery Humans OsteonecrPelvic Bones/blood supply

Jugular Veins/embryology Laryngeal NeLymph NoMale

Humans Male Middle A Radial Artery/anatomy & h

Child Female Humans Knee Joint/anatomy & hist

Female Humans Male Nerve Compression Syndr

Female Humans Male Scapula

Phylogeny

Lipids/chemistry Membranes, ArMicroscopPhosphatidylcholines/chem

Micelles Models, MoleResearch Research Support, U.S. Go

Dithionitrobenzoic Acid Humans MuramidaPapain/analysis

Genetics, Population Haplotypes Humans Male

Research Support, Non-U.S. Gov't Seeds/genetiSeeds/meSequence Analysis, DNA

Phylogeny ProteobacterProteobactProteobacteria/isolation &

Hydrogenase/chemistry* Models, MoleProtein S Reproducibility of Results

Humans Intensive Ca Netherla Outcome Assessment (Hea

Imaging, Three-Dimensional/methods* Membrane ProMicroscopMotion

Fungi/pathogenicity* Haplotypes* Models, GMolecular Sequence Data

DNA, Complementary Expressed S Fatty Aci Fatty Acids/metabolism

Evolution* Likelihood F Molecula Multigene Family

Ecosystem PaleontologyPhylogen Research Support, Non-U.S. Gov't

In Situ Hybridization Mollusca/embMollusca/Muscles/embryology*

Carrier Proteins/metabolism Conserved S DrosophilDrosophila/growth & dev

Carrier Proteins/physiology* Cell Adhesio Cell Mov Cell Physiology*

Bismuth/chemistry Bismuth/metCysteine/Dimerization

Deoxyguanosine/analogs & derivatives DeoxyguanosFemale Humans

Cytochromes c* Electrons Heme/cheLigands

Comparative Study Crystallogra DesulfoviDesulfovibrio vulgaris/che

Hydrogen-Ion Concentration Light MetallopoNickel

Membrane Proteins* Models, MoleMolecula Oxidation-Reduction

Helix-Loop-Helix Motifs Iron-Sulfur P Iron-Sulf Metalloproteins/chemistry

Glucose/pharmacokinetics Humans Insulin/p Mice

Cloning, Molecular DNA, CompleDNA, ComGene Expression Regulatio

Betaproteobacteria/genetics* ChromatiaceaChromati Chromatiaceae/genetics

Colonic Neoplasms/genetics* Gene ExpressGene ExprGenes, src*

Lipoproteins/classification* Lipop Protein Sorting Signals/genetics

Electron Spin Resonance SpEscheFerredoxins/chemistry

Humans Male Middle Aged

Male Middl Netherlands

Vertebrates/anatomy & histology*

R01DC00663/DC/NIDCD

Research Support, Non-U.S.ReseaSubstances:

Arabidopsis/genetics Arabi Cadmium Chloride/pharmacology

Substances: AlkanFluorocarbons

Male NucleNucleic Acid Hybridization/method

Coenzyme A Ligases/metabCoumaCoumaric Acids/chemistry

Gene Expression RegulationIsoen Nitric Oxide/pharmacology*

Solvents/chemistry ThermWater/chemistry

Drosophila melanogaster/geGene Gene Order/genetics

Lymph Nodes/blood supply LymphLymphedema/etiology

Pelvic Bones/injuries Pelvi Pelvic Bones/surgery

Middle Aged

Ulnar Artery/anatomy & his UpperUpper Extremity/blood supply*

Ligaments, Articular/anatomMagneMale

Sphenoid Bone/anatomy & hZygomZygoma/innervation*

Shoulder/blood supply*

Sphingomyelins/chemistry* SubstLipid Bilayers

Solvents/chemistry SubstColloids

Proteins/analysis* Prote Pyridines

Microsatellite Repeats Pater Poland

Trypsin/metabolism TrypsiTrypsin Inhibitors/metabolism

Soil Microbiology* SubstrSubstances:

Research Support, Non-U.S.Struc Temperature

Quality Assurance, Health CRegis Registries/statistics & numerical d

Nanotechnology* Porin Protein Conformation

Phylogeny Plant Selection (Genetics)

Gene Expression Profiling* Gene Gene Frequency

Neurons/metabolism OrganPhylogeny

Research Support, Non-U.S. Gov't

Muscles/metabolism* Phylo RNA, Messenger/genetics

Drosophila Proteins/chemistDrosoDrosophila Proteins/metabolism

Cells/cytology* DrosoGene Expression Regulation

Fluorescence Gene Glycine/genetics

Iron/blood* LymphMale

Magnetic Resonance SpectrMagneMolecular Sequence Data

Electron Spin Resonance SpIron-SIron-Sulfur Proteins/isolation & puri

Oxidation-Reduction OxidoOxidoreductases/metabolism*

Photosynthetic Reaction Ce PhotoPhotosystem I Protein Complex*

Metalloproteins/metabolismModelMolecular Sequence Data

Molecular Mimicry ReprodResearch Support, Non-U.S. Gov't

Genes, Plant/genetics* In Sit MADS Domain Proteins/genetics*

Comparative Study Envir Gammaproteobacteria/classificatio

Humans Pyrid Pyrimidines/pharmacology

Sensitivity and Specificity Sequence Analysis, Protein/methods

Iron-Sulfur Proteins/biosynthesis* Molecular Sequence Data

Pneumonia/diagnosis* Positive-Pressure Respiration/instrumentation*

Nursing Staff, Hospital/organization &Thoracic Surgical Procedures/nursing*

DNA Primers Abscisic Acid

Diterpenes/pharmacology* Drug Resistance/genetics

Oligonucleotide Array Sequence Anal Polymerase Chain Reaction

Coumaric Acids/metabolism Coumaric Acids/pharmacology

Oligonucleotide Array Sequence AnalyOxidoreductases/genetics*

Substances: 2-thiolumazine

Genes, Insect/genetics Genome*

Lymphedema/surgery* Mammaplasty/methods*

Middle Aged

Lipids Phosphatidylcholines

Solvents

Reproducibility of Results Research Support, Non-U.S. Gov't

Research Support, Non-U.S. Gov't Y Chromosome/genetics*

Variation (Genetics) Substances:

Culture Media Glucose

Thiocapsa roseopersicina/enzymologySubstances:

Severity of Illness Index* Statistics, Nonparametric

Research Support, Non-U.S. Gov't Substances:

Sequence Alignment Sequence Analysis, DNA

Gene Library Glycolysis/genetics

Research Support, Non-U.S. Gov't Sequence Alignment

RNA, Messenger/metabolism Research Support, Non-U.S. Gov't

Evolution, Molecular Gene Expression Regulation, Developmental

Humans Microfilament Proteins/chemistry

Models, Molecular Operon

Middle Aged Research Support, Non-U.S. Gov't

Protein Conformation Research Support, Non-U.S. Gov't

Models, Molecular Molecular Sequence Data

Oxygen/chemistry Phosphothreonine/analogs & derivatives

Protein Conformation Protein Subunits

Nickel/metabolism* Peptides/chemistry*

Toxicity Tests Vanadium Compounds/chemical synthesis

Molecular Sequence Data Phylogeny

Gammaproteobacteria/enzymology Gammaproteobacteria/genetics*

Rats Research Support, Non-U.S. Gov't

Substances: Lipoproteins Protein Sorting Signals

Mutation Research SuppResearch SupResearch SuSaccharomyceSchizosaccharo

Prospective StuRespiratory D Statistics, Nonparametric

Time and Motion Studies

Grant Support: GM-44640/GM/NIGMS

Fungi/drug effe Gene ExpressiMolecular S Phylogeny Plant Diseas Plant Proteins/g

Research SupporTechnology Assessment, Biomedical*

Flax/cytology Flax/enzymol Flax/metaboHydrogen-ILignans/bios Lignans/isolatio

Reactive OxygeResearch SuppSignal TransTime FactoTrans-ActivatSubstances:

Gases Pteridines Solvents Water

Molecular Sequ Multigene FamOlfactory M Phylogeny Receptors, OReceptors, Odor

Radiation Injuri Skin/blood su Surgical Flaps*/blood supply*

SphingomyelinsG(M1) GanglioCholesterol 1-palmitoyl-2-oleoylphosphatidylcholine

Sensitivity and Serum AlbuminSpectrophotoSulfhydryl Sulfhydryl Sulfhydryl Reag

Genetic Marker Trypsin Inhibi Trypsin

Amino Acids Protein Subunnickel-iron Hydrogenase

Aquaporins Escherichia coMembrane PrOprF protePorins aqpZ protein, E

Triticum/geneti Triticum/microbiology*

OligonucleotidePlant Leaves/ Plant Roots/ Zea mays/ Zea mays/geSubstances:

Sequence AnalysSnails/embryoSnails/genetTranscripti Substances: DNA-Binding Pro

Substances: Homeodomain RNA, Messenger

Humans Protein Bindi RNA TranspoRNA, MesseRNA, MessenResearch Suppor

Microfilament PMicrofilament Models, Mol Protein Co Research SupSubstances:

Point Mutation Promoter RegiProtein Con Repressor Repressor PrResearch Suppor

Substances: Ascorbic Acid Iron 8-oxo-7-hyDeoxyguanosine

Solutions Substances: Cytochrome Ligands Solutions cyanoferricytoc

Multienzyme CoProtein Confo Research SuResearch SuSequence HoSynchrotrons

PhosphothreoniResearch SuppSpectrophotoSulfides/c Sulfites/chemSubstances:

Proteins/chemisProteins/metaResearch SuResearch SuSubstances: Iron-Sulfur Prot

Peptides/metabProtein FoldinResearch SuResearch SuResearch SuppSubstances:

Vanadium CompVanadium Co Substances:Vanadium Insulin Glucose

Research SupporSequence Ali Sequence AnSequence Zea mays/geSubstances:

Gene Dosage Molecular Se NitrosomonasNitrosomo NitrosomonasOperon

Research SupporReverse TransUp-Regulati SubstancesPD 180970 Pyridones

SchizosaccharomycesSequence Homology, Spectroscopy, MossbaTranscription Factors

Research Support, NoSequence Homology, Sodium Chloride/pha Substances:

Molecular Structure Phenylalanine AmmonPodophyllotoxin/analoPodophyllotoxin/biosy

Cytochrome c Group Isoenzymes Reactive Oxygen SpecNitric Oxide

Research Support, NoResearch Support, U.S.Sequence Alignment/ Sequence Analysis,

1-palmitoyl-2-oleoylphosphatidylcholine

Substances: Disulfides Proteins Pyridines

Bacteriorhodopsins

Carbocyanines DNA Probes DNA, ComplementaryFatty Acids

Transcription Factorssnail family transcription factors

Sequence Homology, Zebrafish/genetics Zebrafish/growth & d Zebrafish Proteins/ge

Actins Carrier Proteins Microfilament Protein fascin

Research Support, U.SSpectrophotometry/mStaphylococcus aureuSubstances:

Heme Cytochromes c

Substances: Bacterial Proteins Iron-Sulfur Proteins Multienzyme Complex

Metalloporphyrins Sulfides Sulfites titanium citrate

Membrane Proteins Photosynthetic React Photosystem I Protei Protein Subunits

Iron-Sulfur Proteins Metalloproteins Peptides Cysteine

DNA, ComplementaryMADS Domain ProteinSecondary Source ID: GENBANK/AJ271208

Oxidoreductases/geneProtein Structure, Se Research Support, NonResearch Support, U.S

Pyrimidines Grant Support: 6120-119-L0-A/PHS CA77049-02/CA/NCI

Transcription Factor Transcription Substances: Cross-Linking DNA-Binding PFerredoxins

ATP-Binding CassettDiterpenes Plant ProteinsTUR2 protein, Cadmium ChloAbscisic Acid

Podophyllotoxin/chePodophyllotoxResearch SuppSpectrum AnalSubstances: Carbon Isotop

Oxidoreductases alternative oxidase

Variation (Genetics) Substances: Drosophila Pr Receptors, Ododorant-bindi Grant Support

Serum Albumin, BovSulfhydryl C Sulfhydryl Re 4,4'-dipyridyl DithionitrobenMuramidase

cyanine dye 3 cyanine dye 5

Zebrafish Proteins/ Substances: Carrier Protei Drosophila Pr RNA, MessengZebrafish Prot

Bacterial Proteins CadC protein, Repressor ProCysteine Glycine Bismuth

prismane protein, DeAldehyde Oxi carbon monoxSecondary SouPDB/1GN9 PDB/1GNL

7-mercaptoheptanoyPhosphothreoChloroform factor F430 Nickel Citric Acid

Proteins photosystem ISecondary SouPDB/1K0T

Nickel Grant SupportGM28856/GM/NIGMS

GENBANK/AJ307056 GENBANK/AJ318098

Sequence Homology,Variation (GenSubstances: Ammonia Oxidoreducta ammonia monooxygenase

CA85052-A1/CA/NCI CA85429-01/CHL59781/HL/NHLBI

ISA1 protein, Iron-Sulfur Pr SaccharomycesTranscription Cysteine Alanine

sclareol Sodium Chlori2,4-Dichlorophenoxyacetic Acid

Cinnamates Coumaric Aci Lignans ferulic acid 3-(3,4-dimethPodophyllotox

5R01NS31231/NS/NINDS

Papain

partner of paired protein, Drosophila

Grant SupportGM42569/GM/NIGMS

PDB/1GNT Grant SupportGM5600/GM/NIGMS

Oxygen polysulfide Oxidoreducta methyl coenzyme M reductase

ammonia monooxygenase

Grant SupportGM08512-03/ GM59953/GM/NIGMS

sinapinic acid deoxypodophy3,4,5-trimeth Alcohol Oxidocinnamyl alcoAldehyde Oxi

cinnamoyl Co Phenylalanin Coenzyme A Lhydroxycinnamate-CoA ligase

Referencety. AVAILABILITY: Academic users should send their request for the perl program for calculating likelihood probabilities at [email protected]. SUPPLEMENTARY INFORMATION: The materials can be viewed at http://www.astrazeneca-montreal.com/AZRDM_info/supporting_info.pdf. Publication Types: Evalumber of classes in data (cancerous and normal). AVAILABILITY: JAVA software of dynamic SOM tree algorithm is available upon request for academic use. SUPPLEMENTARY INFORMATION: A comparison of rectangular and hexagonal topologies for GSOM is available from http://www.mame.mu.oz.au/mechatronics/journss data. Their capability of predicting protein functions generally falls between that of the Y2H data and that of the MIPS protein complex data. The supplementary information is available at the following Web site: http://www-hto.usc.edu/-msms/AssessInteraction/. PMID: 12603024 [PubMed - indexed foomparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods. SUPPLEMENTARY INFORMATION: http://www.stat.ohio-state.edu/~yklee/msvm.htm Publication Types: Evaluation Studies Validation Studies PMID: 12801874 [Pub ones to functionally annotate novel protein sequences from genomic projects. AVAILABILITY: MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html SUPPLEMENTARY INFORMATION: The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repairation is available at http://www.pathogenomics.sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors. SUPPLEMENTARY INFORMATION: An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/ures estimation, statistical significance test and extent prediction. AVAILABILITY: The software is available at: http://www.chgb.org.cn/lda/lda.htm. SUPPLEMENTARY INFORMATION: Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre versinteractions among gene products. Further, it integrates the capability of conducting both deterministic and stochastic simulations. AVAILABILITY AND SUPPLEMENTARY INFORMATION: Dynetica 1.0, example models, and the user's guide are available at http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.dy subjects. AVAILABILITY: Information on obtaining the executable code, example data, example analysis, and documentation is available upon request. SUPPLEMENTARY INFORMATION: All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR. PMID: 12584123 [PubMed - indexed fces (MIPS, mips.gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data. The supplementary data is available at www-hto.usc.edu/~msms/ProteinFunction. PMID: 14980019 [PubMed - indexed for MEDLINE]2). The option to directly submit probe sequences to the probe match tool of the Ribosomal Database Project II (RDP-II) further allows one to extract supplementary information on probe specificities. The two main features of probeBase, 'search probeBase' and 'find probe set', help researchers to fins available at http://www.imtech.res.in/raghava/propred1/. Mirror site of this server is available at http://bioinformatics.uams.edu/mirror/propred1/ Supplementary information: Matrices and document on server are available at http://www.imtech.res.in/raghava/propred1/page2.html Publication Types: Evclear receptor proteins, which took 11 min on a DEC Alpha 6100 computer Availability: RASCAL is available at ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL. SUPPLEMENTARY INFORMATION: http://bioinfo-igbmc.u-strasbourg.fr/BioInfo/RASCAL/paper/rascal_supp.html Publication Types: Evaluation Studies Validation

names or the correct closest spelling for a query compound name, if it exists. AVAILABILITY: Web-based interface available at http://ibb.uab.es/snow/ SUPPLEMENTARY INFORMATION: http://ibb.uab.es/snow/snow_moreinfo.html Publication Types: Evaluation Studies Validation Studies PMID: 14668242 [PubMed - disease phenotype due to the expansion potential of repeats present in them. The list of genes and other details of analysis are given in the online supplementary data (http://www.ingenovis.com/tripletrepeats). PMID: 12651711 [PubMed - indexed for MEDLINE]this information novel biological hypotheses may be addressed. AVAILABILITY: Venn Mapper is freely available on http://www.erasmusmc.nl/gatcplatform. SUPPLEMENTARY INFORMATION: http://www.erasmusmc.nl/gatcplatform/vennmapper.html. Publication Types: Evaluation Studies Validation Studies PMID: 145947rotocols. AVAILABILITY: The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/) Publicationplete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html Publication Types: Evaluationintensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment. SUPPLEMENTARY INFORMATION: http://sigwww.cs.tut.fi/TICSP/SpotQuality/. Publication Types: Evaluation Studies Validation Studies PMID: 14594707 [PubMedhe rate of false positives. AVAILABILITY: This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). SUPPLEMENTARY MATERIAL: ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf Publication Types: Evaluation Studies Validation Studies MeSH Terms:th the literature. AVAILABILITY: The implementation of this algorithm is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml Supplementary Information: Supplementary material is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml Publication Types: Esults. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/ PMID: 14512358 [PubMed - indexed for MEDLINE]publicly available data of TIGR (The Institute for Genomic Research). 1744 distinct RGAs were identified, 597 of which belonged to the NBS-LRR class. Supplementary data (sequences and annotations) is available on the web site http:/gkoczyk.bioinfo.pl/CMBL. PMID: 14668919 [PubMed - indexed for MEDLINreely available from http://www.bio.vu.nl/microb/research/tumor.html provided one adheres to the end-user license agreement in the associated manual. SUPPLEMENTARY INFORMATION: Above website also supplies the in- and output files used in the example run. PMID: 14555635 [PubMed - indexed for MEDLINE] can be trained on relatively small data sets to provide prediction more accurate than those based on previously published methods or on MHC binding. SUPPLEMENTARY INFORMATION: Data for 203 synthesized peptides is available at http://linus.nci.nih.gov/Data/LAU203_Peptide.pdf Publication Types: Evaluon of signals) we have shown that the novel system for comparative analysis of the properties of information-bearing biomolecules works as in theory. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/wavepaper. Publication Types: Evaluation Studies Validation Studies PMID: 14594705 [PubMed - indexed f

ion of the analysed experimental data to the databases. AVAILABILITY: ARIA 1.2 is available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/. SUPPLEMENTARY INFORMATION: XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the conversion of various NMR data formats and the re(or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf Publication Types: Evaluation Studies Validation Studies PMID: 1451s less than a second. For images with high expression rates ( approximately 90%) the registration time is even smaller, around a quarter of a second. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf PMID: 14512355 [PubMed - indexed for MEDLINE]d background model alleviates the drawbacks of MAP (maximum a posteriori log likelihood) scores. AVAILABILITY: Available on request from the authors. SUPPLEMENTARY INFORMATION: Data and the results presented in this paper are available on the web at http://compbio.ornl.gov/mira/index.html Publicatio by-product of bagged clustering are the cluster votes which can be used to assess the confidence of cluster assignments for individual observations. SUPPLEMENTARY INFORMATION: For supplementary information on datasets, analyses, and software, consult http://www.stat.berkeley.edu/~sandrine and http: each of the K queries, but BLAST++ completes the processing in a much shorter time. AVAILABILITY: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Supplementary information: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Publication Types: Evaluation Studies Validation Studies PMID: 14630666 lary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. SUPPLEMENTARY INFORMATION: http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guideequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a co1 and samples of input data sets on Windows PC are available at http://www.clab.kwansei.ac.jp/mining/discas/discas.html upon request from the author. SUPPLEMENTARY INFORMATION: Summary of prediction results and cross validations is accessible via http://www.clab.kwansei.ac.jp/~okada/BIJ/BIJsupple.htor high-throughput characterization of functional regions in proteins. AVAILABILITY: The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION: A set of examples is available at http://consurf.tau.ac.il under 'GALLERY'. PMID: 12499312 [PubMed - indexed for MEDLINE]d breast cancer, that we are able to identify partitions that elude standard clustering analysis. AVAILABILITY: Free, at http://ctwc.weizmann.ac.il.. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/ Publication Types: Evaluation Studies Validation Studies PMID:nts Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data Availability: Free, at http://ctwc.weizmann.ac.il. SUPPLEMENTARY INFORMATION: The site has a link to an example which provides figures and detailed explanations PMID: 12801877 [PubMed - indexed for MEDods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html Supplementary information: http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html Publication Types: Evaluation Studies Validation Studies PMID: 14512346 [PubMed - indexed for MEDLINE]

dels. In addition to accuracy, our method also provides comprehensible rules to help elucidate the translation between raw data and useful knowledge. Supplementary information: http://sdmc.i2r.a-star.edu.sg/GEDatasets/supplementaldata/eccb2003/ECCB2003.html . Contact: [email protected] PMID: B files including modeled disulfides. Validation demonstrates a high level of accuracy for the algorithm. AVAILABILITY: http://www.ehscenter.org/dbd/ Supplementary information: http://www.ehscenter.org/dbd/ Publication Types: Evaluation Studies Validation Studies PMID: 14512360 [PubMed - indexed forUpon request from the corresponding author. Free for academic users (license agreement). Special contracts are available for industrial corporations. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer. Publication Types: Evaluation Studies PMID: 12538248 [PubMed - index and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html Supplementary information: http://www.chip.org/~ge/gedihome.html PMID: 14630665 [PubMed - indexed for MEDLINE]at the same time being more specific. Availability: A web interface for AUGUSTUS and the executable program are located at http://augustus.gobics.de. Supplementary Information: The datasets used for testing and training are available at http://augustus.gobics.de/datasets/ Contact: [email protected] PMsition to breast cancer, and the method is used to identify a set of significant genes. The method is also applied successfully to the leukemia data. SUPPLEMENTARY INFORMATION: http://stat.tamu.edu/people/faculty/bmallick.html. Publication Types: Evaluation Studies Validation Studies PMID: 12499298 red so as to be easily modified for viewing data from any database that stores gene structures. AVAILABILITY: The GeneComber public web interface and supplementary information is located at http://bioinformatics.ubc.ca/genecomber The source code is released under the GNU General Public License and ilso provides an explanation mechanism that traces every finding to the pertinent data. AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp. Publication Types: Evaluation Studies PMID: 12584124 [that GA-based algorithms may represent a powerful new tool in the analysis and exploration of complex multi-class gene expression data. AVAILABILITY: Supplementary information, data sets and source codes are available at http://www.omniarray.com/bioinformatics/GA. Publication Types: Evaluation Studisequence analysis. AVAILABILITY: gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below. Supplementary information: http://genome.imim.es/software/gfftools/GFF2APLOT.html Publication Types: Evaluation Studies PMID: 14668236 [PubMed - indexwork integrities. Such difference between different experimental methods can provide insight into the systematic bias present among these techniques. SUPPLEMENTARY INFORMATION: The full list of our results can be found in the supplemental web site http://www.nas.nasa.gov/Groups/SciTech/nano/msamantath operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation. AVAILABILITY: Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html Publication Types: Evaluation Studies Vathod outperforms existing methods for numerical data. Availability: Programs transforming input data into LP format files are available upon request. Supplementary information: http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/supplement.html Contact: [email protected] PMID: 14534173 [

idea when combined with a learning algorithm, such as the support vector machine that does not suffer from the curse of dimensionality. AVAILABILITY: Supplementary data at www.cs.columbia.edu/compbio/hiclust. Software source code available by request. Publication Types: Evaluation Studies Validationously published by Cho et al. (Nat. Genet., 27, 48-54, 2001). AVAILABILITY: The Rosetta system is available at http://www.idi.ntnu.no/~aleks/rosetta. SUPPLEMENTARY INFORMATION: http://www.lcb.uu.se/~hvidsten/bioinf_cho/ Publication Types: Evaluation Studies Validation Studies PMID: 12801872 [PubMed d if the bias is rational. AVAILABILITY: Java code of the algorithm can be found at http://www.csse.monash.edu.au/~lloyd/tildeProgLang/Java2/Biased/. SUPPLEMENTARY INFORMATION: Examples of applications to Plasmodium falciparum genomic DNA can be found at the above URL. PMID: 12835276 [PubMed - index clusters obtained. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html SUPPLEMENTARY INFORMATION: http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html Publication Types: Evaluation Studies Validation Studies PMID: 14668243 in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html SUPPLEMENTARY INFORMATION: The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html ains having different genotypes under various environmental conditions, and automated pathway layout creation. AVAILABILITY: http://mbel.kaist.ac.kr/ Supplementary information: A manual for MetaFluxNet is available as PDF file. PMID: 14594721 [PubMed - indexed for MEDLINE]of multiple reporters per gene, use of replicate experiments, and sample referencing schemes in measurements based on expression change. AVAILABILITY/SUPPLEMENTARY INFORMATION: Expression data and supplementary information are available at http://www.rii.com/publications/2003/HE_SDS.htm Publication

environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/promot PMID: 12801880 [PubMed - indexed for MEDLINE] allows for ranking of their predicted functional consequences based on conservation in multiple sequence alignments. AVAILABILITY: http://mutdb.org/ Supplementary information: http://mutdb.org/about/about.html PMID: 14512363 [PubMed - indexed for MEDLINE] newly developed software. AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/ Supplementary information: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodiOur program provides an optimal method for performing this task. AVAILABILITY: The software is available, free of charge, on request from Oxagen Ltd. SUPPLEMENTARY INFORMATION: http://www.oxagen.co.uk PMID: 12538255 [PubMed - indexed for MEDLINE]her database systems over the network, and it represents a complete solution for the management of the entire manufacturing process. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html PMID: 12538251 [PubMed - indexed for MEDLINE]tware for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002 Publication Types: Evaluation Stuanother independent data sets are also presented to show the strength of our method. AVAILABILITY: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information. Publication Types: Evaluation Studies Validation Studies PMID: 12499295 [PubMed - indexed for MEDLINE]

at lies within a given distance of a real SNP. AVAILABILITY: The software is available, free of charge, for academic use on request from the authors. SUPPLEMENTARY INFORMATION: www.oxagen.co.uk PMID: 14594720 [PubMed - indexed for MEDLINE]Y: An academic version of the algorithm (full source listing in standard C language) can be freely downloaded (http://www.caspur.it/~castri/STRING/). SUPPLEMENTARY INFORMATION: Some illustrative figures and some sample results are provided as supplementary material at: http://www.caspur.it/~castri/SABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/ Publication Types: Evaluation Studies provides good approximations to the responses of this complex system. AVAILABILITY: FUNDER is available from http://bbm1.ucm.es/torralba/funder/down/ SUPPLEMENTARY INFORMATION: http://bbm1.ucm.es/torralba/funder/ Publication Types: Evaluation Studies Validation Studies PMID: 14668227 [PubMed - index have a high reliability and separating them from tags that carry an inherent ambiguity in their capacity to discriminate between genes. To this end, supplementary information in the form of a web companion to this paper is located at http:// biobase.biotech.kth.se/tagseq. PMID: 12682372 [PubMed - i intervals. AVAILABILITY: The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site. SUPPLEMENTARY INFORMATION: http://www.ime.usp.br/~rvencio/SAGEci/ Publication Types: Evaluation Studies Validation Studies PMID: 14668232 [PubMed - inicle if you access the article at http://dx.doi.org/10.1007/s00894-003-0118-0. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Structure 1 of the N15m cluster, showing bond distances in A and bond angles in degrees PMID: 12707803 [PubMed - in prole if you access this article at http://dx.doi.org/10.1007/s00122-002-1182-z. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: Animals Diptera/physiology* Genes, Plant* Poaceae/genetics* Polyploidy* Research Support, Non-U.S. Gov't Transfectsurements of positions of cells in 3D matrices by eliminating the need to perform optical sectioning and can be used with any brightfield microscope. Supplementary material for this article can be found at http://www.interscience.wiley.com/jpages/0196-4763/suppmat/54_2/v54.125.html Copyright 2003 Wihis report presents two new cases of CPLS, and suggests that the CPLS phenotype may represent the mild end of the Fryns syndrome phenotypic spectrum. Supplementary material for this article can be found on the Birth Defects Research (Part A) website (http://www.interscience.wiley.com/ jpages/1542-07

transcriptionally active cell responsive to environmental stimuli and capable of a complex series of both early and late changes in gene expression. Supplementary material for this article can be found on the Journal of Cellular Biochemistry website (http://jws-edci.interscience.wiley.com:8998/jpaget allows a safe diagnostic FOB with BAL in patients with hypoxemic ARF, avoiding gas exchange deterioration, and endotracheal intubation. Electronic supplementary material: is available if you access this article at http://dx.doi.org/10.1007/s00134-002-1554-5. On that page (frame on the left side),fter cardiothoracic surgery alters nursing activity; it reduces the time for documentation and increases the time devoted to patient care. Electronic supplementary material: is available if you access this article at http://dx.org/10.1007/s00134-002-1542-9. On that page (frame on the left side), a l

icle if you access the article at http://dx.doi.org/10.1007/s00894-003-0116-2. A link in the frame on the left on that page takes you directly to the supplementary material. PMID: 12838399 [PubMed - in process]

icle if you access the article at http://dx.doi.org/10.1007/s00894-002-0114-9. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Docking structures of1 and2 binding with oligonucleotide: l-Ser-Hism.5'-TpTpdC-3'(left), d-Ser-Hism.5'-TpTpdC-3'(right)cific expression, genomic organization and evolutionary conservation of the different PAD isotypes will be discussed in detail. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2003/25/v25.1106.htmwork properties shed new light on the basis of human cognitive diseases including schizophrenia, autism, Huntington's disease and mental retardation. Supplementary material for this article can be found on the BioEssays website http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html. Ces well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/bioinformatics/ Publication Types: Evaluation Studies PMID: 12874056 [PubMed - indexed for MEDLINE]istalsis was demonstrated on cine MR using ultrafast MRI. Direction and frequency of peristaltic waves are closely related to menstrual cycle phases. Supplementary material for this article can be found on the JMRI website at http://www.interscience.wiley.com/jpages/1053-1807/suppmat/index.html. Copof W3110 in the absence of MgCl(2). The expression ratios of a total of 232 genes were <0.75 in all three strains (the supplemental data are shown at http://www.nara.kindai.ac.jp/nogei/seiken/array.html), suggesting that the PhoP/PhoQ system is involved directly or indirectly in the transcription of

Live?

No

no

no

no

No

no

NO

no

no

no

no

No

No

no

no

no

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

Yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

Yes

yes

yes

yes

yes

yes

yes

Yes

yes

yes

yes

yes

Yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

yes

no

Journal?

n 64: Bioinformati

n 18: Bioinformati

n 55: Pac Symp Bi

n 44: Bioinformati

n 37: Bioinformati

n 57: Bioinformati

n 15: Bioinformati

n 56: Bioinformati

n 59: Bioinformati

n 1: J Comput Biol

n 66: Nucleic Acid

n 50: Bioinformati

n 42: Bioinformati

n 4: Bioinformatic

n 53: Bioinformati

n 20: Bioinformati

n 49: Bioinformati

n 65: Bioinformati

n 21: Bioinformati

n 1: Bioinformatic

n 14: Bioinformati

n 31: Bioinformati

n 2: Cell Mol Biol

n 23: Bioinformati

n 24: Bioinformati

n 22: Bioinformati

n 60: Bioinformati

n 33: Bioinformati

n 32: Bioinformati

n 25: Bioinformati

n 46: Bioinformati

n 12: Bioinformati

n 10: Bioinformati

n 67: Nucleic Acid

n 40: Bioinformati

n 68: Bioinformati

n 47: Bioinformati

n 43: Bioinformati

n 34: Bioinformati

n 27: Bioinformatic

n 30: Bioinformati

n 63: Bioinformati

n 13: Bioinformati

n 26: Bioinformatic

n 69: Bioinformati

n 38: Bioinformati

n 58: Bioinformati

n 71: Bioinformati

n 5: Bioinformatic

n 9: Bioinformatic

n 48: Bioinformati

n 28: Bioinformatic

n 19: Bioinformati

n 45: Bioinformati

n 39: Bioinformati

n 3: Bioinformatic

n 7: Bioinformatic

n 16: Bioinformati

n 51: Bioinformati

n 41: Bioinformati

n 29: Bioinformati

n 11: Bioinformati

n 61: Bioinformati

n 62: Bioinformati

n 72: Bioinformati

n 70: Bioinformati

n 17: Bioinformati

n 35: Bioinformati

n 54: Bioinformati

n 8: Bioinformatic

n 52: Nucleic Acid

n 6: Bioinformatic

y 12: J Mol Model

y 11: Theor Appl

y 8: Cytometry A.

y 7: Birth Defects

y 9: J Cell Biochem

y 16: Intensive Ca

y 17: Intensive Ca

y 10: J Mol Model

y 13: J Mol Model

y 5: Bioessays. 20

y 2: Bioessays. 20

y 36: Bioinformati

y 3: J Magn Reson

n

1: J Bacteriol. 2003 Jul;185(13):3696-702.

A naive Bayes model to predict coupling between receptors and PMID: 12538244 [PubMed - indexed for MEDLINE]

An unsupervised hierarchical dynamic self-organizi discovery and PMID: 14594719 [PubMed - indexed for MEDLINE]

Assessment of the reliability of protein-protein inte function predicPMID: 12603024 [PubMed - indexed for MEDLINE]

Classification of multiple cancer types by multicat using gene expPMID: 12801874 [PubMed - indexed for MEDLINE]

Identifying property based sequence motifs in protesuperfamilies: PMID: 12874050 [PubMed - indexed for MEDLINE]

IslandPath: aiding detection of genomic islands in p Hsiao W, Wan IPMID: 12584130 [PubMed - indexed for MEDLINE]

LDA--a java-based linkage disequilibrium analyzer. Ding K, Zhou KPMID: 14594722 [PubMed - indexed for MEDLINE]

Modeling biological systems using Dynetica--a simuYou L, Hoonlor PMID: 12584138 [PubMed - indexed for MEDLINE]

Multifactor dimensionality reduction software for d gene-environmePMID: 12584123 [PubMed - indexed for MEDLINE]

Prediction of protein function using protein-protein Deng M, Zhang PMID: 14980019 [PubMed - indexed for MEDLINE]

probeBase: an online resource for rRNA-targeted ol Loy A, Horn M PMID: 12520066 [PubMed - indexed for MEDLINE]

ProPred1: prediction of promiscuous MHC Class-I binSingh H, Ragh PMID: 12761064 [PubMed - indexed for MEDLINE]

RASCAL: rapid scanning and correction of multiple Thompson JD, TPMID: 12801878 [PubMed - indexed for MEDLINE]

SNOW: standard nomenclature wizard to help searchstandardized PMID: 14668242 [PubMed - indexed for MEDLINE]

Triplet repeats in human genome: distribution and tand other genoPMID: 12651711 [PubMed - indexed for MEDLINE]

Venn Mapping: clustering of heterologous microarr co-occurring d PMID: 14594711 [PubMed - indexed for MEDLINE]

3D-Jury: a simple approach to improve protein strucGinalski K, Elo PMID: 12761065 [PubMed - indexed for MEDLINE]

A comparison of normalization methods for high dendata based on PMID: 12538238 [PubMed - indexed for MEDLINE]

A novel strategy for microarray quality control usi Hautaniemi S, PMID: 14594707 [PubMed - indexed for MEDLINE]

A random variance model for detection of differenti microarray ex PMID: 14668230 [PubMed -

A simple and efficient algorithm for gene selection uregression. PMID: 14630653 [PubMed - indexed for MEDLINE]

A tool-kit for cDNA microarray and promoter analysiShah NH, King PMID: 14512358 [PubMed - indexed for MEDLINE]

An assessment of the resistance gene analogues of their presencePMID: 14668919 [PubMed - indexed for MEDLINE]

Analysing gene expressions with GRANK. de Boer WP, OuPMID: 14555635 [PubMed - indexed for MEDLINE]

Application of support vector machines for T-cell epZhao Y, Pinilla PMID: 14555632 [PubMed - indexed for MEDLINE]

Applying signal theory to the analysis of biomoleculKauer G, BlockPMID: 14594705 [PubMed - indexed for MEDLINE]

ARIA: automated NOE assignment and NMR structureLinge JP, Habe PMID: 12538267 [PubMed - indexed for MEDLINE]

Automatic registration of microarray images. I. RectGalinsky VL. PMID: 14512354 [PubMed - indexed for MEDLINE]

Automatic registration of microarray images. II. HexGalinsky VL. PMID: 14512355 [PubMed - indexed for MEDLINE]

Background rareness-based iterative multiple sequeregulatory ele PMID: 14555629 [PubMed - indexed for MEDLINE]

Bagging to improve the accuracy of a clustering pr Dudoit S, Fridl PMID: 12801869 [PubMed - indexed for MEDLINE]

BLAST++: BLASTing queries in batches. Wang H, Ooi BCPMID: 14630666 [PubMed - indexed for MEDLINE]

caCORE: a common infrastructure for cancer informaCovitz PA, Har PMID: 14668224 [PubMed - indexed for MEDLINE]

CATMA: a complete Arabidopsis GST database. Crowe ML, SeriPMID: 12519971 [PubMed - indexed for MEDLINE]

Characteristic substructures and properties in chemthe cascade mPMID: 12835263 [PubMed - indexed for MEDLINE]

ConSurf: identification of functional regions in pro phylogenetic i PMID: 12499312 [PubMed - indexed for MEDLINE]

Coupled two-way clustering analysis of breast canc expression datPMID: 12801868 [PubMed - indexed for MEDLINE]

Coupled two-way clustering server. Getz G, DomanPMID: 12801877 [PubMed - indexed for MEDLINE]

DDBASE2.0: updated domain database with improved domains. PMID: 14512346 [PubMed - indexed for MEDLINE]

Discovery of significant rules for classifying cancer Li J, Liu H, Ng PMID: 14534178 [PubMed - in process]

Disulfide by Design: a computational method for the bonds in protePMID: 14512360 [PubMed - indexed for MEDLINE]

FluxAnalyzer: exploring structure, pathways, and flunetworks on inPMID: 12538248 [PubMed - indexed for MEDLINE]

Gene Expression Dynamics Inspector (GEDI): for inteexpression profPMID: 14630665 [PubMed - indexed for MEDLINE]

Gene prediction with a hidden Markov model and a Stanke M, WaaPMID: 14534192 [PubMed - in process]

Gene selection: a Bayesian variable selection approLee KE, Sha N,PMID: 12499298 [PubMed - indexed for MEDLINE]

GeneComber: combining outputs of gene prediction Shah SP, McVicPMID: 12835277 [PubMed - indexed for MEDLINE]

GenePath: a system for automated construction of data. PMID: 12584124 [PubMed - indexed for MEDLINE]

Genetic algorithms applied to multi-class predictionexpression datPMID: 12499291 [PubMed - indexed for MEDLINE]

gff2aplot: Plotting sequence comparisons. Abril JF, Guigo PMID: 14668236 [PubMed - indexed for MEDLINE]

Global snapshot of a protein interaction network-a Chin CS, SamaPMID: 14668225 [PubMed - indexed for MEDLINE]

Hierarchical analysis of dependency in metabolic n Gagneur J, Jac PMID: 12761067 [PubMed - indexed for MEDLINE]

Inferring strengths of protein-protein interactions linear progra PMID: 14534173 [PubMed - in process]

Kernel hierarchical gene clustering from microarrayQin J, Lewis D PMID: 14594715 [PubMed - indexed for MEDLINE]

Learning rule-based models of biological process f profiles using PMID: 12801872 [PubMed - indexed for MEDLINE]

Longest biased interval and longest non-negative suAllison L. PMID: 12835276 [PubMed - indexed for MEDLINE]

Machaon CVE: cluster validation for gene expressio Bolshakova N, PMID: 14668243 [PubMed - indexed for MEDLINE]

Metabolic pathways in three dimensions. Rojdestvenski IPMID: 14668228 [PubMed - indexed for MEDLINE]

MetaFluxNet: the management of metabolic reactionmetabolic flux PMID: 14594721 [PubMed - indexed for MEDLINE]

Microarray standard data set and figures of merit f methods and ePMID: 12761058 [PubMed - indexed for MEDLINE]

Modular modeling of cellular systems with ProMoT/DGinkel M, KremPMID: 12801880 [PubMed - indexed for MEDLINE]

MutDB: annotating human variation with functionallMooney SD, AlPMID: 14512363 [PubMed - indexed for MEDLINE]

NCL: a C++ class library for interpreting data files Lewis PO. PMID: 14630669 [PubMed - indexed for MEDLINE]

Pedstrip: extracting a maximal subset of available, pedigree. PMID: 12538255 [PubMed - indexed for MEDLINE]

QuickLIMS: facilitating the data management for DNKokocinski F, PMID: 12538251 [PubMed - indexed for MEDLINE]

Representation of DNA sequences with virtual potent(SEQREP) KohoPMID: 12499290 [PubMed - indexed for MEDLINE]

Simple rules underlying gene expression profiles of acute lymphoblPMID: 12499295 [PubMed - indexed for MEDLINE]

SNP cherry picker: maximizing the chance of findingdisease SNP. PMID: 14594720 [PubMed - indexed for MEDLINE]

STRING: finding tandem repeats in DNA sequences. Parisi V, De FoPMID: 14512342 [PubMed - indexed for MEDLINE]

Subnetwork hierarchies of biochemical pathways. Holme P, Huss PMID: 12611809 [PubMed - indexed for MEDLINE]

Susceptibility of non-linear systems as an approach Torralba AS. PMID: 14668227 [PubMed - indexed for MEDLINE]

Transcript identification by analysis of short sequenlength, restric PMID: 12682372 [PubMed - indexed for MEDLINE]

Using credibility intervals instead of hypothesis tes Vencio RZ, BrePMID: 14668232 [PubMed - indexed for MEDLINE]

A computer-aided quantum chemical study of the N(1Cheng L, Li Q, PMID: 12707803 [PubMed - in process]

A new Hessian fly resistance gene (H30) transferredtriuncialis to PMID: 12748776 [PubMed -

An aperture-shifting light-microscopic method for raof cells in 3D PMID: 12879459 [PubMed -

Cleft-palate lateral synechia syndrome: insight int Fryns syndromPMID: 12962292 [PubMed -

Erratum in: J Cell Biochem PMID: 12858349 [PubMed -

Fiberoptic bronchoscopy during noninvasive positivedelivered by h PMID: 12528033 [PubMed -

Intensive care information system reduces documentcardiothoracic PMID: 12528027 [PubMed -

Molecular crystals: the crystal field effect on molecuYatsenko AV. PMID: 12838399 [PubMed - in process]

Molecular modeling of diastereoisomeric aggregateswith 5'-TpTpdCPMID: 12707801 [PubMed - in process]

PAD, a growing family of citrullinating enzymes: ge in disease. PMID: 14579251 [PubMed -

Synapse signalling complexes and networks: machinGrant SG. PMID: 14635258 [PubMed -

The connectivity structure, giant strong component networks. PMID: 12874056 [PubMed - indexed for MEDLINE]

Uterine peristalsis shown on cine MR imaging using Nakai A, TogasPMID: 14635158 [PubMed -

Escherichia colPMID: 12813061 [PubMed - Identification and molecular characterization of the Mg2+ stimulon of







MeSH Terms: Algorithms* Analysis of Varia







PMID: 14534178 [PubMed - in process]




















MeSH Terms: Animals Diptera/physiolog

MeSH Terms: Calibration Cell Line, Tumor

MeSH Terms: Abnormalities, MAbnormalities, Mu

MeSH Terms: Cluster Analysis Comparative Stud





MeSH Terms: Amino Acid Seq Animals

MeSH Terms: Animals Humans


MeSH Terms: Adult Female

MeSH Terms: Bacterial Protei Bacterial Protein

Comparative Study False Positive Reactions Gene Expression Profiling/me

Genes, Plant* Poaceae/genetics* Polyploidy*

Cells/cytology* Collagen/chemistry Humans

Adhesions/congenital Adhesions/genetics Adhesions/pathology

Escherichia coli/chemistry Gene Expression/drug effGene Expression Profiling/me

Anoxemia/diagnosis Bronchoalveolar Lavage Bronchoscopy/methods*

Cardiac Surgical Procedures/nursi Efficiency, OrganizationalFemale

Arthritis, Rheumatoid/enzymologyHumans Hydrolases/classification

Models, Biological Models, Theoretical Nerve Net*

Humans Image Processing, CompuMagnetic Resonance Imaging,

Base Sequence DNA Footprinting Deoxyribonucleases/metaboli

Models, Genetic* Models, Statistical*

Research Support, Non-U.S. Gov't Transfection*

Image Processing, Computer-Assi Microscopy/methods*

Alveolar Process/abnormalities Cleft Palate/genetics

Humans Lipopolysaccharides/pharmacology*

Female Fiber Optics*

Hospital Information Systems* Humans

Hydrolases/genetics* Hydrolases/metabolism*

Neurons/physiology* Protein Binding

Menstrual Cycle/physiology* Uterine Contraction/physiology*

Escherichia coli/genetics Escherichia coli/metabolism*

Oligonucleotide Array Seq Reproducibility of Results Sample Size

Triticum/genetics*

Microscopy, Fluorescence Microscopy, Video Research Support, U.S. Gov't,

Cleft Palate/pathology* DNA/analysis Diseases in Twins*

Multigene Family Neutrophil Activation/drug effects Neutrophil Activation/physio

Head Protective Devices* Humans Male

Intensive Care Units* Male Middle Aged

Isoenzymes/classification Isoenzymes/genetics* Isoenzymes/metabolism*

Receptors, N-Methyl-D-AspResearch Support, Non-U.S. Gov't Signal Transduction*

Escherichia coli Proteins/g Escherichia coli Proteins/metabolism* Gene Expression Profiling

Sensitivity and Specificity Sequence Analysis, DNA/methods*

Substances: Collagen

Face/abnormalities Fatal Outcome

Neutrophils/drug effects* Neutrophils/physiology

Middle Aged Pneumonia/diagnosis*

Netherlands Nursing Staff, Hospital/organization & administration

Molecular Sequence Data Multigene Family

Synapses/physiology* Substances:

Gene Expression RegulatioMagnesium/pharmacology*

Variation (Genetics)

Grant Support: R24-CA-56591/CA/NCI

Female Humans Infant, Newborn

Oligonucleotide Array SequencRNA/analysis RNA/genetics

Positive-Pressure Respiration/ Prospective Studies Respiratory Distress

Thoracic Surgical Procedures/ Time and Motion Studies

Multiple Sclerosis/enzymologyPhylogeny Protein Conformation

Receptors, N-Methyl-D-Aspartate

Molecular Sequence Data Oligonucleotide Array Sequence AnPromoter Regions (Ge

Minisatellite Repeats/gMouth AbnormaMouth AbnormalitiPolymerase Chain Reacti

Research Support, NonResearch SuppoSubstances: Lipopolysaccharides

Statistics, Nonparametric

Psoriasis/enzymology Sequence Ali Substances: Isoenzymes

Research Support, NonSignal Transd Transcription, GenSubstances:

Research Support, Non-Syndrome Twins, MonozSubstances: DNA

RNA Grant Support: R01-DK54369/DK/NIDDK

Hydrolases protein-arginine deiminase

Bacterial Proteins Escherichia coli Protein PhoQ proteinPhoP protein, Bacteri Magnesium

Deoxyribonucleases

Reference interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications. Publication Types: Evaluation Studies PMID: 15613400 [PubMed - isting programs (ADHoRe and LineUp) for chromosomal homology detection and found that in general CloseUp compares favorably. AVAILABILITY: CloseUp and supplementary information are available at http://www.igb.uci.edu/servers/cgss.html CONTACT: [email protected]. Publication Types: Evaluation Studiegnments. In all experiments, the sample temperature was 120 degrees C, to ensure a homogeneous solution and sufficient molecular mobility. Electronic Supplementary Material: Supplementary material (1D 13C NMR spectra of the 13C-labeled and unlabeled polymers) is available in the online version of thed gene order from annotated genomes. AVAILABILITY: Available free of charge for Unix/Linux/Cygwin platforms at ftp://159.149.110.11/pub/GeneSyn_1.0/ SUPPLEMENTARY INFORMATION: ftp://159.149.110.11/pub/GeneSyn_1.0/ Publication Types: Evaluation Studies PMID: 14976031 [PubMed - indexed for MEDLINE]tally testable hypotheses. AVAILABILITY: Supplementary data and Matlab computer source code will be made available on the web at the URL given below. SUPPLEMENTARY INFORMATION: http://public.kgi.edu/~wild/LDS/index.htm Publication Types: Evaluation Studies Validation Studies PMID: 14962938 [PubMed -rogression of cancer. Although some genetic changes were associated only with the 8p pathway, most secondary genetic changes appear in both pathways. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair. AVAILABILITY: http://genecards.weizmann.ac.il/geneannot/ SUPPLEMENTARY INFORMATION: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html Publication Types: Evaluation Sn for arbitrary natural and random sequences. AVAILABILITY: paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass SUPPLEMENTARY INFORMATION: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnassbiology and differentiation-specific expression patterns and gives important clues related to the possible cellular origin of these pediatric tumors. Supplementary material for this article is available at the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7strate that our method has improved power in finding physically close residues in crystal structures, compared to that of Ranganathan and colleagues. SUPPLEMENTARY INFORMATION: www.afodor.net/bioinfosup.html Publication Types: Evaluation Studies Validation Studies PMID: 14962924 [PubMed - indexed foor the late and continuous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html

h E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences. SUPPLEMENTARY INFORMATION: All the kinetic data are available via http://www.e-cell.org PMID: 14962921 [PubMed - indexed for MEDLINE]parison of individuals with NS and individuals with VCFS, a correct identification rate of 95% was achieved for both syndromes. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/

ible methods, log ratio values and a list of genes showing significant variations between conditions. AVAILABILITY: http://www.bionet.espci.fr/varan/ SUPPLEMENTARY INFORMATION: http://www.bionet.espci.fr/varan/help.html PMID: 14962915 [PubMed - indexed for MEDLINE]mportant results. AVAILABILITY: The software module dChipSNP implementing these methods is available at http://biosun1.harvard.edu/complab/dchip/snp/ SUPPLEMENTARY INFORMATION: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart. Publication Types: Evalesidues that have potential structural or functional importance. AVAILABILITY: The ConSeq web server is available at http://conseq.bioinfo.tau.ac.il/ SUPPLEMENTARY INFORMATION: The ConSeq methodology, a description of its performance in a set of five well-documented proteins, a comparison to other m and the characteristics of the subgraphs resulting from the application of our software to the revised datasets. AVAILABILITY: Complete datasets and supplementary material may be downloaded from http://helix.ex.ac.uk/metabolism. The software for the creation of enzyme-centric graphs from reaction dmonline.unibas.ch/; http://germonline.igh.cnrs.fr/), Japan (http://germonline.biochem.s.u-tokyo.ac.jp/) and USA (http://germonline.yeastgenome.org/). SUPPLEMENTARY INFORMATION: Extended documentation of the database is available through the link 'About GermOnline' at the websites. PMID: 14751982 [Pu needed to bring under control the tobacco-related lung cancer epidemic in European women before it reaches the high level observed in North America. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7bly information. Results are output in spreadsheets containing information that facilitates manual validation. AVAILABILITY: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/ CONTACT: [email protected]. PMID: 15585532 [PubMed -d adapted by groups working on diverse EST sequencing projects. AVAILABILITY: The system and source code are available upon request from the authors. Supplementary information: http://EST-PAGE.binf.gmu.edu PMID: 14734326 [PubMed - indexed for MEDLINE]mining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athenated annealing heuristic. LVB runs fast and gives high quality results. AVAILABILITY: The software is available at http://www.rubic.reading.ac.uk/lvb/ Supplementary information: Supplementary information may be downloaded from http://www.rubic.reading.ac.uk/~daniel/ Publication Types: Evaluation Studf the probe set. AVAILABILITY: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. Supplementary information: http://pbil.univ-lyon1.fr/roso Publication Types: Evaluation Studies Validation Studies PMID: 14734320 [PubMed - indexed fo found by other clustering methods. AVAILABILITY: The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/ Publication Types: Evaluation Studies Validation Studies PMID: 1 as some novel genes. AVAILABILITY: R code for the empirical Bayes adjustment and step-down P-value calculation via resampling are available from the supplementary web-site. Supplementary information: http://www.mathstat.gsu.edu/~matsnd/EB/supp.htm Publication Types: Evaluation Studies Validation St

emonstrate the feasibility of using automated microscopy as a high-throughput screen for identifying modulators of large-scale chromatin folding. The Supplementary Material referred to in this article can be found at the CYTO Part A website (http://www.interscience.wiley.com/jpages/0196-4763/suppmational feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below). Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer Publication Types: Evaluation Studies Validation Studies PMID: 147343ical pieces of evidence to be considered in order to enhance the therapeutic benefit of a strategy that is currently being tested in clinical trials. Supplementary Material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7VAILABILITY: The program has been implemented in ANSI C and is freely available for academic use at http://www.cse.wustl.edu/~zhang/projects/rna/ilm/ Supplementary information: http://www.cse.wustl.edu/~zhang/projects/rna/ilm/ Publication Types: Evaluation Studies Validation Studies PMID: 14693809 [ces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Oryza sativa, Arabidopsis thaliana and a subset of all human proteins. AVAILABILITY: Supplementary information and subcellular location annotations for eukaryotes are available at http://166.111.30.65/hying/fuzzy_loc.htm Publication Tyels of disulphide-rich short polypeptides. The database can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/dsdbase.html. Supplementary information can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/nar/suppl.htm. PMID: 14681394 [PubMed - indeclassification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: e proposed for data normalized using methods established in the field of proteomics. AVAILABILITY: Software is available on request from the authors. SUPPLEMENTARY INFORMATION: There is supplementary material available online at http://www.flychip.org.uk/kreil/pub/2dgels/ Publication Types: Evaluatio SFTPC mutation from interstitial lung disease to PAP. Notably, the reported mutations do not appear to be dominant negatives. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/methods we propose are capable of deducing and quantifying functional interactions within and across cellular gene, signaling and metabolic networks. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dbi.tju.edu/bioinformatics2004.pdf Publication Types: Evaluation Studies e use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt. Publication, standardized exercise testing and training programs appear to be underused in German CF centers, despite a high degree of interest in the topic. Supplementary material for this article can be found on the Pediatric Pulmonology website (http//www.interscience.wiley.com/jpages/8755-6863/suppmat).

matic change in the gene expression program during the transition of fetal liver progenitor cells from an undifferentiated to a differentiated state. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Mer these loci. However, the differences between the two populations suggest that population specific locus heterogeneity exists. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/ted in cancer. Our results have provided further insight into the roles of TERT and ATM by identifying genes likely to be involved in their function. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-225downloaded from http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN. It underlies the GPL version 2. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~f it possible to target most of the known HLA alleles with known specificities using only a few peptides, and may be used in construction of vaccines. Supplementary material is available at http://www.cbs.dtu.dk/researchgroups/immunology/supertypes.html. MeSH Terms: Amino Acid Motifs Cluster AnalysisGene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/ven two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. AVAILABILITY: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/ Publication Types: Evaluation Studies Meich may be used as candidate markers for diagnosing the early onset of HCC in high-risk populations and may guide new strategies for chemoprevention. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me mRNA levels, controlling most, if not all, intracellular events from early signaling to the final secretion of proteins involved in innate immunity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me to a better understanding of the clinical evolution of familial adenomatous polyposis and to finding of new prophylactic and therapeutic approaches. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7cuss these issues and some methodological approaches that can detect multilocus effects, using hypertension as a model disease. This article contains supplementary material, which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html. Copyrigest possible mechanisms of action of the core elements in the promoters with multiple transcription start sites. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf. Publication Types: Eva membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis. AVAILABILITY: Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm Publication Types: Evaluation Studies Validation Studies M

d that the salivary proteins are less conserved than the housekeeping proteins, and therefore are changing at a faster evolutionary rate. Tabular and supplementary material containing the cDNA sequences and annotations are available at http://www.ncbi.nlm.nih.gov/projects/Mosquito/A_darlingi_sialomedata set on acute lymphocytic leukemia. AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml. Publication Types: Evaluation Studies PMID: 15572464 [PubMed - indeults demonstrate that mammalian viral genome types differ in their amino acid preference. AVAILABILITY: The tools used to format and analyze data and supplementary material are available at http://www.cse.sc.edu/~rose/aminoPreference/index.html CONTACT: [email protected]. Publication Types: EvaluationILABILITY: The software is publicly available under the GNU general public licence from http://www.cs.may.ie/distributed CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Full documentation and a user manual is available from http://www.cs.may.ie/distributed. Publication Types: Evaluation Studf signal pathway databases. AVAILABILITY: The pipeline software components are freely available on request to the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://stateslab.bioinformatics.med.umich.edu/software.html. PMID: 15564295 [PubMed - indexed for MEDLINE]mes are 30-40% faster for M-ZDOCK. AVAILABILITY: M-ZDOCK is freely available to academic users at http://zlab.bu.edu/m-zdock/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://zlab.bu.edu/m-zdock. Publication Types: Evaluation Studies PMID: 15613396 [PubMed - indexed for MEDLINE] were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html. Publicatio provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network. Publication Types: Evaluation Studies Validation Studies PMID: 15531ic interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/. MeSH Terms: Adaptation, Physioloring of microarray signals. AVAILABILITY: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Screenshots and instructions for use are available at the above website. Publication Types: Evaluation Studies PMID: 155095quence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org. PMID: 15509596 [PubMed - indexed for MEDLINE]www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: [email protected], [email protected] SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html. Publication Types: Evaluation Studies PMID: 15501914 [PubMed - indexed vel follow-up analysis. AVAILABILITY: The R package arrayMagic is available with BSD license at http://www.bioconductor.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow. PMI

automated assignment program. AVAILABILITY: APART is available from http://sir.lanl.gov/NMR/APART.htm CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APARTblically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Four tables available at the above site. Publication Types: Evaluation Studies PMID: 15388519 [PubMed - indexed for MEDLINEatabase of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani Publication Types: Evaluation Studies Validation Studies PMID: 15377508 [PubMed - indexed forntal plate and paraxial mesoderm. Deducing the mechanical influences on cell behavior is critical, if we are to understand vertebral axis patterning. Supplementary material for this article is available online at http://www.mrw.interscience.wiley.com/suppmat/1542-975X/suppmat/72/v72.266.html. (c) 20e drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded froretin (through cAMP) and adrenergic receptor agonist activation (through Ca(2+)/PKC) induces maximal ductal bicarbonate secretion in liver diseases. (Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Meee MIAME compliance. AVAILABILITY: The application is available from the author at http://www.ansorge-group.embl.de/bloader CONTACT: [email protected] SUPPLEMENTARY INFORMATION: For more details on BLoader visit the above web page. PMID: 15613394 [PubMed - indexed for MEDLINE]scribed below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de SUPPLEMENTARY INFORMATION: database model, semantic mapping table. PMID: 15374875 [PubMed - indexed for MEDLINE]intosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request. PMID: 15374874 [PubMed - indexedLITY: The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html. Publication Types: Evaluation Studies PMID: 1ion on time-lagged co-regulation between genes/gene clusters. AVAILABILITY: The software is available upon request. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary tables and figures for this paper can be found at http://www.comp.nus.edu.sg/~jiliping/p2.htm. Publication Tyion but also on its own mechanism of regulation: genes in the same altered region responded very differently to the gain or loss of genetic material. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22n sequences. AVAILABILITY: The program is freely available for non-profit organizations, upon request to the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analys

s against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method. SUPPLEMENTARY INFORMATION: http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs. Publication Types: Evaluation Studies Validation Studies PMID: 15374856 [Pnsional functional genomics datasets, VizRank can systematically find relevant biological patterns. AVAILABILITY: http://www.ailab.si/supp/bi-vizrank SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-vizrank. PMID: 15358614 [PubMed - indexed for MEDLINE]. These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available AILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4. PMID: 15353449 [PubMed - indexed for MEDLINE] downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu. PMID: 1535344

d improve metabolomics by multidisciplinary cooperation. AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/ PMID: 15613389 [PubMed - indexed for MEDLINE]of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. Publication Types: Evaluation Studies PMID: 1534757D scores, NPL scores, P-values and other parameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. PMID: 15347576 [PubMed - indexed for MEDLINE]he reported patients appear to have the same condition as the family reported by Kantaputra [2002: Am J Med Genet 111:420-428]. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses. AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html. Publication Types: Evaluation Studies PMID: 15347574 [PubMed - indexed for MEDLINE]plain the phenotype observed in the family. Thus, the exon skipping resulted from a nonsense-associated altered splicing (NAS). This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/or factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual. PMID: 15347571 [PubMed - indexed for MEDLINE]COL6A2, and/or COL18A genes located on the distal portion of chromosome 21q, which are lost when the ring chromosome is formed. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/pare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/S

ns; (3) PS affects more males than females; and 4) the published diagnostic criteria are useful for clinical care and research. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/ simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, i phenotypes of Cx45(-/-) mice. Our results indicate that Cx45 is an essential connexin for coordinated conduction through early cardiac myocytes. The Supplementary Material referred to in this article can be found at the Anatomical Record website (http://www.interscience.wiley.com/jpages/0003-276X/sta flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog. PMID: 15308546 [PubMed - indexed for MEDLINE]f techniques to capture both morphological and functional data from the CPCS will further improve with continued interdisciplinary collaboration. The Supplementary Material referred to in this article can be found at the Anatomical Record website (http://www.interscience.wiley.com/jpages/0003-276X/seasured over different subsets of patients. A possible biological explanation for these properties is discussed. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/ Publication Types: Evaluation Studies Validation Studie oculo-palato-cerebral syndrome, supporting autosomal recessive inheritance, and a detailed comparison with the previous cases. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/ve full control of their tools. AVAILABILITY: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/ SUPPLEMENTARY INFORMATION: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/e TXNIP gene, based on its intronic, exonic, and 5' UTR sequences, is not involved as a major contributor to the FCH phenotype. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/ork models fit the PPI networks. We show that the structure of PPI networks is better modeled by a geometric random graph than by a scale-free model. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://www.cs.utoronto.ca/~juris/data/data/ppiGRG04/ Publication Types: Evaluatioatics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material. Publication Types: Evaluation Studies PMID: 15613384 [PubMed lying zeroth, first, second and third order partial correlation analysis can be downloaded at: http://mendes.vbi.vt.edu/tiki-index.php?page=Software. SUPPLEMENTARY INFORMATION: Supplementary information can be found at: URL to be decided. Publication Types: Evaluation Studies PMID: 15284096 [PubMed mmatory stimuli and support the possibility that the phenomenon of jaundice of sepsis" represents an adaptive physiological response to endotoxemia. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co"

ective in recovering biological networks from experimentally collected data. AVAILABILITY: Source code and simulated data are available upon request. SUPPLEMENTARY INFORMATION: http://www.jarvislab.net/Bioinformatics/BNAdvances/ Publication Types: Evaluation Studies Validation Studies PMID: 15284094ly stages of liver development, and the extracellular matrix components may play important roles in biliary differentiation and vascular development. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Cob web-site offers a database of NMR raw datasets, ordered by spectral characteristics. AVAILABILITY: NMRb is available from: http://nmrb.cbs.cnrs.fr. SUPPLEMENTARY INFORMATION: General organization of NMRb figure, relational model organization, and XML structure files are available from http://nmrb.the AE. Random reactivation of the original HBV pool, rather than a sequential evolution of one strain, also contributes to the onset of repeated AE. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Coam runs relatively fast and is suitable for analyzing alignments containing large number of sequences. AVAILABILITY: ftp://iole.swmed.edu/pub/PCOAT/. SUPPLEMENTARY INFORMATION: The PCOAT ftp site contains a detailed description of the program, and the results of PCOAT analysis on C2H2 alignment and l tool to characterize protein families and to optimize the alignments for comparative modelling. AVAILABILITY: http://bioserv.cbs.cnrs.fr/VITO/DOC/. SUPPLEMENTARY INFORMATION: http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html. PMID: 15271783 [PubMed - indexed for MEDLINE] network allowing biologists to explore gene relationships at the system level. AVAILABILITY: Download from http://genenetwork.sbl.bc.sinica.edu.tw/. SUPPLEMENTARY INFORMATION: Supplement documentation of algorithms for the four approaches is downloadable at the above location. PMID: 15271782 [PubMeers previously determined by manual searching. AVAILABILITY: ORFcurator and all associated scripts are freely available as supplementary information. SUPPLEMENTARY INFORMATION: http://www.genomecurator.org/ORFcurator/ Publication Types: Evaluation Studies PMID: 15271781 [PubMed - indexed for MEDLINE

ical analysis of both empirical data and methods designed to detect natural selection. AVAILABILITY: http://www.stats.ox.ac.uk/mathgen/software.html. SUPPLEMENTARY INFORMATION: http://www.stats.ox.ac.uk/mathgen/software.html. PMID: 15271777 [PubMed - indexed for MEDLINE]ated up-regulation of gene expression. In conclusion, this study suggests a role of NS5A and NF-kappaB in HCV pathogenesis and related liver disease. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Cots. The success of the predictions is validated by examining the predictions in the context of the three-dimensional structures of protein complexes. SUPPLEMENTARY INFORMATION: http://www.public.iastate.edu/~chhyan/ISMB2004/list.html PMID: 15262822 [PubMed - in process] HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. Supplementary material for this article can be found on the HEPATOLOGY Web site (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html) Costead of years, and uncover homologs missed by heuristic techniques to speed CM searches. AVAILABILITY: Software in development; contact the authors. SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-ISMB-2004 (Additional technical details on the method; predicted homologs.)

cells resistant to TNFalpha-mediated apoptosis and acquisition of sensitivity to death stimuli is an implicit feature of the differentiation process. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co

s on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability SUPPLEMENTARY INFORMATION: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http:lable. AVAILABILITY: A software package implementing our method is freely available under the GNU general public license (GPL) at http://ghmm.org/gql SUPPLEMENTARY INFORMATION: Supplemental material can be found at http://algorithmics.molgen.mpg.de/ExpMix PMID: 15262810 [PubMed - in process]has been significantly perturbed across the conditions of the expression dataset used. AVAILABILITY: Freely available (in Supplementary information). SUPPLEMENTARY INFORMATION: Available at the following URL http://arep.med.harvard.edu/kharchenko/mep/supplements.html PMID: 15262797 [PubMed - in proccausal networks affecting the traits in a multigenic manner. AVAILABILITY: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/ SUPPLEMENTARY INFORMATION: See http://omicspace.riken.jp/info/traitmap.html PMID: 15262794 [PubMed - in process] is a suitable tool for detecting putative cell cycle regulators in the realm of known human transcription factors. AVAILABILITY: Further details and supplementary data can be obtained from http://corg.molgen.mpg.de/cellcycle PMID: 15262788 [PubMed - in process]

increases. We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction. SUPPLEMENTARY INFORMATION: The datasets built specifically for this paper as well as the full set of results are available at http://genome.imim.es/daDemonstration web server and software download, subject to the Virginia Tech Noncommercial License are available at http://gaia.biotech.vt.edu/goat/. SUPPLEMENTARY INFORMATION: Updates, installation and configuration information are available at http://gaia.biotech.vt.edu/goat. PMID: 15256414 [PubMepare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/Sal preferences for ubiquitin ligation to target proteins, and compartment-specific amino acid patterns in close proximity to the modified side chain. SUPPLEMENTARY INFORMATION: http://www.people.fas.harvard.edu/~catic. PMID: 15256413 [PubMed - indexed for MEDLINE]y, it suggests multiple options for storage and queries of the dog RH database. AVAILABILITY: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html. SUPPLEMENTARY INFORMATION: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html. PMID: 15256409 [PubMed - indexn the predicted risk groups and the receiver operator characteristics analysis. AVAILABILITY: R programs are available upon request from the authors. SUPPLEMENTARY INFORMATION: http://dna.ucdavis.edu/~hli/bioinfo-surv-supp.pdf. Publication Types: Evaluation Studies Validation Studies PMID: 15256406 numerous independent experiments as well as by the analysis of spike-in data. AVAILABILITY: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. SUPPLEMENTARY INFORMATION: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. PMID: 15256405 [PubMed - indexed for MEDLINE]analysis results and R functions for the proposed methods can be found at http://www.biostat.umn.edu/~baolin/research CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.biostat.umn.edu/~baolin/research. Publication Types: Evaluation Studies Validation Studies PMID: 15598833 [PubMe

o simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer. SUPPLEMENTARY INFORMATION: http://stat.tamu.edu/people/faculty/bmallick.html. Publication Types: Evaluation Studies Validation Studies PMID: 15256404 BILITY: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. SUPPLEMENTARY INFORMATION: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/say outweigh the benefit of saving on microarray cost. The microarray data from both platforms show that the major assumption of pooling may not hold. SUPPLEMENTARY INFORMATION: Supplementary material referenced in the text is available at http://linus.nci.nih.gov/brb/TechReport.htm. Publication Typetech.res.in/raghava/gpcrpred/. We have also suggested subfamilies for 42 sequences which were previously identified as unclassified ClassA GPCRs. The supplementary information is available at http://www.imtech.res.in/raghava/gpcrpred/info.html. Publication Types: Evaluation Studies PMID: 15215416 [Pagnostic scan time, expand the target population, improve patient comfort, and facilitate targeted, interventional treatment of infarcted myocardium. Supplementary material for this article can be found on the MRM website at http://www.interscience.wiley.com/jpages/0740-3194/suppmat/index.html. MeSH of transcription regulatory regions in eukaryotes and can be directly applied to clusters of co-expressed genes obtained in gene expression studies. Supplementary information is available at http://www.mit.edu/ approximately kreiman/resources/cisregul/. Publication Types: Evaluation Studies PMID: 1ns--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. AVAILABILITY: Supplementary data at http://noble.gs.washington.edu/proj/sdp-svm Publication Types: Evaluation Studies PMID: 15130933 [PubMed - indexed for MEDLINE]n one would expect from a random substitution model, indicating a cooperative behaviour for these surfaces residues in terms of this single variable. SUPPLEMENTARY INFORMATION: Additional plots for all of the proteins examined in this paper can be found at: http://www.ebi.ac.uk/~shanahan/PCon/index.OP and CATH classifications of proteins, based on their FSSP Z-scores. AVAILABILITY: Free at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/ SUPPLEMENTARY INFORMATION: The site contains links to additional figures and tables. Publication Types: Evaluation Studies PMID: 15059833 [PubMed - inree from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html. SUPPLEMENTARY INFORMATION: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfoach of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. SUPPLEMENTARY INFORMATION: http://bidd.nus.edu.sg/group/trmp/sm.pdf PMID: 15059817 [PubMed - indexed for MEDLINE]eover, its presence in a restricted number of bacteria suggests a possible use for marking plant pathogenicity. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data (Figures S1 and S2 and Table S1) and the alignment in clustal format are available at http://www.bork.emWin32 platform and is free of charge for academic use. For details, visit the web page http://www.bioinfo-hr.org/inca or contact the author directly. SUPPLEMENTARY INFORMATION: Software is accompanied with a user manual and a short tutorial. PMID: 15059815 [PubMed - indexed for MEDLINE]

alias/ and as a web service using a SOAP interface. The complete tool, including sources and data, is available for local installations upon request. SUPPLEMENTARY INFORMATION: Technical documentation is available at http://cbi.labri.fr/outils/alias/asdoc.pdf PMID: 15059813 [PubMed - indexed for MEDchical organization. It furthermore has the advantage over both methods of capturing overlapping modules in the presence of combinatorial regulation. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/~barkai/modules Publication Types: Evaluation Studies Validation Studies PMID: 15044247 [PubMed -i-lognormal mixture assigns observations to subgroups with the lowest uncertainty. AVAILABILITY: Software is available upon request from the authors. SUPPLEMENTARY INFORMATION: http://www-rcf.usc.edu/~kims/SupplementaryInfo.html Publication Types: Evaluation Studies Validation Studies PMID: 15044245 be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes. SUPPLEMENTARY INFORMATION: Matlab code and test data are available at http://www.ee.nthu.edu.tw/~bschen/quantitative/regulatory_network.htm Publicatioologies generated is significantly more likely than the others, Kishino-Hasegawa, Shimodaira-Hasegawa and ELW tests are implemented. Availability and SUPPLEMENTARY INFORMATION: http://www.plantbio.uga.edu/~russell/software.html PMID: 15044241 [PubMed - indexed for MEDLINE]

ray experiments, with minimal user intervention and time investment. AVAILABILITY: microGENIE is freely available from http://www.cs.vu.nl/microgenie SUPPLEMENTARY INFORMATION: The web site above supplies examples of input and output files. PMID: 15044238 [PubMed - indexed for MEDLINE] a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html Publication Types: Evaluation Studies Validation Studies PMID: 15044235 [Pubhly conserved non-protein-coding elements in the human genome thus contains rich family-like structures, which merit in-depth analysis. AVAILABILITY: Supplementary material to this work is available at http://www.soe.ucsc.edu/~jill/dark.html PMID: 15262779 [PubMed - in process]e proposed for data normalized using methods established in the field of proteomics. AVAILABILITY: Software is available on request from the authors. SUPPLEMENTARY INFORMATION: There is supplementary material available online at http://www.flychip.org.uk/kreil/pub/2dgels/ Publication Types: Evaluatimethods we propose are capable of deducing and quantifying functional interactions within and across cellular gene, signaling and metabolic networks. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dbi.tju.edu/bioinformatics2004.pdf Publication Types: Evaluation Studies d during the measurements. AVAILABILITY: All programs used for this publication are available on request from the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information about the model and its interpretation can be downloaded from http://www.imb-jena.de/tsb/pad. Pubotal proteome. AVAILABILITY: MITOPRED program is freely accessible at http://mitopred.sdsc.edu. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Training data sets are also available at http://mitopred.sdsc.edu Publication Types: Evaluation Studies Validation Studies t studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/bioinformatics/ PMID: 15037506 [PubMed - indexed for MEDLINE]

ons. AVAILABILITY: R code is freely available from http://www.davidbickel.com and may become available from www.r-project.org or www.bioconductor.org SUPPLEMENTARY INFORMATION: Applications to cancer microarrays, an application in the absence of differential expression, pseudocode, and a guide to cuof traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteeduch weaker than tRNA genes. Based on the conservation of studied sRNA genes, we also give clues to estimate the total number of sRNA genes in E.coli. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://www.bioinfo.org.cn/SM/sRNAconservation.htm Publication Types: Evaluation Say outweigh the benefit of saving on microarray cost. The microarray data from both platforms show that the major assumption of pooling may not hold. SUPPLEMENTARY INFORMATION: Supplementary material referenced in the text is available at http://linus.nci.nih.gov/brb/TechReport.htm. Publication TypeL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data. AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output. PMID: 15 of three or four states. AVAILABILITY: LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/. SUPPLEMENTARY INFORMATION: Supplementary data for the SVM method can be downloaded from the Website www.cs.columbia.edu/compbio/backbone. Publication rom http://www.ncbs.res.in/~faculty/mini/imot/iMOTserver.html. Supplementary Material can be accessed from: http://www.ncbs.res.in/~faculty/mini/imot/supplementary.html. MeSH Terms: Amino Acid Motifs* Databases, Protein Internet Protein Folding Protein-Tyrosine-Phosphatase/classification Sequence Angeneral and could be easily adopted by other projects. AVAILABILITY: The R package matchprobes is available under LGPL at http://www.bioconductor.org SUPPLEMENTARY INFORMATION: The package contains documentation in the form of a vignette and manual pages. PMID: 14988118 [PubMed - indexed for MEDLINEicle if you access the article at http://dx.doi.org/10.1007/s00216-004-2494-4. A link in the frame on the left on that page takes you directly to the supplementary material. MeSH Terms: Comparative Study Culture Media/chemistry Culture Media/pharmacology Escherichia coli K12/chemistry* Escherichia chree-dimensional protein structures across eukaryotic organisms. AVAILABILITY: SEDB is publicly available at http://glinka.bio.neu.edu/SEDB/SEDB.html SUPPLEMENTARY INFORMATION: On the SEDB Web site. PMID: 14988102 [PubMed - indexed for MEDLINE] various molecular mass distributions (Mathematica). These tools are presented here and briefly compared with other DOSY analysis methods. Electronic Supplementary Material: Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00216-003-2457-1. The d and Drug Administration (FDA). The workshop featured presentations by 22 experts and was attended by 65 individuals. The agenda can be found in the supplementary data at www.toxsci.oupjournals.org. Publication Types: Review PMID: 14976355 [PubMed - indexed for MEDLINE]m is useful mainly to improve local marker ordering in linkage groups obtained in other ways. AVAILABILITY: The source code and supplemental data are http://www.iubio.bio.indiana.edu/soft/molbio/qtl/flipper/ CONTACT: [email protected]. Publication Types: Evaluation Studies Validation Studies MeSH Te

pathways and indicate a large diversity in the functional context of the individual gene family members. AVAILABILITY: The SHOPS tool can be found at http://www.bioinformatics.med.uu.nl/shops supplemental data are available at http://humgen.med.uu.nl/publications/vanbakel/pathway/ Publication Types:

1: Bioinformatics. 2005 Apr 15;21(8):1603-9. Epub 2004 Dec 21.


100: Anal Bioanal Chem. 2004 Mar;378(6):1414-27.

100: Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.


101: Int J Cancer. 2004 Jul 20;110(6):850-6.


103: Bioinformatics. 2004 Jul 10;20(10):1573-82. Epub 2004 Feb 12.

103: Int J Cancer. 2004 Jul 10;110(5):687-94.


105: Bioessays. 2004 May;26(5):567-81.


106: Am J Med Genet A. 2004 May 1;126(4):339-48.


107: Bioinformatics. 2004 May 22;20(8):1233-40. Epub 2004 Feb 10.

108: Bioinformatics. 2004 May 22;20(8):1322-4. Epub 2004 Feb 10.

108: Bioinformatics. 2004 Sep 1;20(13):2050-5. Epub 2004 Apr 8.

109: Bioinformatics. 2004 Mar 22;20(5):808-11. Epub 2004 Jan 29.

109: Int J Cancer. 2004 Jun 10;110(2):155-69.


110: Bioinformatics. 2004 Jan 22;20(2):286-8.






115: Cytometry A. 2004 Apr;58(2):157-66.


116: Int J Cancer. 2004 May 20;110(1):51-60.



119: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D200-2.



123: Bioinformatics. 2004 Sep 1;20(13):2026-34. Epub 2004 Mar 25.

124: Am J Med Genet A. 2004 Apr 1;126(1):18-26.

125: Bioinformatics. 2004 Aug 12;20(12):1877-86. Epub 2004 Mar 22.


131: Pediatr Pulmonol. 2004 Apr;37(4):351-5.

133: Hepatology. 2004 Mar;39(3):617-27.

137: Am J Med Genet A. 2004 Mar 1;125(2):135-44.

138: Genes Chromosomes Cancer. 2004 Apr;39(4):298-310.


141: Immunogenetics. 2004 Mar;55(12):797-810. Epub 2004 Feb 13.

15: Bioinformatics. 2005 Apr 15;21(8):1592-5. Epub 2004 Nov 30.

15: Bioinformatics. 2005 May 1;21(9):1797-806. Epub 2004 Nov 30.

150: Hepatology. 2004 Feb;39(2):518-27.

151: Hepatology. 2004 Feb;39(2):353-64.

153: Int J Cancer. 2004 Mar 20;109(2):200-6.

154: Bioessays. 2004 Feb;26(2):170-9.



163: Insect Mol Biol. 2004 Feb;13(1):73-88.

17: Bioinformatics. 2005 May 1;21(9):2112-3. Epub 2004 Nov 30.





20: Bioinformatics. 2005 Mar 1;21(5):691-3. Epub 2004 Nov 5.


22: Arch Microbiol. 2005 Jan;183(1):27-36. Epub 2004 Nov 13.

22: Bioinformatics. 2005 Mar 1;21(5):689-90. Epub 2004 Oct 27.



25: Bioinformatics. 2005 Feb 15;21(4):554-6. Epub 2004 Sep 28.

26: Bioinformatics. 2005 Mar 1;21(5):680-2. Epub 2004 Sep 23.


28: Bioinformatics. 2005 Jan 15;21(2):239-47. Epub 2004 Sep 17.

28: Birth Defects Res C Embryo Today. 2004 Sep;72(3):267-76.


29: Hepatology. 2004 Nov;40(5):1116-27.






33: Genes Chromosomes Cancer. 2004 Dec;41(4):353-65.










42: Am J Med Genet A. 2004 Oct 1;130(2):181-90.





44: Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19.


45: Bioinformatics. 2005 Jan 15;21(2):208-17. Epub 2004 Aug 19.

46: Anat Rec A Discov Mol Cell Evol Biol. 2004 Oct;280(2):973-9.


47: Anat Rec A Discov Mol Cell Evol Biol. 2004 Oct;280(2):980-9.

47: Bioinformatics. 2005 Jan 15;21(2):171-8. Epub 2004 Aug 12.

48: Am J Med Genet A. 2004 Sep 15;130(1):92-5.

48: Bioinformatics. 2004 Dec 12;20(18):3628-35. Epub 2004 Aug 5.

49: Am J Med Genet A. 2004 Sep 15;130(1):73-5.

49: Bioinformatics. 2004 Dec 12;20(18):3508-15. Epub 2004 Jul 29.



50: Hepatology. 2004 Aug;40(2):424-33.


51: Hepatology. 2004 Aug;40(2):346-55.


52: Hepatology. 2004 Aug;40(2):310-17.






57: Hepatology. 2004 Sep;40(3):708-18.

58: Bioinformatics. 2004 Aug 4;20 Suppl 1:I371-I378.

58: Hepatology. 2004 Sep;40(3):667-76.


59: Hepatology. 2004 Sep;40(3):590-9.

6: Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17.
















73: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W383-9.

74: Magn Reson Med. 2004 Aug;52(2):354-61.

74: Nucleic Acids Res. 2004 May 20;32(9):2889-900. Print 2004.

75: Bioinformatics. 2004 Nov 1;20(16):2626-35. Epub 2004 May 6.


















90: Bioinformatics. 2004 Jul 22;20(11):1785-94. Epub 2004 Mar 22.






95: Bioinformatics. 2004 Jul 22;20(11):1815-7. Epub 2004 Mar 4.


96: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W602-5.





99: Toxicol Sci. 2004 May;79(1):4-9. Epub 2004 Feb 19.


2: Bioinformatics. 2004 Nov 1;20(16):2644-55. Epub 2004 May 14.

Live? Journal?

n/a n Hatzimanikatis

no n Hampson SE, Ga

no n acrylate-co-ca

No n Pavesi G, Mauri

no n models.

no n of allelotyping

no n and GeneCards

No n Voss B, Meyer

No n rhabdomyosarc

no n co-variance in

no n Bioessays. 200

no n scale.

no n Hammond P, Hut

Yes n Golfier G, Dan

yes n loss-of-hetero

yes n in protein seq

yes n Horne AB, Hod

yes n community anno

yes n Int J Cancer.

yes n Li W, Rehmeye

yes n Matukumalli LK

yes n Brodie R, Rope

yes n Barker D.

yes n Reymond N, Cha

yes n protein sequen

yes n differentially

yes n chromatin struc

yes n Klamt S, Gilles

yes n murine colon c

yes n with pseudokn

yes n Huang Y, Li Y.

yes n Vinayagam A,

yes n classification

yes n classification

yes n expression anal

yes n fibrosing lung

yes n expression, pr

yes n Aoki KF, Mamit

yes n Barker M, Hebe

yes n development u

yes n Antioquia-Colo

yes n Baross A, Sche

yes n microarray dat

yes n matrices.

yes n relations.

yes n measure.

yes n cirrhosis.

yes n coverage of th

Yes n De Giovanni C,

yes n equal or why d

yes n analysis.

yes n melanogaster

yes n Calvo E, Ander

yes n Toedling J, Sc

yes n Rose JR, Turke

yes n Keane TM, Nau

yes n statistical met

yes n Pierce B, Ton

yes n Nelson RT, Gr

yes n high-throughpu

Yes n strain EbN1.

yes n Ng JK, Liu WT.

yes n Pond SL, Frost

yes n and insights g

yes n Buness A, Hube

yes n Pawley NH, Gan

yes n relationships i

yes n Leone M, Pagn

yes n vertebral axis

yes n Martin DP, Wil

Yes n Ca(2+)- and P

yes n Schwager C, Bl

yes n phenomics.

yes n Creevey CJ, Mc

yes n replicated gen

yes n Ji L, Tan KL.

yes n material detec

yes n whole genome

yes n protein interac

Yes n learning.

yes n factors.

yes n Shegogue D, Z

yes n Price EW, Carb

yes n Kopka J, Schau

yes n for microbiol

yes n analyses.

yes n Am J Med Gene

yes n Firth AE, Brow

yes n Stickler syndr

yes n annotations.

yes n Rope AF, Hinto

yes n sites.

yes n criteria to pub

yes n Orrell D, Ramse

yes n stem cell-deri

yes n Curk T, Demsar

yes n over the past

yes n Ein-Dor L, Kel

yes n inheritance.

yes n mass fingerpri

yes n hyperlipidemia

Yes n Przulj N, Cornei

yes n machines appr

yes n coefficients.

yes n rats.

yes n observational b

yes n liver developm

yes n Pons JL, Malli

yes n the liver and

yes n Qi Y, Grishin N

yes n Catherinot V,

Yes n microarray dat

yes n organisms.

yes n recombination

yes n microarray an

yes n Yan C, Dobbs

yes n Hepatology. 2

yes n loss of accurac

yes n sensitization

yes n phylogenetic t

yes n HMMs.

yes n Kharchenko P,

yes n biomolecular n

Yes n transcription f

yes n Castelo R, Gui

yes n Kaluszka A, Gi

yes n sites.

yes n Catic A, Colli

yes n canine genome

yes n survival data.

yes n Finocchiaro G,

yes n the improved S

yes n Bae K, Mallick

yes n sequence data

yes y Shih JH, Micha

yes y G-protein coup

yes y interactive MR

yes y sets of co-exp

yes y Lanckriet GR, D

yes y Shanahan HP,

yes y Getz G, Starov

yes y Savva G, Conn J

yes y Zheng CJ, Zhou

yes y Ciccarelli FD,

yes y map.

yes y Iragne F, Barr

yes y Ihmels J, Berg

yes y Siegmund KD, L

yes y yeast cell cycl

yes y inference.

yes y Korotkiy M, Mi

yes y identification

yes y Bejerano G, Ha

yes y expression anal

yes y expression, pr

yes y Beyer A, Wilhe

yes y proteins.

yes y connectivity st

yes y expression dif

yes y Wren JD.

yes y Zhang Y, Zhang

yes y Shih JH, Micha

yes y Haverty PM, W

yes y Kuang R, Lesli

yes y Bhaduri A, Pug

yes y probe element

yes y species with li

yes y structures.

yes y of a broad, fe

yes y Willett KL, Rot

no n A nearest-neig

y n Prokaryotic di



PMID: 152144MeSH Terms: Acrylates/chemistry*



PMID: 151706MeSH Terms: Alleles



PMID: 151465MeSH Terms: Cell Differentiation


PMID: 151122MeSH Terms: Archaeal Proteins/metabolism


PMID: 150982MeSH Terms: Abnormalities, Multiple/pathol




PMID: 150730MeSH Terms: Computer Simulation


PMID: 150696MeSH Terms: Europe/epidemiology








PMID: 150579MeSH Terms: Animals


PMID: 150548MeSH Terms: Adenoviridae/genetics





PMID: 155855MeSH Terms: Algorithms*


PMID: 150399MeSH Terms: Bronchoalveolar Lavage Fluid/



PMID: 150221MeSH Terms: Adult

PMID: 149996MeSH Terms: Aging/genetics*

PMID: 149817MeSH Terms: Cleft Lip/genetics*

PMID: 149787MeSH Terms: Ataxia Telangiectasia/genetics


PMID: 149636MeSH Terms: Amino Acid Motifs



PMID: 147680MeSH Terms: Antigens, Neoplasm/genetics

PMID: 147679MeSH Terms: Acute Disease

PMID: 147501MeSH Terms: Adenomatous Polyposis Coli/ge



PMID: 147343MeSH Terms: Amino Acid Sequence









PMID: 155510MeSH Terms: Adaptation, Physiological/gene










PMID: 154869MeSH Terms: Adrenergic alpha-Agonists/ph






PMID: 153822MeSH Terms: Chromosomes, Human, Pair 13/










PMID: 153725MeSH Terms: Abnormalities, Multiple/genetic






PMID: 153725MeSH Terms: Diagnosis, Differential




PMID: 153724MeSH Terms: Action Potentials




PMID: 153684MeSH Terms: 5' Untranslated Regions






PMID: 153684MeSH Terms: Aging/metabolism*


PMID: 153684MeSH Terms: Acute Disease






PMID: 153499MeSH Terms: Amino Acid Sequence


PMID: 153499MeSH Terms: Carcinoma, Hepatocellular/class








PMID: 152154MeSH Terms: Amino Acid Motifs*


PMID: 152144MeSH Terms: Comparative Study




MeSH Terms:Crane CF, Crane YM.


pathway. MeSH Terms:PMID: 15145814 [PubMed - indexed for MEDLINE]

Carbon Isotopes/chemiCarbon Monoxide/chemistry* Ethylenes/chemistry*

Bayes Theorem Chromosome Aberrations* Chromosomes, Human

Cell Line, Tumor Child Cyclin D1/biosynthes

Bacterial Proteins/met Cell Nucleolus*/chemistry Cell Nucleolus*/meta

Adolescent Adult Child

Databases, Protein* Enzymes/chemistry* Enzymes/metabolism

Female Humans Male

Automation CHO Cells Chromatin/chemistry

Animals Antibodies, Monoclonal/therapeutic Antigens, CD

Cluster Analysis Computer Simulation Gene Expression Prof

Bayes Theorem Comparative Study Computer Simulation

Child, Preschool Cohort Studies Comparative Study

Cell Physiology* Computer Graphics Computer Simulation

Attitude of Health Per Child Cystic Fibrosis/physi

Animals Animals, Newborn/growth & develo Animals, Newborn/ph

Cleft Lip/pathology Cleft Palate/genetics* Cleft Palate/patholog

Cell Cycle Proteins Cells, Cultured Child

Cluster Analysis Histocompatibility Antigens Class I/cHistocompatibility Ant

Cluster Analysis DNA Mutational Analysis/methods Evolution, Molecular

Carcinoma, HepatocellCarcinoma, Hepatocellular/genetics Cell Adhesion Molecu

Adult Aged Aged, 80 and over

Adenomatous PolyposiAdenomatous Polyposis Coli/patholoAdenomatous Polyposi

Disease* Disease Models, Animal* Epistasis, Genetic

Animals Chitinase/chemistry* Chitinase/classificati

Anopheles/genetics* Brazil Comparative Study

Amino Acid Sequence Animals Base Sequence

Aerobiosis Anaerobiosis Azoarcus/genetics

Body Patterning/physi Cell Movement/physiology* Cell Physiology*

Animals Bicarbonates/metabolism Bile/secretion

Chromosomes, Human, Chromosomes, Human, Pair 6/genetiExpressed Sequence

Abnormalities, Multipl Child Dwarfism/pathology*

Abnormalities, Multipl Base Sequence Child, Preschool

Abnormalities, Multipl Aorta/abnormalities* Chromosomes, Human,

Female Humans Kidney Diseases/comp

Calcium/metabolism Cell Differentiation Comparative Study

Animals Embryo*/cytology Embryo*/innervation

Cleft Palate/genetics* Consanguinity* Craniofacial Abnormal

Adult Aged Animals

Bilirubin/pharmacolog Bilirubin/physiology* Carrageenan

Animals Animals, Newborn/growth & develo Animals, Newborn/me

Adult Base Sequence Carrier State

Binding Sites Calcium/metabolism Carcinoma, Hepatocel

Carcinoma, HepatocellCarcinoma, Hepatocellular/mortalityGene Expression Prof

Apoptosis/drug effectsCell Differentiation Cell Line

Binding Sites Comparative Study Protein Binding

Computer Simulation Contrast Media/administration & do Humans

Comparative Study Gene Expression Profiling/methods* Models, Genetic*

Databases, Protein Internet Protein Folding

Culture Media/chemistCulture Media/pharmacology Escherichia coli K12/

Algorithms* Chromosome Mapping/methods* Comparative Study

Algorithms Carrier Proteins/genetics* Carrier Proteins/met

Isotope Labeling Magnetic Resonance Spectroscopy/methods Molecular

Chromosomes, Human, Pair 9 Cyclin-Dependent Kinase Inhibitor p16/genetics Genes, p

DNA Primers/pharmacology DNA-Binding Proteins/biosynthesis Disease P

Databases, Factual Evolution* Models, B

Child, Preschool Comparative Study Craniofac

Metabolism/physiology* Models, Biological* Multienz

Neoplasms/mortality* Research Support, Non-U.S. Gov't Time Factors

Chromatin/genetics Chromatin/metabolism* Chromati

Cell Movement Colonic Neoplasms/therapy* Dendritic

Genetic Markers/genetics* Models, Genetic* Oligonucl

Data Interpretation, Statistical Electrophoresis, Gel, Two-Dimensional/methods* Electroph

Female Humans Infant

Gene Expression Profiling/methods* Gene Expression Regulation/physiology* Models, B

Cystic Fibrosis/rehabilitation* Exercise Test/methods Exercise

Embryonic and Fetal Development Fetus/physiology Gene Exp

Colombia Comparative Study Family He

Comparative Study DNA-Binding Proteins Expresse

Humans Markov Chains Research

Models, Genetic* Models, Statistical Pattern R

Gene Expression Regulation, NeoplastHumans Liver Cir

Cytokines/genetics Databases, Genetic Female

Animals Cell Differentiation Cytoskele

Genetic Predisposition to Disease Humans Hypertens

Chitinase/genetics* Databases, Protein Drosophi

DNA, Complementary/classification* Databases, Genetic Electroph

Chromosome Mapping/methods* Comparative Study DNA, Vira

Bacterial Proteins/genetics Betaproteobacteria/classification Betaprote

Chick Embryo Extracellular Matrix/physiology* Microscop

Bile Ducts/cytology Bile Ducts/metabolism* Bile Duct

Gene Dosage* Gene Expression Profiling Humans

Family Health Female Humans

Codon, Nonsense/genetics* Collagen Type XI/genetics* DNA Mutat

Humans In Situ Hybridization, Fluorescence Infant

Male Proteus Syndrome/complications Proteus S

Connexins/genetics Connexins/physiology* Electroph

Embryo*/metabolism Heart Conduction System/cytology Heart Co

Dwarfism/genetics Eye Abnormalities/genetics* Female

Carrier Proteins/genetics* Exons Female

Cell Line Cytoprotection Endotoxe

Bile Ducts, Extrahepatic/embryology Bile Ducts, Extrahepatic/growth & development Bile Duct

Comparative Study Female Genome, V

Carrier Proteins/physiology Gene Expression Profiling Gene Expr

Humans Liver/metabolism Liver Neo

Cell Lineage Glutathione/physiology Liver/cyt

Research Support, U.S. Gov't, Non-P.HSequence Alignment/methods* Sequence

Magnetic Resonance Imaging/methodMyocardial Infarction/diagnosis* Swine

Models, Statistical Oligonucleotide Array Sequence Analysis/methodRNA, Mes

Protein-Tyrosine-Phosphatase/classifi Sequence Analysis, Protein Sequence

Escherichia coli K12/drug effects Escherichia coli K12/metabolism Selenium

Computer Simulation DNA Mutational Analysis/methods* Gene Del

Comparative Study Copper/metabolism* Evolution

Polymers/analysis* Polymers/chemistry*

Genotype Humans

Fibroblasts/metabolism Gene Expression Regulation, Neopl

Nuclear Proteins/chemistry* Nuclear Proteins/classification*

Face/pathology* Heart Defects, Congenital/patholo

Multienzyme Complexes/met Protein Interaction Mapping/metho

Time Factors

Cricetinae Estrogen Receptor alpha/chemistry

Gene Therapy* Interferon Type II/biosynthesis

Pattern Recognition, Automa Phenotype*

Gene Expression Profiling/meGene Expression Profiling/standard

Infant, Newborn Lung Diseases, Interstitial/genetics

Multienzyme Complexes/met Research Support, Non-U.S. Gov't

Germany Health Services Needs and Deman

Liver/embryology* Liver/physiology*

Female Genes, Dominant

Fibroblasts/chemistry* Fibroblasts/metabolism*

Research Support, U.S. Gov't,Substances:

Phylogeny Recombination, Genetic/genetics*

Liver Cirrhosis/etiology Liver Cirrhosis/genetics*

Gene Expression Genetic Markers

Cytoskeletal Proteins/metaboFemale

Hypertension/physiopathologLinkage (Genetics)

Drosophila melanogaster/genGene Expression Profiling/methods

Gene Library* Research Support, Non-U.S. Gov't

Genome, Viral* Mammals

Betaproteobacteria/metaboli Biodegradation

Photomicrography/methods* Research Support, Non-U.S. Gov't

Bile Ducts, Intrahepatic/metaBiological Transport

In Situ Hybridization, Fluore Lymphoma, T-Cell/genetics*

Male Microcephaly/pathology

Exons/genetics* Face/abnormalities

Karyotyping Male

Urologic Diseases/complications

Gap Junctions/metabolism* Heart Conduction System/metabol

Heart Conduction System/phyHistory, 20th Century

Genes, Recessive Humans

Humans Hyperlipidemia, Familial Combined

Endotoxins/pharmacology* Enzyme Inhibitors/metabolism

Bile Ducts, Intrahepatic/emb Bile Ducts, Intrahepatic/growth &

Hepatitis B e Antigens Hepatitis B virus/genetics

Hepatitis C/etiology* Humans

Liver Neoplasms/genetics Liver Neoplasms/mortality

Liver/drug effects Mitochondria, Liver/drug effects

Transcription Factors/analysi Transcription Factors/chemistry*

Substances: Contrast Media

Reproducibility of Results Sample Size

Software* User-Computer Interface

Selenium Compounds/chemisSelenium Compounds/metabolism

Genetic Markers/genetics* Genetics, Population*

Gene Expression Profiling/meGene Expression Regulation, Funga


Loss of Heterozygosity Microsatellite Repeats/genetics

Genetic Markers Heparan Sulfate Proteoglycan/biosynthesi

Nuclear Proteins/genetics Nuclear Proteins/metabolism

Humans Imaging, Three-Dimensional/instrumentati

Research Support, Non-U.S. Gov't Signal Transduction/physiology*

Estrogen Receptor alpha/genetics Estrogen Receptor alpha/metabolism*

Interleukin-12/genetics* Interleukin-12/physiology

Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Models, Genetic Models, Statistical

Lung Diseases, Interstitial/metabolis Male

Research Support, U.S. Gov't, Non-P.HResearch Support, U.S. Gov't, P.H.S.

Health Surveys Humans

Oligonucleotide Array Sequence AnalyRats*

Genes, Recessive Genetic Markers*

Fibroblasts/pathology Gene Expression Profiling/methods*

Histocompatibility Antigens Class I Histocompatibility Antigens Class II

Research Support, Non-U.S. Gov't Sequence Alignment/methods*

Liver Neoplasms/epidemiology Liver Neoplasms/genetics*

Hepatitis/genetics* Hepatitis/immunology

Gene Expression Profiling Genes, APC*

Phenotype

Genome* Models, Molecular*

Research Support, U.S. Gov't, P.H.S. Saliva/chemistry*

Models, Genetic Molecular Sequence Data

Chromosomes, Bacterial/genetics DNA, Bacterial/chemistry

Research Support, U.S. Gov't, P.H.S. Grant Support:

Calcium/physiology* Cell Membrane

Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis

Osteochondrodysplasias/pathology Pedigree

Family Health Female

Ring Chromosomes* Syndrome

Mice/embryology* Myocytes, Cardiac/metabolism*

History, 21st Century Humans

Infant Inheritance Patterns*

Introns Male

Enzyme Inhibitors/pharmacology Heme Oxygenase (Decyclizing)/metabolis

Bile Ducts, Intrahepatic/metabolism Blood Vessels/growth & development

Hepatitis B, Chronic/physiopathology Hepatitis B, Chronic/virology*

Interferon-alpha/therapeutic use Interleukin-1/physiology

Oxidative Stress Rats

Substances: Transcription Factors

Sensitivity and Specificity Variation (Genetics)

Substances: Protein-Tyrosine-Phosphatase

Spectroscopy, Fourier Transform Inf Time Factors

Humans Linkage (Genetics)/genetics

Internet Operon/genetics

Acrylates Carbon Isotopes

Neural Networks (Computer) Research Support, Non-U.S. Gov't

Humans Lipid Metabolism

Phylogeny Protein Structure, Tertiary

Imaging, Three-Dimensional/methods* Infant

Substances: Enzymes

Microscopy, Fluorescence/instrumentation Microscopy, Fluorescence/methods*

Isoantigens/immunology* Mice

Software* Substances:

Oligonucleotide Array Sequence Analysis/met Oligonucleotide Array Sequence Analysis/standar

Mutation* Pedigree

Signal Transduction/physiology* Time Factors

Physical Education and Training/methods Physical Education and Training/statistics & numer

Research Support, U.S. Gov't, P.H.S. Stem Cells/physiology*

Genetic Predisposition to Disease/genetics* Genotype

Gene Expression Regulation/genetics* Gene Expression Regulation/physiology

Grant Support: AI49213-02/AI/NIAID

Sequence Analysis, DNA/methods* Variation (Genetics)/genetics*

Oligonucleotide Array Sequence Analysis* Research Support, U.S. Gov't, P.H.S.

Hepatitis/physiopathology Hepatocytes/immunology

Heterozygote* Intestinal Neoplasms/genetics*

Molecular Sequence Data Phylogeny

Salivary Glands/secretion* Sequence Analysis, DNA

Research Support, U.S. Gov't, Non-P.H.S. Sequence Alignment/methods*

Evolution, Molecular Gene Expression Regulation, Bacterial

R01 HL68855/HL/NHLBI R01 HL73700-03/HL/NHLBI

Cyclic AMP/metabolism* Cyclic AMP-Dependent Protein Kinases/metabolis


Research Support, Non-U.S. Gov't Skin Abnormalities*

Hearing Loss, Sensorineural/pathology Humans

Myocytes, Cardiac/pathology Phenotype

Pacemaker, Artificial*/history

Microcephaly/genetics* Pedigree

Mice Middle Aged

Heme Oxygenase-1 Hindlimb

Blood Vessels/metabolism Cell Aging

Humans Liver/virology*

Intracellular Signaling Peptides and Proteins* Lipid Metabolism

Reactive Oxygen Species Stem Cells/cytology*

Substances: RNA, Messenger

Secondary Source ID: PDB/2HNQ

Substances: Culture Media

Models, Genetic* Models, Statistical

Research Support, Non-U.S. Gov't Saccharomyces cerevisiae/genetics*

Ethylenes Polymers n-butyl ac

Urologic Neoplasms/genetics* Substances: Cyclin-Dependent Kinase Inhibitor p16

Models, Statistical Oligonucleotide Array Sequence ARNA, Com

Proteome/analysis Ribosomal Proteins Ribosome

Infant, Newborn Middle Aged Models, A

Multienzyme Complexes

Protein Structure, Tertiary Recombinant Fusion Proteins/che Recombina

Mice, Inbred BALB C Mice, Inbred C57BL Receptors

Genetic Markers

Research Support, Non-U.S. Gov't Sensitivity and Specificity Sequence

Peptides* Phenotype Pulmonary

User-Computer Interface* Substances: Multienz

Questionnaires Research Support, Non-U.S. Gov't

Grant Support: P30 DK 41296/DK/NIDDK P30 DK 5

Humans Linkage (Genetics)/genetics* Lod Score

Gene Library Genes/genetics Genes/phy

Risk Factors Substances: Antigens,

Hepatocytes/physiology Humans Male

Intestinal Neoplasms/metabolism Intestinal Neoplasms/pathology Mice

Protein Conformation Protein Structure, Tertiary Research

Substances: DNA, Complementary Grant Sup

Sequence Analysis, DNA/methods* Species Specificity Statistics

Gene Transfer, Horizontal Genes, Bacterial Genome, B

Drug Synergism Isoenzymes/metabolism Ligation

Syndrome Tooth Abnormalities*

Knee Joint/pathology Male Molecular

Research Support, Non-U.S. Gov't Stem Cells/cytology* Stem Cell

Netherlands Phenotype Sequence

Inflammation/chemically induced Lipopolysaccharides/pharmacolo Male

Embryo/metabolism Extracellular Matrix Proteins/met Hepatocy

Male Middle Aged Phylogen

Liver Neoplasms/genetics Molecular Sequence Data NF-kappa

Tumor Necrosis Factor-alpha/pharmacSubstances: Reactive

Selenium Compounds

Research Support, U.S. Gov't, Non-P.HSoftware* Substance

Saccharomyces cerevisiae/metabolis Saccharomyces cerevisiae ProteinSaccharom

Carbon Monoxide ethylene

Cyclin-Dependent Kinase Inhibitor p16

RNA, Messenger/metabolism* Repressor Proteins/biosyn Research Support, Non-U.S. Go

Substances: Archaeal Proteins Bacterial Proteins

Noonan Syndrome/pathology* Research Support, Non-U.SSyndrome

Recombinant Fusion Proteins/ Reproducibility of Results Research Support, U.S. Gov't,

Receptors, Nerve Growth Fact Receptors, Tumor Necrosis Receptors, Tumor Necrosis Fa

Sequence Alignment/standardsSequence Analysis, DNA/ Sequence Analysis, DNA/standards

Pulmonary Alveolar ProteinosisPulmonary Alveolar Protei Pulmonary Fibrosis/genetics*

Grant Support: AA08714/AA/NIAAA GM59570/GM/NIGMS

R01 DK 17609/DK/NIDDK R01 DK 59321/DK/NIDDK U24 DK 058768/DK/NIDDK

Male Microsatellite Repeats Ohio

Humans Infant, Newborn Male

Cell Adhesion Molecules tumor-associated antigen GA733

Middle Aged Oligonucleotide Array Se Promoter Regions (Genetics)

Mice, Inbred C57BL Mice, Nude Oligonucleotide Array Sequenc

Research Support, U.S. Gov't, PSequence Alignment/methSequence Analysis, Protein/m

AI29746/AI/NIAID

Viral Proteins/genetics* Substances: DNA, Viral

Hydrocarbons, Aromatic/metabInterspersed Repetitive S Molecular Sequence Data

Male Phenylephrine/pharmacol Protein Isoforms/metabolism

Pedigree Proteins/genetics Research Support, Non-U.S. Go

Substances: Connexins connexin 45

Thioredoxin/genetics* Substances: 5' Untranslated Regions

Nitric Oxide/antagonists & inhi Nitric Oxide/biosynthesis Nitric Oxide/blood

Hepatocytes/physiology Immunohistochemistry Integrins/metabolism*

Research Support, Non-U.S. GoSeverity of Illness Index Species Specificity

Oligonucleotide Array SequencPromoter Regions (GeneticResearch Support, Non-U.S. Go

Tumor Necrosis Factor-alpha Glutathione

Genetic Markers

Sequence Analysis, Protein/meSignal Transduction/physi Software

Reverse TransRhabdomyosarcoma/genetiSarcoma, Ewing'sTrans-Activators/biosynthesis

Nuclear Prote Proteome Ribosomal Proteins

Velopharyngeal Insufficiency/pathology

Sequence DeleTime Factors Substances: Chromatin

Research SuppTransfection Substances: Antibodies, Monoclonal

Sequence Analysis, DNA/standards

Pulmonary FibPulmonary Surfactant-AssocPulmonary SurfacPulmonary Surfactant-Associated Pr

P20-GM64375/GM/NIGMS

Pedigree Prevalence Research SupportResearch Support, U.S. Gov't, P.H.S.

Protein-Serin Research Support, Non-U.S.Retroviridae/genSkin/cytology

RNA, MessengeResearch Support, Non-U.S.Signal TransductSubstances:

Proto-OncogenRNA, Neoplasm/metabolis Research SupportTranscription Factors/genetics

Sequence HomStructure-Activity Relation Substances: Chitinase

Viral Proteins

Multigene FamNitrogen Fixation/genetics Open Reading F Plasmids/genetics

Protein Kinas Protein Kinase C/physiolog Rats Rats, Inbred F344

Syndrome Substances: COL11A2 protei Codon, Nonsense

Calcium

Carrier Protei TXNIP protein, human Thioredoxin

Nitric Oxide S Nitric Oxide Synthase/geneNitric Oxide Syn Nitric Oxide Synthase Type II

Liver/cytologyLiver/embryology* Liver/growth & Liver/metabolism*

Viremia* Substances: Hepatitis B e Antigens

Research SuppoSignal Transduction/physio Transforming GroViral Nonstructural Proteins/physiol

Structure-ActiUser-Computer Interface Variation (Genet Substances:

Tumor MaSubstances: CITED2 prote DNA Primers DNA-Binding PGenetic MarkeHeparan Sulfa

EstrogenRecombinant FGrant SupportR01-GM42516R01-GM58460/GM/NIGMS

AntigensCD137 antige Isoantigens Receptors, NeReceptors, TuInterleukin-12Interferon Type II

ResearchSubstances: Peptides Pulmonary SurSFTPC protei Secondary SouOMIM/178620

Substan Genetic MarkeGrant SupportP60 DE13076 R01 DE 14677/DE/NIDCR

Skin/pat Telomerase/geTelomere/enzTelomere/geneTransduction, Tumor SuppresSubstances:

CytokineGenetic MarkeRNA, Messenger

Transcri Tumor Cells, Wnt Proteins Zebrafish ProtSubstances: Adenomatous PCytoskeletal P

Grant SuP20 RR16475/RR/NCRR

ResearchSequence AnaSequence Ho Substances: Bacterial Prot DNA, BacteriaHydrocarbons,

ReceptorReceptors, AdResearch SuppResearch SuppResearch SuppoSecretin/pha Up-Regulation

CollagenProteins

Oxidore Prostaglandin Rats Rats, Spragu Research SuppoTranscription,Substances:

Liver CirMice Mice, Inbred Receptors, CeResearch SuppSubstances: Extracellular

Substan Carrier Protei Interferon-alp Interleukin-1 Intracellular NF-kappa B NS-5 protein,

ATX1 proCarrier Protei SaccharomycesCopper

RNA, ComplemRNA, MessengRepressor ProTrans-Activat Tumor Markersglypican 3

Interferon Type II

OMIM/178620

Cell Cycle ProDNA-Binding PTumor SuppresProtein-Serin ataxia telang Telomerase

Proto-OncogenRNA, Neoplas Transcription Wnt Proteins Zebrafish Protwnt8b protein, zebrafish

Plasmids Secondary SouGENBANK/CR5GENBANK/CR5GENBANK/CR555308

Substances: Adrenergic al Bicarbonates Isoenzymes Protein Isofo Receptors, Ad

Endotoxins Enzyme InhibiLipopolysacchNitric Oxide Bilirubin Carrageenan

Integrins Receptors, Celextracellular matrix receptor

Transforming Viral Nonstruclatent TGF-bettransforming Calcium Grant Support

Cyclin D1

telomerase reverse transcriptase

wnt8b protein, zebrafish

Secretin Phenylephrin Cyclic AMP Calcium Cyclic AMP-DeProtein Kinas

Nitric Oxide Nitric Oxide S Nos2 protein, Prostaglandin Heme OxygenaHeme Oxygen

2 P30 DK3493DK59771/DK/NIDDK

Grant SupportDK 54208/DK DK58411/DK/NIDDK

Oxidoreducta biliverdin red Grant SupportDK063954/DKDK51679/DK/ DK62628/DK/

OK07727/PHS

Reference

guidance that appears as an appendix in Supplementary data to this paper should

, NetBSD, Solaris and Windows XP. It can be downloaded from http://mesord.sourceforge.net. CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: 'MesoRD User's Guide' and other documents are available at http://mesord.sourceforge.net. PMID: 15817692 [PubMed - indexed

bentities and associate them to biological processes without compromising overall prediction accuracy. AVAILABILITY: Bioconductor compliant R package SUPPLEMENTARY INFORMATION: Complete analyses are available at http://compdiag.molgen.mpg.de/supplements/lottaz05. Publication Types: Evaluation Studieontrary to the assumptions of previous models. AVAILABILITY: Programs are available upon request from the authors in the form of Matlab script files. SUPPLEMENTARY INFORMATION: http://www.cis.upenn.edu/biocomp/manuscripts/bioinformatics_bti245/supp-info.htm l. Publication Types: Evaluation Studies V2% precision at 50% recall, sufficient for inclusion in a high-quality database. AVAILABILITY: Source code is available from the author upon request. SUPPLEMENTARY INFORMATION: ftp.uni-koeln.de/institute/biochemie/pub/brenda/info/diseaseSupp.pdf. Publication Types: Evaluation Studies PMID: 15661799 ith a previous study of the yeast mitochondrial proteome is presented. AVAILABILITY: A demonstration prototype, interSearch, is available on request. SUPPLEMENTARY INFORMATION: http://ijsr32.infj.ulster.ac.uk/~e10110731/interSearch. PMID: 15657100 [PubMed - indexed for MEDLINE] using Java language, and can be executed on the platforms that JVM (Java Virtual Machine) is running. It is available from the authors upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at http://dragon.kaist.ac.kr/gk. Publication Types: Evaluation Studies Validation Studies mes are 30-40% faster for M-ZDOCK. AVAILABILITY: M-ZDOCK is freely available to academic users at http://zlab.bu.edu/m-zdock/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://zlab.bu.edu/m-zdock. Publication Types: Evaluation Studies PMID: 15613396 [PubMed - indexed for MEDLINE]eover, its presence in a restricted number of bacteria suggests a possible use for marking plant pathogenicity. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data (Figures S1 and S2 and Table S1) and the alignment in clustal format are available at http://www.bork.embly information. Results are output in spreadsheets containing information that facilitates manual validation. AVAILABILITY: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/ CONTACT: [email protected]. PMID: 15585532 [PubMed -. These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. Publication Types: Evaluation Studies PMID: 1534757computed genome comparisons, can be viewed online using ACT and are available for download. AVAILABILITY: Freely accessible at http://www.webact.org. SUPPLEMENTARY INFORMATION: User guide and worked examples are available at http://www.webact.org/WebACT/docs. PMID: 16076890 [PubMed - indexed for MED

CONCLUSION: There continues to be marked

nd a web interface for submission of texts to GIFT analysis are available at http://gift.cryst.bbk.ac.uk/gift CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Additional documentation, such as the dictionaries and the reference sets, are available at the GIFT website. PMID: 1601436from other species. AVAILABILITY: The CQS is freely accessible over the Internet at http://moris.csie.ncku.edu.tw/cqs/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://moris.csie.ncku.edu.tw/cqs/ Publication Types: Evaluation Studies PMID: 15998663 [PubMed - indexed for MEDLINE]53 TFBSs are in the promoter region of known genes or associated with previously characterized p53-responsive genes. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at the following URL http://genome.dfci.harvard.edu/~xsliu/HMMTiling/index.html. PMID: 15961467 [PubMed - in proc as mitochondrial in S. cerevicae, D. melanogaster, C. elegans, mouse and human proteome respectively. MitPred developed on above hybrid approach and supplementary data are available at http://www.imtech.res.in/raghava/mitpred or http://www.imtech.ac.in/raghava/mitpred. PMID: 16339140 [PubMed - as s strictly constrained by the mitotic phase of the cell cycle and suggesting additional roles during G- and S-phase progression. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/2005/95/spada.ht ml. (c) 2005 Wiley-Liss, Inc. MeSMT3B. The implications of these findings for the regulation of de novo methyltransferases and genomic imprinting are discussed. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/2005/95/chen.htm l. (c) 2005 Wiley-Liss, Inc. MeSHss in understanding neural tube closure mechanisms and how these studies can inform our search for the genes that underlie human neural tube defects. Supplementary material for this article can be found on the American Journal of Medical Genetics (Part C) website (http://www.mrw.interscience.wiley.cin the critical region. Refined mapping studies need to be performed to further narrow the region and additional candidate genes need to be examined. Supplementary material for this article can be found on the Birth Defects Research (Part A) website (http://www.mrw.interscience.wiley.com/suppmat/154 the CAFASP-DP evaluation results are available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html. Publication Types: Evaluation Studies PMID: 15840708source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.Sienabiogzefix.com/publication. Publication Types: Evaluation Studies PMID: 15827080 [PubMed - indexed for MEDLI

icense) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html. PMID: 16377612 [PubMed -s data in dot plot-like matrix views. AVAILABILITY: software is freely available at www.win.tue.nl/dnavis; the source code is available upon request. SUPPLEMENTARY INFORMATION: Figures are at the publisher's site, other information and examples are at www.win.tue.nl/dnavis. PMID: 16332715 [PubMed -

variation in rates of early retirement due to ill-health within and betweenorganizations that warrants further investigation. The general and specifichelp occupational physicians to make equitable recommendations when assessing

f how genes function in symbiotic processes in both Rhizobia and their host plants. AVAILABILITY: http://nodmutdb.vbi.vt.edu CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Database schema and data curation model are available at http://nodmutdb.vbi.vt.edu. PMID: 15817696 [PubMed - indexed for Me-profile alignment algorithms where the normalization of alignment scores has traditionally been a challenging task. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.eidogen-sertanty.com/Documents/convergent_island_stats_sup.pdf. Publication Types: Evaluation Studies PMID: 1581ide insight into the extent of differential expression across genes. AVAILABILITY: http://www.bioconductor.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Please visit our software webpage on http://compdiag.molgen.mpg.de/software. PMID: 15817688 [PubMed - indexed for MEDLINE]

nts to build pipelines for sequence processing is provided. AVAILABILITY: http://www.lbm.fmvz.usp.br/egene/ CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: http://www.lbm.fmvz.usp.br/egene/ PMID: 15814554 [PubMed - indexed for MEDLINE] be perfectly suited to portray transcriptional regulatory networks. AVAILABILITY: The R code is available on request. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.csie.ntu.edu.tw/~b89x035/yeast/ Publication Types: Evaluation Studies PMID: 15802287 [PubMed - indexed for MEDLId increase in speed over existing programs. AVAILABILITY: Source code for gmap and associated programs is available at http://www.gene.com/share/gmap SUPPLEMENTARY INFORMATION: http://www.gene.com/share/gmap. Publication Types: Evaluation Studies PMID: 15728110 [PubMed - indexed for MEDLINE]onal classes have been affected. MEGO is available free of charge for academic use and may be downloaded from http://www.dxy.cn/mego/MEGOInstall.EXE. Supplementary information can be found on the authors' web page at http://www.dxy.cn/mego/ and at the BioTechniques' web site at http://www. BioTechnimponents in the mixture model, we suggest an alternative criterion, ICL-BIC, which is shown to perform better in selecting the correct mixture model. SUPPLEMENTARY INFORMATION: http://odin.mdacc.tmc.edu/~yuanj/highcorgeneanno.html. PMID: 15713737 [PubMed - indexed for MEDLINE]fference in their size. AVAILABILITY: http://www.dion.che.udel.edu/multiscale/Introduction.html. Fortran 90 code available for academic use by email. SUPPLEMENTARY INFORMATION: Details about the binomial tau-leap algorithm, software and a manual are available at the above website. PMID: 15699024 [Pu

for CADLIVE. AVAILABILITY: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ SUPPLEMENTARY INFORMATION: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ Publication Types: Evaluation Studies PMID: the methods described in this paper and R code for the virtual mass spectrometer are available at http://bioinformatics.mdanderson.org/software.html SUPPLEMENTARY INFORMATION: http://bioinformatics.mdanderson.org/supplements.html. Publication Types: Clinical Trial Validation Studies PMID: 15673564 ith homology to all S.cerevisiae mitochondrially targeted proteins. One hundred twenty eight of these proteins are novel and are of unknown function. SUPPLEMENTARY INFORMATION: Supplementary tables will be available from http://www.sickkids.ca/Robinsonlab/ PMID: 15671119 [PubMed - indexed for MEDLIN

enome, and an expression and cloning approach has been coupled with the predictions of the method. Two genes discovered by this method are discussed. SUPPLEMENTARY INFORMATION: All data used and the results obtained in the cross-validation analysis are available at http://www.soi.city.ac.uk/~conklinfs are consistent with published data regarding the binding specificity of the proteins. AVAILABILITY: THEME is freely available for download. Online SUPPLEMENTARY INFORMATION: http://jura.wi.mit.edu/fraenkel/THEME. PMID: 16332710 [PubMed - as supplied by publisher]ow that these highly central residues are strongly correlated with the presence of hot spots of binding free energy. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.fujirebio.co.jp/support/index.php (under construction). PMID: 15659419 [PubMed - indexed for MEDLINE]emic users at http://ophid.utoronto.ca, both in tab-delimited and PSI-MI formats. Commercial users, please contact I.J. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://ophid.utoronto.ca/supplInfo.pdf. Publication Types: Evaluation Studies PMID: 15657099 [PubMed - indexed for MEDLINE]s illustrated by outlining several current applications. AVAILABILITY: The database is accessible via the world wide web at http://salilab.org/pibase SUPPLEMENTARY INFORMATION: http://salilab.org/pibase/suppinfo.html. PMID: 15657096 [PubMed - indexed for MEDLINE]gorithm. AVAILABILITY: The web tool and a reduced version for local installation are freely available at http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html SUPPLEMENTARY INFORMATION: The website supplies a detailed explanation and illustration of the algorithm at http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHelnative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner. SUPPLEMENTARY INFORMATION: http://www.bioinfo.sfc.keio.ac.jp/research/intron. PMID: 15647298 [PubMed - indexed for MEDLINE]er two popular motif-finding programs, MEME and AlignACE. AVAILABILITY: SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero SUPPLEMENTARY INFORMATION: http://bioinf.nuigalway.ie/sombrero/additional. Publication Types: Evaluation Studies PMID: 15647296 [PubMed - indexed for ific scores in order to obtain reliable and valid estimates. AVAILABILITY: The Selecton web server is available at: http://selecton.bioinfo.tau.ac.il SUPPLEMENTARY INFORMATION: More information is available at http://selecton.bioinfo.tau.ac.il/overview.html. A set of examples is available at http:// (2) multiple tumor subtypes and (3) survival times. AVAILABILITY: Code to implement SAFE in the statistical package R is available from the authors. SUPPLEMENTARY INFORMATION: http://www.bios.unc.edu/~fwright/SAFE. Publication Types: Evaluation Studies Validation Studies PMID: 15647293 [PubMed - inical knowledge. AVAILABILITY: Software is freely available for academic use as a Matlab package, called GENLAB: http://genlab.tudelft.nl/genlab.html. SUPPLEMENTARY INFORMATION: Additional data, results and figures can be found at http://genlab.tudelft.nl/larna.html. PMID: 16332709 [PubMed - as suppl interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications. Publication Types: Evaluation Studies PMID: 15613400 [PubMed - iee MIAME compliance. AVAILABILITY: The application is available from the author at http://www.ansorge-group.embl.de/bloader CONTACT: [email protected] SUPPLEMENTARY INFORMATION: For more details on BLoader visit the above web page. PMID: 15613394 [PubMed - indexed for MEDLINE]

d improve metabolomics by multidisciplinary cooperation. AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/ PMID: 15613389 [PubMed - indexed for MEDLINE]

atics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material. Publication Types: Evaluation Studies PMID: 15613384 [PubMed

s on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability SUPPLEMENTARY INFORMATION: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http:analysis results and R functions for the proposed methods can be found at http://www.biostat.umn.edu/~baolin/research CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.biostat.umn.edu/~baolin/research. Publication Types: Evaluation Studies Validation Studies PMID: 15598833 [PubMed during the measurements. AVAILABILITY: All programs used for this publication are available on request from the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information about the model and its interpretation can be downloaded from http://www.imb-jena.de/tsb/pad. Pubsting programs (ADHoRe and LineUp) for chromosomal homology detection and found that in general CloseUp compares favorably. AVAILABILITY: CloseUp and supplementary information are available at http://www.igb.uci.edu/servers/cgss.html CONTACT: [email protected]. Publication Types: Evaluation Studierve distances between examples in the projected subspaces. AVAILABILITY: http://homes.dsi.unimi.it/~valenti/SW/clusterv/download/clusterv_1.0.tar.gz. SUPPLEMENTARY INFORMATION: http://homes.dsi.unimi.it/~valenti/SW/clusterv. PMID: 16332708 [PubMed - as supplied by publisher]classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: e use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt. Publicatdownloaded from http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN. It underlies the GPL version 2. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~fGene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/venest possible mechanisms of action of the core elements in the promoters with multiple transcription start sites. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf. Publication Types: Evadata set on acute lymphocytic leukemia. AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml. Publication Types: Evaluation Studies PMID: 15572464 [PubMed - indeILABILITY: The software is publicly available under the GNU general public licence from http://www.cs.may.ie/distributed CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Full documentation and a user manual is available from http://www.cs.may.ie/distributed. Publication Types: Evaluation Stud

f signal pathway databases. AVAILABILITY: The pipeline software components are freely available on request to the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://stateslab.bioinformatics.med.umich.edu/software.html. PMID: 15564295 [PubMed - indexed for MEDLINE] were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html. Publicatio

on proteins of known structure. AVAILABILITY: Paircoil2 is freely available as a web application and for download at http://paircoil2.csail.mit.edu. SUPPLEMENTARY INFORMATION: Available at the journal's web site and at the Paircoil2 web site. PMID: 16317077 [PubMed - as supplied by publisher] provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network. Publication Types: Evaluation Studies Validation Studies PMID: 15531ring of microarray signals. AVAILABILITY: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Screenshots and instructions for use are available at the above website. Publication Types: Evaluation Studies PMID: 155095quence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org. PMID: 15509596 [PubMed - indexed for MEDLINE]www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: [email protected], [email protected] SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html. Publication Types: Evaluation Studies PMID: 15501914 [PubMed - indexed vel follow-up analysis. AVAILABILITY: The R package arrayMagic is available with BSD license at http://www.bioconductor.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow. PMIautomated assignment program. AVAILABILITY: APART is available from http://sir.lanl.gov/NMR/APART.htm CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APARTblically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Four tables available at the above site. Publication Types: Evaluation Studies PMID: 15388519 [PubMed - indexed for MEDLINEatabase of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani Publication Types: Evaluation Studies Validation Studies PMID: 15377508 [PubMed - indexed fore drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded froscribed below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de SUPPLEMENTARY INFORMATION: database model, semantic mapping table. PMID: 15374875 [PubMed - indexed for MEDLINE]

slightly exceeded that of the Smith-Waterman algorithm and two Hidden Markov Model-based algorithms. AVAILABILITY: www.inf.u-szeged.hu/~kocsor/CBM05 (supplementary data). PMID: 16317070 [PubMed - as supplied by publisher]intosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request. PMID: 15374874 [PubMed - indexedLITY: The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html. Publication Types: Evaluation Studies PMID: 1ion on time-lagged co-regulation between genes/gene clusters. AVAILABILITY: The software is available upon request. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary tables and figures for this paper can be found at c. Publication Tyn sequences. AVAILABILITY: The program is freely available for non-profit organizations, upon request to the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analyss against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method. SUPPLEMENTARY INFORMATION: http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs. Publication Types: Evaluation Studies Validation Studies PMID: 15374856 [Pnsional functional genomics datasets, VizRank can systematically find relevant biological patterns. AVAILABILITY: http://www.ailab.si/supp/bi-vizrank SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-vizrank. PMID: 15358614 [PubMed - indexed for MEDLINE]AILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4. PMID: 15353449 [PubMed - indexed for MEDLINE] downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu. PMID: 1535344LITY: All data generated in this study are available for download and browsing at http://pedant.gsf.de/ARIA/index.htm. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://pedant.gsf.de/ARIA/index.htm. PMID: 16306393 [PubMed - as supplied by publisher]D scores, NPL scores, P-values and other parameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. PMID: 15347576 [PubMed - indexed for MEDLINE]prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses. AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html. Publication Types: Evaluation Studies PMID: 15347574 [PubMed - indexed for MEDLINE]or factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual. PMID: 15347571 [PubMed - indexed for MEDLINE]pare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/S

simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, ita flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog. PMID: 15308546 [PubMed - indexed for MEDLINE]easured over different subsets of patients. A possible biological explanation for these properties is discussed. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/ Publication Types: Evaluation Studies Validation Studielassification scheme named DALI, which is found to be more accurate, but extremely slow. The software is available upon request from the authors. The supplementary information on ProtClass method can be found at: http://xena1.ddns.comp.nus.edu.sg/ approximately genesis/PClass.htm. PMID: 16305330 [Pu algorithm, BDTree provides a higher prediction accuracy in cross-validations. AVAILABILITY: The software is available upon request from the authors. SUPPLEMENTARY INFORMATION: http://cic.cs.wustl.edu/bdtree/. PMID: 16303796 [PubMed - as supplied by publisher]s successful in estimating gene networks that capture many known relationships as well as several unknown relationships which are likely to be novel. Supplementary information is available at http://bonsai.ims.u-tokyo.ac.jp/~tamada/bayesnet/. PMID: 16374908 [PubMed - in process]he first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera. SUPPLEMENTARY INFORMATION: http://www.unil.ch/comparativegenometrics/collyn_et_al_2005/collyn.htm. PMID: 16303795 [PubMed - as supplied by publisher]iption factor binding sites in non-coding DNA. AVAILABILITY: ACANA software and test sequence data are publicly available at http://BioMedEmpire.org/ SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. CONTACT: [email protected]. PMID: 16301203 [PubMed - in prog facilities to various pathway exchange formats. AVAILABILITY: The Web site is freely accessible to non-commercial users from http://web.patika.org. SUPPLEMENTARY INFORMATION: Detailed information is available on the tool Web site (http://www.cs.bilkent.edu.tr/~patikaweb), including key features, sevise a control strategy that reduces the WNT5A gene's action in affecting biological regulation. AVAILABILITY: The software is available on request. SUPPLEMENTARY INFORMATION: The supplementary Information is available at http://ee.tamu.edu/~edward/tree. PMID: 16286362 [PubMed - as supplied by publith rates of 10-fold or better 10-20% of the time. AVAILABILITY: The software is available for academic research use free of charge by email request. SUPPLEMENTARY INFORMATION: Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html. PMID: 16278238 [PubMed - as supplied bvailable as an R package. AVAILABILITY: ClaNC is freely available from http://students.washington.edu/adabney/clanc CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://students.washington.edu/adabney/clanc/figure2.pdf. PMID: 16269418 [PubMed - in process]d FESTA has been developed based on this algorithm. The program is freely available and can be downloaded at http://www.sph.umich.edu/csg/qin/FESTA/. SUPPLEMENTARY INFORMATION: http://www.sph.umich.edu/csg/qin/FESTA/. PMID: 16269414 [PubMed - as supplied by publisher]tware is implemented in R and is available from Bioconductor or from the first author at [email protected]. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.stat.berkeley.edu/users/nrabbee/693.pdf. PMID: 16267090 [PubMed - in process]

f ncRNA families. AVAILABILITY: The source code is available under GNU Public License at the supplementary web site. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-HeurHmm-2004/ (Technical details, results, C++ code). PMID: 16267089 [PubMedhttp://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://blast.wustl.edu/exalin/exalin-supplement.pdf. PMID: 16267086 [PubMed - in process]ways. AVAILABILITY: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. PMID: 16368768 [PubMed - as supplied by publisher] same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus Contact: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are accessible at http://pir.georgetown.edu/iprolink/biothesaurus/supplement/ PMID: 16267085 [PubMed - iriments. Evaluation of the final version shows further improvement over these results together with a significant speed-up. AVAILABILITY: The server, supplementary information, and the detailed predictions are available at http://www.bio.ifi.lmu.de/SSEP/. PMID: 16267083 [PubMed - as supplied by publtisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/ PMID: 16267082 [PubMed - is in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.inab.org/Help/Main/index.html. PMID: 16257987 [PubMed - in process]e discovery of conserved protein substructures. AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at http://web.mit.edu/bamel/gemoda. PMID: 16257985 [PubMed - in process]m ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W. CONTACT: [email protected] and [email protected] SUPPLEMENTARY INFORMATION: http://www.cmb.dtu.dk/ PMID: 16257984 [PubMed - as supplied by publisher]tasets and has produced very promising results. AVAILABILITY: MATLAB codes are available upon request from the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~hzhang/research.html. PMID: 16249260 [PubMed - in process]atlab source code is available upon request and DNA microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo). Contact: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16249259 [PubMed - in process] system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Contact: [email protected] SUPPLEMENTARY INFORMATION: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PilZ.html. PMID: 16249258 [PubMed - in process]hmark, we blindly identified genes from yeast cell cycles without selecting for periodic or any other anticipated behaviour. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The complete versions of Table 2 and Figure 4, as well as other material, can be found at http://www.lps.ens.fr/~willbran/uvement in our ability to find these sites in genomic sequences. Availability: ICSF is freely available to academic users at http://zlab.bu.edu/ICSF . Supplementary information: http://zlab.bu.edu/ICSF . PMID: 16362906 [PubMed - indexed for MEDLINE]uct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. AVAILABILITY: The program, a web-server and supplementary information are available on http://bioinfo3d.cs.tau.ac.il/ARTS CONTACT: [email protected]. PMID: 16204124 [PubMed - in process]

s cerevisiae and Escherichia coli. AVAILABILITY: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16204114 [PubMed - in process]ar history of gene loss events, and we use this property to predict functional interactions among proteins in our set. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Sequences and trees for the selected orthologous groups can be accessed at http://www.cmbi.kun.nl/~jagabald/table_groupsb.hn when some values were missing. AVAILABILITY: The code is available at http://genome.tugraz.at/BayesianClustering/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The supplementary material is available at http://genome.tugraz.at/BayesianClustering/ PMID: 16204092 [PubMed - in process]ulatory networks obtained for Saccharomyces cerevisiae, one under the normal growth condition and the other under the environmental stress condition. SUPPLEMENTARY INFORMATION: http://kiefer.stat.ucla.edu/lap2/download/bti656_supplement.pdf. PMID: 16144806 [PubMed - indexed for MEDLINE]nts while appropriately controlling the false positives. AVAILABILITY: http://bioinformatics.med.yale.edu/DNACopyNumber CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://bioinformatics.med.yale.edu/DNACopyNumber. PMID: 16131523 [PubMed - indexed for MEDLINE]e Barley Dominant versus Recessive. AVAILABILITY: The algorithm is available upon request from the corresponding author. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://faculty.ucr.edu/~xpcui. Publication Types: Evaluation Studies PMID: 16118260 [PubMed - indexed for MEDLINE]iehs.nih.gov/dirbb/oriogen/index.cfm CONTACT: [email protected] (for statistical questions) and [email protected] (for software support) SUPPLEMENTARY INFORMATION: ORIOGEN has a full set of help files. Also, an example input file is provided with the download. PMID: 16109745 [PubMed - iare freely available at http://www.cs.bgu.ac.il/~meshi; the MESHI API is available at http://www.cs.bgu.ac.il/~meshi/API CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief presailable conformations reveals that the number of preferred local conformations is several orders of magnitude smaller than that suggested previously. SUPPLEMENTARY INFORMATION: www.it.iitb.ac.in/~ashish/bioinfo2005/. PMID: 16096349 [PubMed - indexed for MEDLINE]nd powerful tool to interrogate these very large and complex datasets. AVAILABILITY: The application is freely available for non-commercial research. SUPPLEMENTARY INFORMATION: Documentation, source code and a demonstration version are available at www.bioinformatics.ic.ac.uk/eqtl/. PMID: 16357031 [he position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about lt to find otherwise. Using another dataset, we report a sharply different network structure featuring cellular responses under environmental stress. SUPPLEMENTARY INFORMATION: http://kiefer.stat.ucla.edu/lap2/download/KL_supplement.pdf. PMID: 16076891 [PubMed - indexed for MEDLINE]ular algorithms for generating expression summaries and detection calls. AVAILABILITY: Simpleaffy can be downloaded from http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional information can be found on the supplementary website located at http://bioinformatics.picr.man.ac.uk. PMID: 160al activity, such as atrial fibrillation, which could cause stasis of blood within the left atrial appendage, contributing to left atrial thrombosis. Supplementary data referenced in this paper are not printed in this issue of Toxicologic Pathology. They are available as downloadable files at http:/

: STAR is available as compiled (Linux Fedora 3) or source code from http://pgv19.virol.ucl.ac.uk/download/star_linux.tar CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://pgv19.virol.ucl.ac.uk/download/star_supplement Publication Types: Evaluation Studies PMID: 16046498 [PubMed - indexeiscovery rate for MA and model parameters for HMM. AVAILABILITY: TileMap is freely available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm. SUPPLEMENTARY INFORMATION: http://biogibbs.stanford.edu/~jihk/TileMap/index.htm (includes coloured versions of all figures). PMID: 16046496 [PubMed -

are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, maity of 3'-processing events. AVAILABILITY: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION: Available online at http://harlequin.jax.org/pacdb/supplemental.php. PMID: 16030070 [PubMed - indexed for MEDLINE]rm independent and available free of charge as a Java webstart application at http://mavisto.ipk-gatersleben.de/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Can be found at http://mavisto.ipk-gatersleben.de/ PMID: 16020473 [PubMed - indexed for MEDLINE]near regression models provide a rigorous and unified statistical framework for sample classification and differential gene expression detection. For supplementary information including the computer programs, detailed analysis results, and R functions for the proposed methods, please see http://www.e program RNAcast and is available on the Bielefeld Bioinformatics Server. CONTACT: [email protected], [email protected] SUPPLEMENTARY INFORMATION: Available at http://bibiserv.techfak.uni-bielefeld.de/rnacast/supplementary.html Publication Types: Evaluation Studies PMIDationships. AVAILABILITY: MetNet3D and some sample datasets are available at http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm. SUPPLEMENTARY INFORMATION: Color snapshots and movies are available at http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryIrameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. The current version is v4.01beta. PMID: 16014370 [PubMed - indexed fILITY: The software is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/ptg/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supporting materials is available from http://zhangroup.aporc.org/bioinfo/ptg/bti572supplementary.pdf Publication Types: Evnd results, are available on the website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/ PMIDomplex estimates reported here can be found in the R package apComplex, available at http://www.bioconductor.org CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://daisy.prevmed.northwestern.edu/~denise/pubs/LocalModeling Publication Types: Evaluation Studies PMID: 15998662 [PubMs method on Anopheles gambiae and detected 59 new miRNA genes. AVAILABILITY: This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm. PMID: 15994192 [Pub

tion of protein-protein interactions reported in this manuscript is available at http://timpani.genome.ad.jp/~proj/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The information is also available at the same site as the R script. PMID: 15994190 [PubMed - indexed for MEDLINE]at the prefiltering scheme efficiently separates the two spectra classes. AVAILABILITY: The software tools are available on request from the authors. SUPPLEMENTARY INFORMATION: The Mascot ion score distributions and the C4.5 classification rules can be found at address http://staff.cs.utu.fi/staff/jghly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at http://www.factweb.de. PMID: 15985174 [PubMed - in process]ain solutions that can also describe domain swapping events. The server can be accessed from http://www.ncbs.res.in/~faculty/mini/DIAL/home.html. The Supplementary data can be accessed from http://www.ncbs.res.in/~faculty/mini/DIAL/supplement.html. PMID: 15980441 [PubMed - indexed for MEDLINE]ation with the histology and provide recommendations for applying PCR-based methodology for the detection of mycobacterial DNA in surgical specimens. Supplementary data are available online at http://www.charite.de/ch/patho (rubric Forschung"). Pre-tested specimens are now available for the externa"vergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html. PMID: 15961494 [PubMeial expression more efficiently than two-color loop designs. AVAILABILITY: http://www.jax.org/staff/churchill/labsite/software CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at terparts. AVAILABILITY: Example trees and additional material are available at http://www.stats.ox.ac.uk/~abeln/foldage CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.stats.ox.ac.uk/~abeln/foldage. PMID: 15961490 [PubMed - in process]ty and approximately 90% specificity among unrelated polytopic functional families with the same number of TM domains. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at www.protonet.cs.huji.ac.il/TM/ PMID: 15961481 [PubMed - in process]edictions and additional experimental results are available at http://www.fml.tuebingen.mpg.de/~raetsch/RASE CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.fml.tuebingen.mpg.de/raetsch/RASE. PMID: 15961480 [PubMed - in process]ge processing algorithms can be found at http://www.computableplant.org, together with additional results and simulation movies. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.computableplant.org/ and alternatively for a direct link to the page, http://computableplant.ics.uci.edu/bti1036hieved by using either clinical data or molecular predictors alone. AVAILABILITY: R programs are available at http://www4.stat.ncsu.edu/~li/survipi/. SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~li/survipi/bioinfo-supp.pdf. PMID: 16339281 [PubMed - as supplied by publisher]ins in a dataset containing 9986 protein entries. AVAILABILITY: Requests for software should be made to Dr Jose E. Belizario CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available for academic users at site http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles. PMID: obtaining a Java implementation with a graphical user interface (GUI) is available from http://www.cs.cmu.edu/~jernst/st/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at http://www.cs.cmu.edu/~jernst/st/ PMID: 15961453 [PubMed - in process]

s discriminating test, yielding a marked increase in the number of reported positives at both contact and non-contact sites. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.dimmic.net/supplement/ PMID: 15961449 [PubMed - in process]oritization of repeats. Here we present Satellog, a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism. RESULTS: A total of 5,546 such repeatsation, synthetic shuffling, DHR, ADO and SISDC. AVAILABILITY: Web interface and C++ source code available at http://guinevere.otago.ac.nz/stats.html. SUPPLEMENTARY INFORMATION: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website. PMID: t this approach can aid in the interpretation of the resulting 'significant' gene set. AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study. PMID: 15919728 [PubMed - indexed for MEDLINable at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/. SUPPLEMENTARY INFORMATION: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nuseful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles. AVAILABILITY: Supplementary information and computer code at http://genomics.lbl.gov/llda. Publication Types: Evaluation Studies PMID: 15919724 [PubMed - indexed foVAILABILITY: Various alternative and supplemental networks (not given in the text) as well as source code extensions, are available from the authors. SUPPLEMENTARY INFORMATION: http://bioinformatics.oxfordjournals.org. Publication Types: Evaluation Studies PMID: 15914545 [PubMed - indexed for MEDLINProtein Data Bank files and represents subunit/domain interfaces as two-dimensional networks. AVAILABILITY: http://www.kumc.edu/biochemistry/resmap/. SUPPLEMENTARY INFORMATION: Default definitions and directions for graphically managing networks are available at the same website. PMID: 15914544 [Pubvery small number of expansive protein families led to the evolution of interactomes and seemed to have played a key role in species diversification. SUPPLEMENTARY INFORMATION: http://interactomics.org. Publication Types: Evaluation Studies PMID: 15914543 [PubMed - indexed for MEDLINE]hierarchy. AVAILABILITY: The new algorithm is integrated into the PRIDE2 web servers at http://pride.szbk.u-szeged.hu and http://www.icgeb.org/pride. SUPPLEMENTARY INFORMATION: Detailed documentation and performance evaluation is available in the description section of the PRIDE2 web server. PMID: 1alytical clustervalidation. AVAILABILITY: The software used in the experiments is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/. SUPPLEMENTARY INFORMATION: Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/available at www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. The Spider matlab package is available at www.kyb.tuebingen.mpg.de/bs/people/spider. SUPPLEMENTARY INFORMATION: www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. Publication Types: Evaluation Studies PMID: 15905279 [PubMed - indexed es with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase. SUPPLEMENTARY INFORMATION: A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://l

pate that this approach will be able to accelerate target identification and drug development for tuberculosis in the future. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary Figures 1 through 6 on drug response networks and differential network analyses on cerulenin, chlorpromazine,n probing molecular mechanisms responsible for functional impacts of nsSNPs. AVAILABILITY: http://www.salilab.org/LS-SNP CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://salilab.org/LS-SNP/supp-info.pdf. Publication Types: Evaluation Studies PMID: 15827081 [PubMed - indexed for MEDLINEthe tumor growth and therefore suggest the selection and timing of experiments for measuring the activity of T cells. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.dmi.unict.it/CIG/suppdata_bioinf.html. Publication Types: Evaluation Studies Validation Studies PMID: 15817697 [ificant for the eventual interpretation of the microarray experiments. AVAILABILITY: Java and Matlab codes are available on request from the authors. Supplementary material: available online at http://users.utu.fi/jotatu/GOImpute.html. PMID: 16377613 [PubMed - as supplied by publisher]r data, which showed heterogeneous and low-level methylation of CpG islands, have obvious implications for methylation studies. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16372313 [PubMed - as ion or interaction prediction problems. AVAILABILITY: Data and MhcSF multiple alignment are available on the IMGT website (http://imgt.cines.fr), and supplementary material is downloadable at http://imgt.igh.cnrs.fr/MhcSF-B2M.html. PMID: 16352655 [PubMed - as supplied by publisher]ighly correlated genes were enriched for gene ontology categories involved in the DNA damage response and telomere maintenance. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16323170 [PubMed - as in 3q26.3-q27 in EA revealed multiple genetic alterations that had occurred sequentially and/or concurrently during EA development. This article has supplementary material, available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16320248 [PubMed - as distance properties, such as metric and additivity, appear to have much less effect on the performance of distances. AVAILABILITY: R code GADIST and Supplementary material are available at http://research.stowers-institute.org/bioinfo/ CONTACT: [email protected]. PMID: 16306389 [PubMed - incadherin expression in the SW480 colon cancer cell line indicates that L-plastin plays an important mechanistic role in colorectal cancer metastasis (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7method for suggesting SNP-SNP interactions that may be validated in future studies, using more traditional statistical methods on different datasets (Supplementary material can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat). Pubure clinical cancer response prediction feasible. The TaqMan-validated gene expression patterns provide new gene candidates for multidrug resistance. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7tural part of recombinational DNA repair. Additionally, we find that Rad51C plays an important role in regulating this process. This article contains supplementary material, which may be viewed at the Journal of Cellular Biochemistry website at http://www.interscience.wiley.com/jpages/0730-2312/supp

design algorithm; and check the concordance between the attractor states of the designed network and the data states. AVAILABILITY: The software and supplementary material is available at http://gsp.tamu.edu/Publications/BNs/bn.htm MeSH Terms: Algorithms* Computer Simulation Gene Expression Profili comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation. MeSH Terms: Algorithms Computational Biology/methods* Computer Graphics Database Managemine-tiling oaCGH analysis provides an unprecedented level of resolution, allowing detailed mapping of recurrent unbalanced chromosomal abnormalities. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22oin other broken ends or eroded telomeres, producing massive chromosomal instability at the later passages of the cell culture. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. MeSH Terms: Blotting, Westercentral role in hepatocyte death in fulminant hepatitis through direct and indirect pathways that may have direct therapeutic implications in humans. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me protein with 85% probability is reduced by 20-30% when using the integrated method.The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php. MeSH Terms: Algorithms* Data Interpretation, Statistical Epitopd metabolism. Increased abundance of transcripts linked to cellular proliferation in advanced fibrosis is consistent with a predisposition to cancer. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index/html)e other human HCCs. In conclusion, expression fingerprints may be used for diagnostic purposes and potential new therapeutic intervention strategies. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index/html)e that activity of ERK in the cytoplasm is important for survival during oxidative stress in hepatocytes and that RSK is activated downstream of ERK. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html) in most individuals, the CD8+ T cell responses generated early in HCV infection decline in peripheral blood and are not replaced with new responses. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)undescribed posttranscriptional mechanism. A single mutation inactivated a 5' splice site that is obviously essential for pre-S2/S mRNA accumulation. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)interferon alfa-2b in lamivudine treatment was found to neither enhance the potency of blocking HBV production nor the decay rates of infected cells. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)ly better than the existing gene finders ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted completely correctly. AVAILABILITY: Supplementary material available at http://www.bioinformatics.uwaterloo.ca/supplements/05eh/ CONTACT: [email protected]. PMID: 15961499 [PubMed -

fied a set of candidate genes, including those regulated by RAS signaling, that may contribute to the process of cancer cell invasion and metastasis. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22actions from diverse organisms than from a single organism. AVAILABILITY: The program for computing the protein-protein interaction probabilities and supplementary material are available at http://bioinformatics.med.yale.edu/interaction. Publication Types: Evaluation Studies MeSH Terms: Binding Sitey separate from hematopoietic cells and differentiate into mature, functional hepatocytes in vivo with the capacity for efficient liver repopulation. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)ation during the evolution of cirrhosis. These findings have implications for understanding the evolution of cirrhosis and associated carcinogenesis. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Meigenesis of intrahepatic cholangiocarcinoma and should contribute to the development of diagnostic and therapeutic strategies for this type of tumor. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)toxic carcinogens because the relatively high levels of cell division in the developing animal facilitate the conversion of DNA damage into mutation. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7es an immediate burst of ATP that seems to be a general response of human differentiated keratinocytes to the radiation stress. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/v95.html (c) 2005 Wiley-Liss, Inc. MeSH Terms: Cel in these chimeric animals necessitates a critical review of the observations and conclusions made in experiments with isolated mature" hepatocytes. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)"le can be used as an estimate of the MCID in HCV, and this value may be used as the basis for power calculations in clinical trials evaluating HRQOL. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)differ between family members and controls. CONCLUSIONS: These six TCII polymorphisms do not strongly influence NTD risk in the Irish population. The Supplementary Material for this article can be found on the Birth Defects Research (Part A) website: http://www.mrw.interscience.wiley.com/suppmat/154ning array comparative genomic hybridization and microsatellite analysis in elucidating complex genomic rearrangements in primary human tumor tissue. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-225methylation or expression of ZAC mRNA between localized and advanced tumors, our data indicates that loss of ZAC is a relatively early event in HOC. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7ic differentiation in vitro and could represent an attractive approach for developing stem cell therapies for treatment of hepatic disease in humans. Supplementary material for this article can be found on the HEPATOLOGY website ( http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html

-1; their effects multiplied. In conclusion, combined expression of sFlt-1 and endostatin effectively suppresses HCC growth under in vivo conditions. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wileyocytes has an impact on several other subcellular compartments and metabolic pathways but is not detrimental to the function of the liver parenchyma. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Meducibly expressing a protein of interest. As such they represent a useful research tool for example, to dissect oncogene function(s) in colon cancer. Supplementary material for this article be found at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/94/suppmat_welma n.doc. Copyright roteins and with chromatin, spectrin repeat-containing proteins represent strong candidates for important organizational proteins within the nucleus. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).that the differential activation of the PKC isoenzymes by DCA may be of critical importance for the functional responses of colonic epithelial cells. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7esterol hypersecretion, diosgenin probably does not interact directly with Abcg5/Abcg8, but rather increases cholesterol delivery to the heterodimer. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Merray analysis of new compounds to determine the presence of these expression changes and their usefulness in predicting idiosyncratic hepatotoxicity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience. Wiley.com/jpages/0270-9139/suppmat/index.htnd). Mrrence and therefore benefit from current antiviral therapy, as well as provide a rationale for the future use of novel immunotherapeutic approaches. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience. wiley.com/jpages/0270-9139/suppmat/index.html). M decrease in hepatic necrosis following acetaminophen challenge. This suggests a novel role for LBP in modulating acetaminophen-induced liver injury. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/O270-9139/suppmat/index.html). Mexpressed genes that colocalize in the genome may indicate gene regulatory mechanisms that require further study to evaluate functional coregulation. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7 two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. AVAILABILITY: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/ Publication Types: Evaluation Studies Meults demonstrate that mammalian viral genome types differ in their amino acid preference. AVAILABILITY: The tools used to format and analyze data and supplementary material are available at http://www.cse.sc.edu/~rose/aminoPreference/index.html CONTACT: [email protected]. Publication Types: Evaluationic interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/. MeSH Terms: Adaptation, Physiolo

sociated with ConA-treated cells implies that a mechanism independent of furin may perhaps account for the binding of the MMP-2 species to the cells. Supplementary material for this article can be found at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/94/suppmat_guo.t if. Copyrights were recognized by serum antibodies of melanoma patients but not healthy controls. The role of these antigens in MAR awaits further investigation. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7Ps (132C > T in exon V and 196G > A (val66met) in exon XIIIA) of the BDNF gene may not be associated with Japanese MAP abusers. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:effects of ethanol, dopamine may be critical for initiating drug use and for reinstating drug use during protracted abstinence. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:e allele reported till date at the MJD/SCA3 locus and may greatly reduce the gap between normal and pathological repeat ranges. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299: We found no association between p.V66M or the additionally genotyped variant c.-46C > T and obesity, ADHD or eating disorders. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:ry finding that needs to be replicated in a larger sample of Caucasian males and relationships sought with clinical phenotypes. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299: the diagnosis of prostate cancer. Nevertheless, this risk should not be neglected as it may be of clinical significance under certain circumstances. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7 of unknown function, potentially coding for pharmacologically or microbiologically active substances. Supplemental data to this work can be found at http://www.ncbi.nlm.nih.gov/projects/omes/index.html#Ag2. MeSH Terms: Amino Acid Sequence Animals Anopheles gambiae/genetics* Chromosome Mapping Chromm is useful mainly to improve local marker ordering in linkage groups obtained in other ways. AVAILABILITY: The source code and supplemental data are http://www.iubio.bio.indiana.edu/soft/molbio/qtl/flipper/ CONTACT: [email protected]. Publication Types: Evaluation Studies Validation Studies MeSH Te

Live? Journal?

101: Bioinformatics. 2005 Jun 15;21(12):2923-4. Epub 2005 Apr 7. no n111: Bioinformatics. 2005 May 1;21(9):1987-94. Epub 2005 Feb 2. no n

114: Bioinformatics. 2005 May 1;21(9):1971-8. Epub 2005 Jan 27. no n



121: Bioinformatics. 2005 May 1;21(9):2099-100. Epub 2005 Jan 18.no n


131: Bioinformatics. 2005 Apr 15;21(8):1472-8. Epub 2004 Dec 21. no n

137: Bioinformatics. 2005 Apr 15;21(8):1304-7. Epub 2004 Dec 14. no N

140: Bioinformatics. 2005 Apr 15;21(8):1695-8. Epub 2004 Dec 7. no N

166: Bioinformatics. 2005 Feb 1;21(3):349-56. Epub 2004 Sep 7. no N

169: Bioinformatics. 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3. no N

52: Bioinformatics. 2005 Sep 15;21(18):3665-6. Epub 2005 Aug 2. no N

63: Bioinformatics. 2005 Sep 1;21(17):3582-3. Epub 2005 Jul 12. no N

66: Bioinformatics. 2005 Sep 1;21(17):3469-74. Epub 2005 Jul 5. no N

78: Bioinformatics. 2005 Jun 1;21 Suppl 1:i274-i282. no N

9: J Biol Chem. 2005 Dec 8; [Epub ahead of print] no N

25: J Cell Biochem. 2005 Aug 1;95(5):885-901. no y

33: J Cell Biochem. 2005 Aug 1;95(5):902-17. no y

35: Am J Med Genet C Semin Med Genet. 2005 May 15;135(1):59-68no y

44: Birth Defects Res A Clin Mol Teratol. 2005 Mar;73(3):154-61. no y

96: Bioinformatics. 2005 Jun 15;21(12):2917-20. Epub 2005 Apr 19. No n

98: Bioinformatics. 2005 Jun 15;21(12):2856-60. Epub 2005 Apr 12. No n

177: Bioinformatics. 2005 Dec 23; [Epub ahead of print] n

1: Bioinformatics. 2005 Dec 23; [Epub ahead of print] yes n


No real Link

100: Bioinformatics. 2005 Jun 15;21(12):2927-9. Epub 2005 Apr 7. yes n




105: Bioinformatics. 2005 Jun 15;21(12):2883-90. Epub 2005 Mar 31yes n

106: Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22. yes n

107: Biotechniques. 2005 Feb;38(2):277-83. yes n

108: Bioinformatics. 2005 May 1;21(9):2118-22. Epub 2005 Feb 15. yes n

109: Bioinformatics. 2005 May 1;21(9):2136-7. Epub 2005 Feb 4. yes n11: Bioinformatics. 2005 Dec 6; [Epub ahead of print] yes n110: Bioinformatics. 2005 May 1;21(9):1846-52. Epub 2005 Feb 2. yes n112: Bioinformatics. 2005 May 1;21(9):2083-4. Epub 2005 Feb 3. yes n

113: Bioinformatics. 2005 May 1;21(9):2036-42. Epub 2005 Jan 27. yes n





120: Bioinformatics. 2005 Apr 15;21(8):1311-5. Epub 2005 Jan 19. yes n









130: Bioinformatics. 2005 Apr 15;21(8):1603-9. Epub 2004 Dec 21. yes n

yes n

yes n



134: Bioinformatics. 2005 Apr 15;21(8):1487-94. Epub 2004 Dec 21.yes n

135: Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17. yes n

136: Bioinformatics. 2005 Apr 15;21(8):1565-71. Epub 2004 Dec 14.yes n







144: Bioinformatics. 2005 Apr 15;21(8):1592-5. Epub 2004 Nov 30. yes n

145: Bioinformatics. 2005 Apr 15;21(8):1295-300. Epub 2004 Nov 30yes n

146: Bioinformatics. 2005 May 1;21(9):2112-3. Epub 2004 Nov 30. yes n



149: Bioinformatics. 2005 Mar 1;21(5):691-3. Epub 2004 Nov 5. yes n

15: Bioinformatics. 2005 Nov 29; [Epub ahead of print] yes n


151: Bioinformatics. 2005 Mar 1;21(5):689-90. Epub 2004 Oct 27. yes n



154: Bioinformatics. 2005 Feb 15;21(4):554-6. Epub 2004 Sep 28. yes n

155: Bioinformatics. 2005 Mar 1;21(5):680-2. Epub 2004 Sep 23. yes n


yes n

158: Bioinformatics. 2005 Jan 15;21(2):260-2. Epub 2004 Sep 17. yes n












17: Bioinformatics. 2005 Nov 1;21(Suppl_3):iii49-iii57. yes n




173: Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19. yes n

174: Bioinformatics. 2005 Jan 15;21(2):208-17. Epub 2004 Aug 19. yes n

175: Bioinformatics. 2005 Feb 1;21(3):396-8. Epub 2004 Aug 12. yes n

176: Bioinformatics. 2005 Jan 15;21(2):171-8. Epub 2004 Aug 12. yes n

18: J Comput Biol. 2005 Nov;12(9):1221-41. yes n


2: J Bioinform Comput Biol. 2005 Dec;3(6):1295-313. yes n


21: Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13. yes n











4: Genome Inform Ser Workshop Genome Inform. 2005;16(1):49-58.yes n


33: Bioinformatics. 2006 Jan 1;22(1):106-11. Epub 2005 Oct 27. yes n






39: Bioinformatics. 2005 Oct 15;21(20):3859-64. yes n

4: Genome Inform Ser Workshop Genome Inform. 2005;16(1):49-58.yes n

40: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii47-ii53. yes n




44: Bioinformatics. 2005 Nov 1;21(21):4033-8. Epub 2005 Sep 6. yes n

45: Bioinformatics. 2005 Oct 15;21(20):3811-7. Epub 2005 Aug 30. yes n




49: Bioinformatics. 2005 Sep 15;21(18):3622-8. Epub 2005 Aug 11. yes n


50: Bioinformatics. 2005 Nov 1;21(21):4060-6. Epub 2005 Aug 9. yes n



54: Toxicol Pathol. 2005;33(5):517-32. yes n

55: Bioinformatics. 2005 Sep 1;21(17):3535-40. Epub 2005 Jul 26. yes n


57: Proteomics. 2005 Aug;5(13):3537-45. yes n











69: Bioinformatics. 2005 Sep 1;21(17):3482-9. Epub 2005 Jun 30. yes n


70: BMC Bioinformatics. 2005 Jun 28;6:161. yes n

71: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W130-2. yes n

72: Virchows Arch. 2005 Sep;447(3):573-85. Epub 2005 Jun 21. yes n

73: Bioinformatics. 2005 Jun 1;21 Suppl 1:i478-i486. yes n










83: BMC Bioinformatics. 2005 Jun 10;6(1):145. yes n

84: Bioinformatics. 2005 Aug 1;21(15):3314-5. Epub 2005 Jun 2. yes n

85: Bioinformatics. 2005 Aug 1;21(15):3324-6. Epub 2005 May 26. yes n










95: Bioinformatics. 2005 Jun 15;21(12):2898-905. Epub 2005 Apr 19yes n




2: Genes Chromosomes Cancer. 2005 Dec 21; [Epub ahead of print]yes n


4: Genes Chromosomes Cancer. 2005 Dec 1; [Epub ahead of print] yes n

5: Genes Chromosomes Cancer. 2005 Nov 30; [Epub ahead of print]yes n

6: Bioinformatics. 2005 Nov 1;21 Suppl 3:iii3-iii11. yes n

7: Int J Cancer. 2005 Nov 14; [Epub ahead of print] yes n

8: Int J Cancer. 2005 Oct 10;118(7):1790-1797 [Epub ahead of print]yes n

9: Int J Cancer. 2005 Oct 10;118(7):1699-1712 [Epub ahead of print]yes n

10: J Cell Biochem. 2005 Dec 15;96(6):1095-109. yes y

12: Bioinformatics. 2005 Nov 1;21(21):4021-5. Epub 2005 Sep 8. yes y

13: Bioinformatics. 2005 Sep 15;21(18):3674-6. Epub 2005 Aug 4. yes y

14: Genes Chromosomes Cancer. 2005 Nov;44(3):305-19. yes y

15: Genes Chromosomes Cancer. 2005 Dec;44(4):339-50. yes y

16: Hepatology. 2005 Aug;42(2):372-80. yes y

17: Eur J Immunol. 2005 Aug;35(8):2295-303. yes y



20: Hepatology. 2005 Jul;42(1):200-7. yes y




24: Bioinformatics. 2005 Jun 1;21 Suppl 1:i57-i65. yes y

26: Genes Chromosomes Cancer. 2005 Sep;44(1):37-51. yes y

28: Bioinformatics. 2005 Aug 1;21(15):3279-85. Epub 2005 May 19. yes y


30: Hepatology. 2005 Jun;41(6):1262-71. yes y

31: Hepatology. 2005 Jun;41(6):1339-48. yes y

32: Int J Cancer. 2005 Nov 1;117(2):182-7. yes y

34: J Cell Biochem. 2005 Jun 1;95(3):620-31. yes y

36: Hepatology. 2005 Apr;41(4):847-56. yes y


38: Birth Defects Res A Clin Mol Teratol. 2005 Apr;73(4):239-44. yes y

39: Genes Chromosomes Cancer. 2005 Jun;43(2):181-93. yes y

40: Int J Cancer. 2005 Jul 10;115(5):690-700. yes y




45: J Cell Biochem. 2005 Apr 15;94(6):1148-62. yes y

46: Bioessays. 2005 Feb;27(2):144-52. yes y

47: Int J Cancer. 2005 May 10;114(6):887-95. yes y

48: Hepatology. 2005 Jan;41(1):141-50. yes y




52: Int J Cancer. 2005 Apr 20;114(4):590-7. yes y

54: Bioinformatics. 2005 May 1;21(9):1797-806. Epub 2004 Nov 30. yes y

55: Bioinformatics. 2005 Apr 15;21(8):1349-57. Epub 2004 Nov 30. yes y

56: Arch Microbiol. 2005 Jan;183(1):27-36. Epub 2004 Nov 13. yes y

57: J Cell Biochem. 2005 Feb 15;94(3):446-59. yes y

58: Int J Cancer. 2005 Mar 10;114(1):88-93. yes y

59: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):70-3yes y

60: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):29- yes y

61: Am J Med Genet B Neuropsychiatr Genet. 2005 Feb 5;133(1):124yes y

62: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):96-9yes y

63: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):100yes y

64: Int J Cancer. 2005 Jan 10;113(2):290-7. yes y

1: J Exp Biol. 2005 Oct;208(Pt 20):3971-86. yes no

2: Bioinformatics. 2005 Apr 15;21(8):1579-91. Epub 2004 Nov 25. no no





PMID: 15937898 [PubMMeSH Terms: Acetylation

PMID: 15861382 [PubMMeSH Terms: Cells, Cultured

PMID: 15806594 [PubMMeSH Terms: Animals














PMID: 15699024 [PubMed - indexed for MEDLINE]PMID: 16332714 [PubMed - as supplied by publisher]PMID: 15691858 [PubMed - indexed for MEDLINE]PMID: 15691853 [PubMed - indexed for MEDLINE]




PMID: 16150807 [PubMMeSH Terms: Algorithms*

PMID: 16081474 [PubMMeSH Terms: Algorithms

PMID: 16075461 [PubMMeSH Terms: Chromosome Breakage*

PMID: 16052508 [PubMMeSH Terms: Blotting, Western



PMID: 15986378 [PubMMeSH Terms: Actins/analysis*



PMID: 15962289 [PubMMeSH Terms: Acute Disease

PMID: 15962285 [PubMMeSH Terms: Carrier State/immunology

PMID: 15962284 [PubMMeSH Terms: Adult


PMID: 15929091 [PubMMeSH Terms: Cell Line, Tumor

PMID: 15905281 [PubMMeSH Terms: Binding Sites


PMID: 15880761 [PubMMeSH Terms: Adaptation, Physiological


PMID: 15880493 [PubMMeSH Terms: Aging

PMID: 15832339 [PubMMeSH Terms: Cells, Cultured


PMID: 15791608 [PubMMeSH Terms: Case-Control Studies

PMID: 15782407 [PubMMeSH Terms: Alleles

PMID: 15770670 [PubMMeSH Terms: Astrocytoma/genetics*

PMID: 15751035 [PubMMeSH Terms: Apoptosis


PMID: 15739185 [PubMMeSH Terms: Angiogenesis Inhibitors/genetic

PMID: 15732085 [PubMMeSH Terms: Adenosine Triphosphate/metabo

PMID: 15669025 [PubMMeSH Terms: Blotting, Western


PMID: 15645414 [PubMMeSH Terms: Butyric Acids/pharmacology*

PMID: 15619238 [PubMMeSH Terms: ATP-Binding Cassette Transport



PMID: 15619225 [PubMMeSH Terms: Acetaminophen*/poisoning




PMID: 15551059 [PubMMeSH Terms: Adaptation, Physiological/genet


PMID: 15523688 [PubMMeSH Terms: Antigens, Neoplasm/analysis*


PMID: 15457501 [PubMMeSH Terms: Alcoholism/physiopathology*

PMID: 15457499 [PubMMeSH Terms: Aged

PMID: 15457498 [PubMMeSH Terms: Adolescent

PMID: 15457497 [PubMMeSH Terms: Adolescent

PMID: 15389512 [PubMMeSH Terms: Humans

Anopheles gambiae. PMID: 16215223 [PubMed - indexedMeSH Terms:

Crane CF, Crane YM. PMID: 15564296 [PubMed - indexedMeSH Terms:

Animals Chromatin/metabolism* G1 Phase/physiol

DNA (Cytosine-5-)-MethyDNA (Cytosine-5-)-Methyltransferas DNA Methylation

Disease Models, Animal Embryonic Development* Humans

Cloning, Molecular Cytogenetic Analysis DNA, Complemen

Computer Simulation Gene Expression Profiling/methods* Gene Expression

Computational Biology/ Computer Graphics Database Manag

Chromosomes, Human, PChromosomes, Human, Pair 17* Genome, Human

Cell Culture Techniques Cell Line Chromosomal Inst

Antigens, CD40/analysisAntigens, CD40/physiology* Apoptosis*

Data Interpretation, StatEpitopes, T-Lymphocyte/immunolog Epitopes, T-Lym

Adult Female Gene Expression P

Carcinoma, HepatocellulCytoskeletal Proteins/genetics* Gene Expression P

Cell Survival/drug effectCell Survival/physiology Cells, Cultured

Adolescent Adult CD8-Positive T-

Clone Cells Hepatitis B/physiopathology Hepatitis B/virol

Antiviral Agents/therapeBiomechanics Female

DNA, Neoplasm/genetic Gene Amplification Humans

Biodiversity Caenorhabditis elegans Proteins/cheCaenorhabditis e

Cell Separation/method Cells, Cultured Epithelial Cells*

Animals Bile Ducts Biological Marke

Aged Bile Duct Neoplasms/genetics Bile Duct Neopl

Aminobiphenyl CompoundAnimals Animals, Newbor

Energy Metabolism/geneEnergy Metabolism/radiation effectsGamma Rays*

Blood Proteins/metabol Hepatitis B/metabolism Hepatitis B/path

Delphi Technique Health Status* Hepatitis C/phys

Case-Control Studies Female Gene Frequency

Base Sequence Brain Neoplasms/genetics* Chromosomes, Hu

Cell Cycle Proteins/geneCell Cycle Proteins/metabolism* Cell Proliferation

Cell Differentiation Cell Movement Cell Survival

Animals Cell Line, Tumor Endostatins/gene

Animals Cells, Cultured Disease Models,

Cell Line, Tumor Cytomegalovirus/genetics Doxycycline/pha

Cell Membrane/metabolCell Nucleus/metabolism* Cell Nucleus/phy

Cell Culture Techniques Colon/cytology* Colon/pathology

Animals Biliary Tract/drug effects* Biliary Tract/secr

Cells, Cultured Fluoroquinolones/poisoning* Gene Expression/

Aged Antibody Formation Antiviral Agents/

Acute-Phase Proteins/geAcute-Phase Proteins/metabolism* Acute-Phase Prot

Blotting, Western Cell Transformation, Neoplastic DNA Primers/che

Cluster Analysis DNA Mutational Analysis/methods Evolution, Molecu

Amino Acid Sequence Animals Base Sequence

Aerobiosis Anaerobiosis Azoarcus/genetic

Cells, Cultured Furin/antagonists & inhibitors Gelatinase A/met

Antigens, Neoplasm/genBlotting, Northern Cell Line, Tumor

Alleles Amphetamine-Related Disorders/eti Amphetamine-Rel

Brain/physiopathology Dopamine/physiology* Humans

Alleles Atrophy Base Sequence

Attention Deficit Disord Body Mass Index Brain-Derived Ne

Adult Aged Amino Acid Subst

Ileum/physiology* Immunohistochemistry In Situ Hybridizat

Amino Acid Sequence Animals Anopheles gambi

Algorithms* Chromosome Mapping/methods* Comparative Stu

Gene Expression RegulationHela Cells Histones/Histones/metabolism*

Genomic Imprinting Glutathione Transferase/geneGlutathio Humans

Nerve Tissue Proteins/physiNeural Tube Defects/embryo Neural TuResearch Support, Non-U.S. G

DNA-Binding Proteins/genetDNA-Binding Proteins/metaboLinkage ( Mice

Models, Biological* Pattern Recognition, Automa ProteomeResearch Support, N.I.H., Ext

Databases, Protein Gene Expression Profiling/m Genome Genomics*

Humans In Situ Hybridization, Fluore Neurobla Nucleic Acid Hybridization/m

Chromosome Painting Chromosomes, Human, Pair ComparatDNA/genetics

CD4-Positive T-Lymphocyte CD40 Ligand/physiology* ConcanavaHepatitis/pathology*

Histocompatibility Antigens Histocompatibility Antigens Humans Hydrolysis

Hepatitis C/complications* Humans ImmunohiLiver/metabolism*

Genes, ras* Genotype GlutamatHumans

Cytoplasm Extracellular Signal-Regulat HepatocytHepatocytes/metabolism

Female Hepatitis C/immunology* Humans Male

Hepatitis B Surface Antige Hepatitis B virus/genetics Hepatitis Hepatitis B virus/physiology*

Hepatitis B e Antigens/imm Hepatitis B, Chronic/drug the Hepatitis Humans

Nucleic Acid Hybridization Oligonucleotide Array SequenPancreatiPoint Mutation

Computer Simulation Drosophila Proteins/chemistr DrosophilModels, Biological*

Fetus/cytology Liver/cytology* Liver/embMice

Cell Cycle Cell Cycle Proteins/metaboli Cell Proli Cyclin-Dependent Kinase Inhi

Bile Ducts, Intrahepatic* Cholangiocarcinoma/geneticsCholangi Cluster Analysis

Carcinogens/toxicity* DNA/genetics DNA/metaDNA Adducts/metabolism*

Humans Keratinocytes/cytology KeratinocMitochondria/enzymology*

Hepatitis C/metabolism Hepatitis C/pathology Humans Liver/metabolism*

Hepatitis C/psychology Hepatitis C/therapy Hepatitis Humans

Humans Male Neural TuNeural Tube Defects/genetics

DNA Primers Humans MicrosateNucleic Acid Hybridization

DNA Methylation* Disease Progression Female Gene Expression Profiling*

Cells, Cultured Embryo/cytology* Green FluGrowth Substances/physiolog

Gene Therapy* Liver Neoplasms, ExperimentLiver NeoLiver Neoplasms, Experiment

Endoplasmic Reticulum/ultr Gene Expression Glucose/ Hepatocytes/ultrastructure*

Electrophoresis, Polyacryla Gene Expression Regulation, Humans Plasmids

Chromatin/chemistry Cytoplasm/metabolism EvolutionFungal Proteins/chemistry

Colorectal Neoplasms/etiol Colorectal Neoplasms/preventCytoskeleDeoxycholic Acid/pharmacolo

Cholesterol/secretion* Diosgenin/pharmacology* Female Kinetics

Glutathione/antagonists & inHepatocytes/drug effects* HepatocyHumans

CD4-Positive T-Lymphocyte CD8-Positive T-Lymphocytes Female Hepacivirus/immunology*

Adenoviridae Animals Carrier P Carrier Proteins/metabolism*

Down-Regulation Fibroblasts/metabolism Gene ExprGenes, erbB-2*

Models, Genetic* Models, Statistical Pattern RPhylogeny

Chromosome Mapping/methComparative Study DNA, ViraGenome, Viral*

Bacterial Proteins/genetics Betaproteobacteria/classificaBetaproteBetaproteobacteria/metaboli

Metalloendopeptidases/metMyocardium/cytology Myocardi Rats

DNA, Complementary/analysDNA, Neoplasm/analysis Gene LibrHumans

Brain-Derived Neurotrophic Female Gene Fre Genotype

Models, Biological Polymorphism, Genetic Receptor Receptors, Dopamine D2/phys

Brain Stem/pathology Cerebellum/pathology Family HeFemale

Child Chromatography, High PressuComparatDNA/chemistry

Catechol O-Methyltransfera Comparative Study European Female

Male Prostate-Specific Antigen/anaProstate- Prostatic Neoplasms/diagnosi

Chromosome Mapping Chromosomes/genetics Cluster A Computational Biology

Computer Simulation DNA Mutational Analysis/metGene Del Genetic Markers/genetics*

Humans Immunoblotting

Immunoprecipitation Isoenzymes

Substances: Nerve Tissue Proteins

Mice, Inbred BALB C Microsatellite Repeats

Research Support, U.S. Gov't, Signal Transduction/physio

Information Storage and Retri Internet

Oligonucleotide Array SequencReverse Transcriptase Pol

Epithelial Cells/cytology* Female

Hepatocytes/pathology* Immunohistochemistry

Predictive Value of Tests Proteasome Endopeptidas

Liver Cirrhosis/metabolism* Male

Liver Neoplasms/genetics* Male

Hydrogen Peroxide/pharmacol Male

Prospective Studies Research Support, N.I.H.,

Humans Mutation

Interferon Alfa-2a/therapeutic Lamivudine/therapeutic us

Proto-Oncogene Proteins/genetRNA, Messenger/genetics*

Models, Chemical Protein Binding

Research Support, N.I.H., Extr Research Support, Non-U.S

Cyclin-Dependent Kinases/antagHepatocytes/metabolism*

Dissection Down-Regulation

Liver/drug effects Liver/pathology*


Liver/pathology* Liver/ultrastructure

Neuropsychological Tests Quality of Life*

Polymorphism, Single Nucleoti Research Support, N.I.H.,

Polymorphism, Genetic Research Support, Non-U.S

Gene Silencing* Genes, Tumor Suppressor

Hepatocytes/cytology* Hepatocytes/metabolism

Male Neovascularization, Pathol

Liver/metabolism Liver/ultrastructure

Promoter Regions (Genetics) Research Support, Non-U.S

Humans Models, Biological

Detergents/pharmacology* Enzyme Activation

Lipoproteins/metabolism* Male

Liver Diseases/chemically ind Male

Hepatitis C/complications* Hepatitis C/drug therapy

Carrier Proteins/pharmacology Cytochrome P-450 Enzyme

Genome Glycoproteins/metabolism

Recombination, Genetic/genetiResearch Support, Non-U.S

Mammals Models, Genetic

Biodegradation Chromosomes, Bacterial/g

Research Support, Non-U.S. GoTissue Inhibitor of Metall

Melanoma/immunology* Paraneoplastic Syndromes

Humans Japan

Research Support, U.S. Gov't, Research Support, U.S. Gov

Haplotypes Humans

DNA/genetics DNA Mutational Analysis

Genotype Homovanillic Acid/cerebros

Protease Inhibitors/metabolismReproducibility of Results

DNA Transposable Elements Female

Genetics, Population* Humans

Immunoprecipitation Mice Mitosis*

Kidney/cytology Kidney/metabolism Protein Binding

Research Support, Non-U.S. Gov't Sequence Analysis, DNA Transcription Factors/gene

Trans-Activation (Genetics)/physiology Transcription Factors/met Substances:

Oligonucleotide Array Sequence Analysis Research Support, Non-U.SSequence Alignment

Translocation, Genetic*

Fluorescent Antibody Technique, Direct Fluorescent Dyes Humans

Interleukin-12/biosynthesis Male Mice

Protein Binding Research Support, N.I.H., Research Support, Non-U.S

Middle Aged Oligonucleotide Array Seq Research Support, N.I.H.,

Mice Mice, Inbred C3H Mutation

Models, Animal Oxidants/pharmacology* Oxidative Stress

Research Support, U.S. Gov't, P.H.S. Grant Support: K08 DA11880/DA/NIDA

Research Support, Non-U.S. Gov't Virus Activation* Virus Latency*

Male Middle Aged Models, Biological

RNA, Neoplasm/genetics RNA, Neoplasm/isolation & Research Support, Non-U.S

Protein Interaction Mapping/methods* Research Support, U.S. GovResearch Support, U.S. Gov

Research Support, U.S. Gov't, P.H.S. Grant Support: P30 DK41296/DK/NIDDK

Hepatocytes/pathology* Humans Ki-67 Antigen/metabolism

Female Gene Expression* Gene Expression Profiling

Male Mice Mice, Inbred Strains

Liver Transplantation* Mice Mice, SCID

Research Support, Non-U.S. Gov't Research Support, U.S. GovResearch Support, U.S. Gov

Research Support, U.S. Gov't, P.H.S. Risk Factors Transcobalamins/genetics*

Substances: DNA Primers

Genomic Imprinting Humans In Situ Hybridization

Hepatocytes/transplantation Liver/metabolism* Liver Cirrhosis/pathology

Rats Research Support, Non-U.SSolubility

Mice Mice, Knockout Mitochondria, Liver/ultrast

Subcellular Fractions/metabolism Transgenes Substances:

Plant Proteins/chemistry Protein Binding Protein Structure, Tertiary

Epithelium Humans Isoenzymes

Mice Mice, Inbred Strains Mice, Knockout

Microarray Analysis* Mitochondria/drug effects Naphthyridines/poisoning*

Hepatitis C/prevention & control Humans Immunity*

Cytokines/metabolism Endotoxins/blood Gene Transfer Techniques

Humans Mice NIH 3T3 Cells

Sequence Alignment/methods* Sequence Analysis, DNA/mVariation (Genetics)/genetics*

Molecular Sequence Data Research Support, U.S. GovSequence Alignment/meth

DNA, Bacterial/chemistry Evolution, Molecular Gene Expression Regulation

Up-Regulation Substances: Tissue Inhibitor of Metallo

RNA, Neoplasm/analysis Research Support, Non-U.SRetinal Diseases/immunol

Male Methamphetamine/poisoniMiddle Aged

Reward* Synaptic Transmission/phySyndrome

India Machado-Joseph Disease/gMachado-Joseph Disease/p

Eating Disorders/genetics Gene Frequency Genotype

Humans Hydroxyindoleacetic Acid/cLinkage Disequilibrium

Research Support, Non-U.S. Gov't Reverse Transcriptase Pol Tissue Distribution

Gene Expression Profiling* Gene Expression Regulati Insect Proteins/chemistry

Linkage (Genetics)/genetics Models, Genetic* Models, Statistical

NIH 3T3 Cells Protein Processing, Post-Translational

Research Support, N.I.H., Ext Research Support, Non-U.S. Gov't

Transcription Factors/metabol Substances:

Proteome Transcription Factors

Sequence Analysis, Protein Software*

In Situ Hybridization, Fluores Indoles

Mice, Inbred C57BL Research Support, Non-U.S. Gov't

Research Support, U.S. Gov't, T-Lymphocytes, Cytotoxic/immunolog

Research Support, Non-U.S. GoResearch Support, U.S. Gov't, P.H.S.

Phenotype Research Support, Non-U.S. Gov't

Rats Rats, Wistar

R01 DK57998/DK/NIDDK U19 AI40035/AI/NIAID

Substances: Hepatitis B Surface Antigens

Polyethylene Glycols/therapeuResearch Support, Non-U.S. Gov't

Research Support, U.S. Gov't, Substances:

Saccharomyces cerevisiae ProSaccharomyces cerevisiae Proteins/m

R01 DK17609/DK/NIDDK

Ligation Liver Cirrhosis/pathology*

Genome, Human* Humans

Mutagenicity Tests Mutagens/toxicity

Mice, Transgenic Microscopy, Electron

Severity of Illness Index Viral Load

Vitamin B 12/metabolism Substances:

Ovarian Neoplasms/genetics* Ovarian Neoplasms/pathology*

Liver Cirrhosis/physiopathologLiver Cirrhosis/surgery

Treatment Outcome Vascular Endothelial Growth Factor R

Oxidation-Reduction Oxidative Stress

Plasmids Doxycycline

Research Support, Non-U.S. GoSpectrin/chemistry*

Protein Kinase C/pharmacokineProtein Kinase C/pharmacology*

Research Support, Non-U.S. GoResearch Support, U.S. Gov't, P.H.S.

Oxidative Stress RNA/drug effects

Liver Failure/surgery* Liver Failure/virology*

Genetic Vectors Glutathione/metabolism

Neovascularization, PathologicOligonucleotide Array Sequence Analy

Variation (Genetics)/genetics*

Sequence Analysis, DNA/methSpecies Specificity

Gene Transfer, Horizontal Genes, Bacterial

Furin Metalloendopeptidases

Reverse Transcriptase PolymeRhodopsin/immunology

Polymorphism, Genetic* Substances:

Substances: Receptors, Dopamine D2

Magnetic Resonance Imaging Male

Humans Linkage Disequilibrium

Male Mental Disorders/cerebrospinal fluid

Tissue Kallikreins/biosynthesisSubstances:

Insect Proteins/genetics* Molecular Sequence Data

Research Support, U.S. Gov't, Software*

Research Support, Non-U.S. Gov't S Phase/physiology*

Research Support, U.S. Gov't, P.H.SSaccharomyces cerevisiae

DNA, Complementary DNA-Binding Proteins

Grant Support: CA 90301/CA/NCI

User-Computer Interface

Karyotyping Mammary Glands, Human/cyto

Tumor Necrosis Factor-alpha/biosy Substances:

T-Lymphocytes, Cytotoxic/metabol Substances:

Substances: Actins

Signal Transduction Trans-Activators/genetics*

Reactive Oxygen Species Ribosomal Protein S6 Kinases,

Treatment Outcome Viral Load*

DNA, Neoplasm KRAS2 protein, human

Sequence Analysis, Protein/methodSignal Transduction/physiolog

Liver Cirrhosis/physiopathology Male

Immunohistochemistry/methods Lasers

Mutation* Substances:

Models, Animal* Research Support, Non-U.S. Go

Grant Support: AG-02-004/AG/NIA

Transcobalamins Vitamin B 12

Polymerase Chain Reaction Prognosis

Mice Mice, Inbred Strains

Vascular Endothelial Growth FactorSubstances:

Peroxisomes/ultrastructure* Receptors, Cytoplasmic and Nu

Spectrin/physiology* Substances:


Substances: ABCG5 protein, mouse

Rats Rats, Sprague-Dawley

Liver Transplantation/immunology*Male

Liver/drug effects Liver/metabolism

Receptor, erbB-2/metabolism* Research Support, Non-U.S. Go

Statistics Viral Proteins/genetics*

Genome, Bacterial* Hydrocarbons, Aromatic/metab

Gelatinase A membrane-type matrix metalloproteinase

Serologic Tests/methods* Skin Neoplasms/immunology*

Brain-Derived Neurotrophic Factor Methamphetamine

Dopamine Grant Support:

Nerve Tissue Proteins/genetics* Pedigree

Mutation* Obesity/genetics

Mental Disorders/genetics* Methoxyhydroxyphenylglycol/ce

Protease Inhibitors Tissue Kallikreins

RNA, Messenger/genetics RNA, Messenger/metabolism

Substances: Genetic Markers

Urochordata Substances: Chromatin Histones

Two-Hybrid System Techniques Substances: Isoenzymes DNMT3L protein

Transcription Factors grainy head-like 3, mouse

Metaphase Nucleic Acid HResearch Support, Non-U.S. GTelomerase/anal

Antigens, CD40 Tumor NecrosiConcanavalin A CD40 Ligand

Epitopes, T-Lymphocyte Histocompatibitransporter associated with Proteasome Endopeptidase Complex

Grant Support: U19 AI 40035/AI/NIAID

beta Catenin Substances: CTNNB1 protein, human Catnb protein,

Ribosomal Protein S6 Kinases, 9 Substances: Oxidants Reactive Oxygen

Substances: Antiviral AgenHepatitis B e Antigens Polyethylene Gl

Proto-Oncogene Proteins RNA, MessengRNA, Neoplasm

Species Specificity Substances: Caenorhabditis elegans ProteDrosophila Prote

Mice Mice, Inbred SMice, Knockout Mitosis*

Lymphatic Metastasis/genetics Male Middle Aged Oligonucleotide

Aminobiphenyl Compounds Carcinogens DNA Adducts Mutagens

Transplantation Chimera* Transplantati Urinary Plasminogen ActivatoUrinary Plasmin

P20-MD00148-01/MD/NCMHHD

RNA, Messenger/biosynthesis Research SuppTranscription Factors/geneticTranscription F

Research Support, Non-U.S. Gov' Stem Cells/cy Stem Cells/metabolism* Substances:

Angiogenesis Inhibitors Endostatins Vascular Endothelial Growth Factor Receptor-1

Research Support, Non-U.S. Gov' Zellweger Sy Zellweger Syndrome/patholo Substances:

Chromatin Fungal Protei Plant Proteins Spectrin

Butyric Acids Detergents Isoenzymes isobutyric acid

ABCG8 protein, mouse ATP-Binding CLipoproteins Diosgenin

Transcription, Genetic/drug effec Substances: Fluoroquinolones Naphthyridines

Middle Aged Phenotype Postoperative Period Prospective Stu

Liver/pathology Liver Disease Liver Diseases/prevention & Membrane Glycop

Reverse Transcriptase PolymerasSignal Transd Transfection Up-Regulation

Substances: DNA, Viral Viral Proteins

Interspersed Repetitive Sequenc Molecular Se Multigene Family Nitrogen Fixatio

membrane-type matrix metalloproteinase

Substances: Antigens, Ne DNA, Complementary DNA, Neoplasm

K05-AA00219/AA/NIAAA R37-AA07112/AA/NIAAA

Phenotype Polymorphism,Research Support, Non-U.S. GTrinucleotide R

Polymorphism, Single Nucleotide Polymorphism,Research Support, Non-U.S. GSubstances:

Middle Aged Minisatellite Monoamine Oxidase/cerebrospMonoamine Oxid

Prostate-Specific Antigen

Research Support, N.I.H., IntramuResearch SuppSalivary Glands/metabolism* Transcription, G

DNA (Cytosine-5- Glutathione T Grant SupportGM50575/GM/GM64378-01/GM/NIGMS

Telomere/metaboSubstances: Fluorescent DIndoles DAPI DNA

Interleukin-12

Proteasome Endopeptidase Complex

Cytoskeletal Prot Trans-Activat beta Catenin Glutamate-Ammonia Ligase

Hydrogen Peroxi Extracellular Ribosomal Protein S6 Kinases, 90-kDa

peginterferon alf Lamivudine Interferon Alfa-2a

Saccharomyces cerevisiae Proteins

Research Support,Research SuppoStress/metaboSubstances: Biological MarCDKN1A prote

Research SupportReverse TransStaining and Up-Regulation

DNA 4-biphenylamine

Substances: Blood Protein Urinary Plasminogen Activator

Tumor Cells, Cult Zinc Fingers Substances: Cell Cycle ProPLAGL1 prote RNA, Messeng

Growth Substanc Green Fluorescent Proteins

Vascular Endothelial Growth Factor Receptor-1

PXR1 protein Receptors, CyGlucose Adenosine Triphosphate

Deoxycholic Acid Protein Kinase C

Cholesterol Grant SupportHL060613/HL/NHLBI

trovafloxacin RNA Glutathione

Recurrence Research SuppResearch SuppoT-LymphocyteSubstances: Antiviral Agen

Membrane GlycopMembrane GlyMice Mice, Inbred Mice, KnockouPortal System

Substances: DNA Primers GlycoproteinsReceptor, erbB-2

Open Reading Fr Plasmids/geneResearch SuppSequence AnaSequence Ho Substances:

RNA, Neoplasm Rhodopsin

Trinucleotide RepSubstances: ATXN3 protei Nerve Tissue Proteins

Brain-Derived NeuDNA

Polymorphism, GePromoter RegiResearch SuppoSubstances: Homovanillic Methoxyhydro

Substances: DNA TransposInsect ProteinRNA, Messenger

Telomerase

Cdkn1a prote Cell Cycle ProCyclin-DependKi-67 Antigen Cyclin-DependGrant Support

Transcription Factors

Grant SupportR01 DK60590/DK/NIDDK

Rats Research SuppResearch SuppoSubstances: Acute-Phase PCarrier Protei

Bacterial Prot DNA, BacteriaHydrocarbons,Plasmids Secondary SouGENBANK/CR5

HydroxyindoleMonoamine OxCatechol O-MeGrant SupportMH48514/MH/MH62185/MH/NIMH

R01 DK49615/DK/NIDDK

Cytokines Endotoxins Genetic VectoMembrane GlylipopolysacchaAcetaminoph

GENBANK/CR5GENBANK/CR555308

MH62185/MH/NIMH

Glutathione Cytochrome PGrant SupportDK53296/DK/ GM60205/GM/NIGMS

no 11: Bioinf

yes 1: Bioinfo

yes 2: Mol Bio

yes 3: Bioinfo

yes 4: Bioinfo

yes 5: Genes

etworks and to infer activity profiles of hidden variables. AVAILABILITY: Supplementary data and Matlab code will be made available at the URL below. SUPPLEMENTARY INFORMATION: http://www.chems.msu.edu/groups/chan/ssm.zip. PMID: 16403793 [PubMed - as supplied by publisher]

itoylation sites. AVAILABILITY: CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/. SUPPLEMENTARY INFORMATION: The supplementary materials, including the details of the algorithm, could be visited from: http://bioinformatics.lcd-ustc.

s can be partly attributed to highly mobile domains. Duplication/deletion has been found in modular proteins such as peptide synthases. Availability: Supplementary material can be found at: http://www.uni-muenster.de/Biologie.Botanik/ebb/projects/cp/ PMID: 16431849 [PubMed - as supplied by publisher

suggest how to find a suitable direction for the extension of a constantly-growing ontology such as GO. AVAILABILITY: http://autogo.biopathway.org/. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. PMID: 16428805 [PubMed - as supplied by publisher]

dy that analyzes a large number of microarrays, prepared with RNA from breast tumor samples from each of 295 patients. AVAILABILITY: The software and supplementary material are available at http://public.tgen.org/tgen-cb/support/testbed/. PMID: 16428263 [PubMed - as supplied by publisher]

ry still-unknown cryptic genomic alterations that could affect a gene or genes of importance in the disease progression of CML. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2006 Wiley-Liss, Inc. PMID: 16425296 [PubMed - as

yes 6: Bioinfo

yes 7: Genes

yes 8: Bioinfo

yes 9: Bioinfo

yes 10: Bioinf

yes 12: Nuclei

ct of annotation bias to significantly improve performance. AVAILABILITY: SUSPECTS is freely available at http://www.genetics.med.ed.ac.uk/suspects/. SUPPLEMENTARY INFORMATION: A quick-start guide in Macromedia Flash format is available at http://www.genetics.med.ed.ac.uk/suspects/help.shtml. Excel

e propose that breakage at specific cFS could derive from early epigenetic events at loci involved in radiation carcinogenesis. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2006 Wiley-Liss, Inc. PMID: 16419058 [PubMed - as

SC genome browser). Availability: TAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal/. SUPPLEMENTARY INFORMATION: http://neoref.ils.unc.edu/tamal/. PMID: 16418238 [PubMed - as supplied by publisher]

ties. Using this method, we make function predictions for multiple proteins, and experimentally confirm predictions for proteins involved in mitosis. SUPPLEMENTARY INFORMATION: Results for the 105 selected GO classes and predictions for 1059 unknown genes are available at: http://function.princeton.

exons. Our results show that GenASAP provides accurate predictions for over one third of the total events, as verified by independent RT-PCR assays. SUPPLEMENTARY INFORMATION: http://www.psi.toronto.edu/GenASAP. PMID: 16403798 [PubMed - as supplied by publisher]

t monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle b

yes 13: Bioinf

yes 14: Bioinf

yes 15: Bioinf

yes 16: Bioinf

yes 18: Bioinf

yes 19: Bioinf

iption factor binding sites in non-coding DNA. AVAILABILITY: ACANA software and test sequence data are publicly available at http://BioMedEmpire.org/ SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. CONTACT: [email protected]. PMID: 16301203 [PubMed - in pro

vailable as an R package. AVAILABILITY: ClaNC is freely available from http://students.washington.edu/adabney/clanc CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://students.washington.edu/adabney/clanc/figure2.pdf. PMID: 16269418 [PubMed - in process]

tware is implemented in R and is available from Bioconductor or from the first author at [email protected]. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.stat.berkeley.edu/users/nrabbee/693.pdf. PMID: 16267090 [PubMed - in process]

f ncRNA families. AVAILABILITY: The source code is available under GNU Public License at the supplementary web site. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-HeurHmm-2004/ (Technical details, results, C++ code). PMID: 16267089 [PubMed

same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus Contact: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are accessible at http://pir.georgetown.edu/iprolink/biothesaurus/supplement/ PMID: 16267085 [PubMed - i

tisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/ PMID: 16267082 [PubMed - i

yes 20: Bioinf

yes 21: Bioinf

yes 22: Bioinf

yes 23: Bioinf

yes 24: Bioinf

yes 25: Bioinf

s in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www.inab.org/Help/Main/index.html. PMID: 16257987 [PubMed - in process]

e discovery of conserved protein substructures. AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Available at http://web.mit.edu/bamel/gemoda. PMID: 16257985 [PubMed - in process]m ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W. CONTACT: [email protected] and [email protected] SUPPLEMENTARY INFORMATION: http://www.cmb.dtu.dk/ PMID: 16257984 [PubMed - as supplied by publisher]

tasets and has produced very promising results. AVAILABILITY: MATLAB codes are available upon request from the authors. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~hzhang/research.html. PMID: 16249260 [PubMed - in process]

atlab source code is available upon request and DNA microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo). Contact: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16249259 [PubMed - in process]

system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Contact: [email protected] SUPPLEMENTARY INFORMATION: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PilZ.html. PMID: 16249258 [PubMed - in process]

yes 26: Int J

yes 27: Int J

yes 28: Int J

yes 17: Bioinf

eats may be associated with endometrial carcinogenesis because of AR's reduced ability to recruit coregulators and other transcriptional components. (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7

ow 2 Ras isoforms regulate disparate biologic processes, revealing a number of genes whose deregulated expression may influence colon carcinogenesis (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7

tages of disease. Our data suggest that cSHMT, Tbx3 and utrophin can be used as components of multiparameter monitoring of ovarian and breast cancer (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7

http://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://blast.wustl.edu/exalin/exalin-supplement.pdf. PMID: 16267086 [PubMed - in process]

Using a state-space model with hidden variables to infer transcription factor

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy

Evolution of Circular Permutations in Multi-Domain Proteins.

Automatic extension of gene ontology with flexible identification of candidate

Genetic test bed for feature selection.

Genomewide screening of DNA copy number changes in chronic myelogenous leukemia

SUSPECTS: enabling fast and effective prioritization of positional candidates.

Chromosomal fragile sites FRA3B and FRA16D show correlated expression and

TAMAL: an integrated approach to choosing SNPs for genetic studies of human

Hierarchical multi-label prediction of gene function.

Inferring global levels of alternative splicing isoforms using a generative

HvrBase++: a phylogenetic database for primate species.

Accurate anchoring alignment of divergent sequences.

ClaNC: point-and-click software for classifying microarrays to nearest

A genotype calling algorithm for affymetrix SNP arrays.

Sequence-based heuristics for faster annotation of non-coding RNA families.

BioThesaurus: a web-based thesaurus of protein and gene names.

libSRES: a C library for stochastic ranking evolution strategy for parameter

Intelligent client for integrating bioinformatics services.

A generic motif discovery algorithm for sequential data.

Robust multi-scale clustering of large DNA microarray datasets with the

Gene selection using support vector machines with non-convex penalty.

Integrating time-course microarray gene expression profiles with cytotoxicity

PilZ domain is part of the bacterial c-di-GMP binding protein.

Androgen receptor polymorphisms and endometrial cancer risk.

Microarray analysis of the differential transformation mediated by Kirsten and

Increased expression of cSHMT, Tbx3 and utrophin in plasma of ovarian and breast

Improved spliced alignment from an information theoretic approach.

activities.

(CSS).

Weiner J 3rd, Bornberg-Bauer E.

terms.

Choudhary A, Brun M, Hua J, Lowey J, Suh E, Dougherty ER.

with the use of high-resolution array-based comparative genomic hybridization.

Adie EA, Adams RR, Evans KL, Porteous DJ, Pickard BS.

association with failure of apoptosis in lymphocytes from patients with thyroid

complex traits.

Barutcuoglu Z, Schapire RE, Troyanskaya OG.

model of microarray data.

Kohl J, Paulsen I, Laubach T, Radtke A, von Haeseler A.

Huang W, Umbach DM, Li L.

centroids.

Rabbee N, Speed TP.

Weinberg Z, Ruzzo WL.

Liu H, Hu ZZ, Zhang J, Wu C.

estimation.

Navas-Delgado I, Rojano-Munoz Mdel M, Ramirez S, Perez AJ, Andres Leon E,

Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN.

consensus algorithm.

Zhang HH, Ahn J, Lin X, Park C.

for identification of biomarkers in primary rat hepatocytes exposed to cadmium.

Amikam D, Galperin MY.

McGrath M, Lee IM, Hankinson SE, Kraft P, Hunter DJ, Buring J, De Vivo I.

Harvey Ras oncogenes in a human colorectal adenocarcinoma cell line.

cancer patients.

Zhang M, Gish W.



PMID: 16049973 [PubMed - indexed for MEDLINE] MeSH Terms:


Breast Neoplasms/pathology* Case-Control Studies Cytosol/chemistry

Electrophoresis, Gel, Two-Dimensional Female Gene Expression Profiling

Glycine Hydroxymethyltransferase/biosynthesis Glycine Hydroxymethyltransferase/blood*

Humans Neoplasm Staging/methods Ovarian Neoplasms/blood*

Research Support, Non-U.S. Gov't Spectrum Analysis, Mass

T-Box Domain Proteins/biosynthesis T-Box Domain Proteins/blood*

Tumor Markers, Biological/blood Utrophin/biosynthesis Utrophin/blood* Substances:

T-Box Domain Proteins Tumor Markers, Biological Utrophin Glycine Hydroxymethyltransferase

Glycine Hydroxymethyltransferase

# Live? Journal?1 y y2 y y3 y y4 y y5 y y6 n/a mis- n/a7 y y8 y y9 y y

10 y y11 y y12 y y13 y y14 y y15 y y16 y y17 y y18 y y19 y y20 y y21 y Y22 n y- online23 y y24 y y25 y y26 y y27 y y28 y y29 y y30 y y31 y y32 y y33 y y34 y y35 y y36 y y37 y y38 y y39 y y40 y y41 y y42 y y43 no -ref n44 y y45 y y46 y y47 y y48 y y49 y y50 y y51 y y52 y y

53 y y54 y y55 y y56 y y57 y y58 y y59 y y60 y y61 y y

ReferenceBarbe V, Vallenet D, Fonknechten N, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucl. Acids Res. %R 10.1093/nar/gkh910. October 28, 2004 2004;32(19):5766-5779.Bene A, Kurten RC, Chambers TC. Subcellular localization as a limiting factor for utilization of decoy oligonucleotides. Nucl. Acids Res. %R 10.1093/nar/gnh139. October 21, 2004 2004;32(19):e142-.Cardoso J, Molenaar L, de Menezes RX, et al. Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucl. Acids Res. %R 10.1093/nar/gnh142. October 28, 2004 2004;32(19):e146-.Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM. Protein-mediated error correction for de novo DNA synthesis. Nucl. Acids Res. %R 10.1093/nar/gnh160. November 23, 2004 2004;32(20):e162-.Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucl. Acids Res. %R 10.1093/nar/gkh988. December 14, 2004 2004;32(22):6501-6510.Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucl. Acids Res. %R 10.1093/nar/gkh978. December 7, 2004 2004;32(21):6414-6424.D'Anjou H, Chabot C, Chartrand P. Preferential accessibility to specific genomic loci for the repair of double-strand breaks in human cells. Nucl. Acids Res. %R 10.1093/nar/gkh952. November 23, 2004 2004;32(20):6136-6143.Doe CL, Osman F, Dixon J, Whitby MC. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucl. Acids Res. %R 10.1093/nar/gkh853. October 14, 2004 2004;32(18):5570-5581.Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. %R 10.1093/nar/gkh973. December 1, 2004 2004;32(21):6321-6326.Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucl. Acids Res. %R 10.1093/nar/gkh885. October 12, 2004 2004;32(18):5452-5463.Glockner G, Lehmann R, Romualdi A, et al. Comparative analysis of the Borrelia garinii genome. Nucl. Acids Res. %R 10.1093/nar/gkh953. November 16, 2004 2004;32(20):6038-6046.Guglielmi B, van Berkum NL, Klapholz B, et al. A high resolution protein interaction map of the yeast Mediator complex. Nucl. Acids Res. %R 10.1093/nar/gkh878. October 11, 2004 2004;32(18):5379-5391.Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ. Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucl. Acids Res. %R 10.1093/nar/gkh984. December 7, 2004 2004;32(21):6437-6444.Hannoush RN, Min K-L, Damha MJ. Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors. Nucl. Acids Res. %R 10.1093/nar/gkh948. November 29, 2004 2004;32(21):6164-6175.Hartig JS, Kool ET. Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities. Nucl. Acids Res. %R 10.1093/nar/gnh149. November 1, 2004 2004;32(19):e152-.Hashiguchi K, Stuart JA, de Souza-Pinto NC, Bohr VA. The C-terminal {alpha}O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial {beta}-Ogg1 lacks this domain and does not have glycosylase activity. Nucl. Acids Res. %R 10.1093/nar/gkh863. October 19, 2004 2004;32(18):5596-5608.Hodas NO, Aalberts DP. Efficient computation of optimal oligo-RNA binding. Nucl. Acids Res. %R 10.1093/nar/gkh1008. December 17, 2004 2004;32(22):6636-6642.Horisawa K, Tateyama S, Ishizaka M, et al. In vitro selection of Jun-associated proteins using mRNA display. Nucl. Acids Res. %R 10.1093/nar/gnh167. December 2, 2004 2004;32(21):e169-.Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucl. Acids Res. %R 10.1093/nar/gkh828. October 5, 2004 2004;32(17):5260-5279.Jacobs JL, Dinman JD. Systematic analysis of bicistronic reporter assay data. Nucl. Acids Res. %R 10.1093/nar/gnh157. November 23, 2004 2004;32(20):e160-.Janssen CS, Phillips RS, Turner CMR, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucl. Acids Res. %R 10.1093/nar/gkh907. October 26, 2004 2004;32(19):5712-5720.Janzen CJ, Lander F, Dreesen O, Cross GAM. Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei. Nucl. Acids Res. %R 10.1093/nar/gkh991. December 15, 2004 2004;32(22):6575-6584.Jin VX, Leu Y-W, Liyanarachchi S, et al. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucl. Acids Res. %R 10.1093/nar/gkh1005. December 17, 2004 2004;32(22):6627-6635.Kroeger KM, Goodman MF, Greenberg MM. A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh873. October 11, 2004 2004;32(18):5480-5485.Le K, Mitsouras K, Roy M, et al. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucl. Acids Res. %R 10.1093/nar/gnh173. December 14, 2004 2004;32(22):e180-.Le Meur N, Lamirault G, Bihouee A, et al. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucl. Acids Res. %R 10.1093/nar/gkh870. October 8, 2004 2004;32(18):5349-5358.Lindenbaum M, Perkins E, Csonka E, et al. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucl. Acids Res. %R 10.1093/nar/gnh169. December 7, 2004 2004;32(21):e172-.Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh911. October 27, 2004 2004;32(19):5721-5731.Maniura-Weber K, Goffart S, Garstka HL, Montoya J, Wiesner RJ. Transient overexpression of mitochondrial transcription factor A (TFAM) is sufficient to stimulate mitochondrial DNA transcription, but not sufficient to increase mtDNA copy number in cultured cells. Nucl. Acids Res. %R 10.1093/nar/gkh921. November 16, 2004 2004;32(20):6015-6027.Mao Y, Luo C, Deng W, et al. Reversibly switchable DNA nanocompartment on surfaces. Nucl. Acids Res. %R 10.1093/nar/gnh145. October 26, 2004 2004;32(19):e144-.Matsubara M, Tanaka T, Terato H, et al. Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase. Nucl. Acids Res. %R 10.1093/nar/gkh859. October 5, 2004 2004;32(17):5291-5302.May T, Hauser H, Wirth D. Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization. Nucl. Acids Res. %R 10.1093/nar/gkh887. October 14, 2004 2004;32(18):5529-5538.Navarro A-E, Spinelli N, Moustrou C, Chaix C, Mandrand B, Brisset H. Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution. Nucl. Acids Res. %R 10.1093/nar/gkh874. October 5, 2004 2004;32(17):5310-5319.Ohtani N, Yanagawa H, Tomita M, Itaya M. Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucl. Acids Res. %R 10.1093/nar/gkh917. November 1, 2004 2004;32(19):5809-5819.Otsuki K, Hayashi Y, Kato M, Yoshida H, Yamaguchi M. Characterization of dRFX2, a novel RFX family protein in Drosophila. Nucl. Acids Res. %R 10.1093/nar/gkh895. October 19, 2004 2004;32(18):5636-5648.Perez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucl. Acids Res. %R 10.1093/nar/gkh954. November 23, 2004 2004;32(20):6144-6151.Pincas H, Pingle MR, Huang J, et al. High sensitivity EndoV mutation scanning through real-time ligase proofreading. Nucl. Acids Res. %R 10.1093/nar/gnh150. October 28, 2004 2004;32(19):e148-.Qin L-X, Kerr KF, Contributing Members of the Toxicogenomics Research C. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucl. Acids Res. %R 10.1093/nar/gkh866. October 12, 2004 2004;32(18):5471-5479.Quere R, Manchon L, Lejeune M, et al. Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucl. Acids Res. %R 10.1093/nar/gnh161. November 23, 2004 2004;32(20):e163-.Ruepp A, Zollner A, Maier D, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl. Acids Res. %R 10.1093/nar/gkh894. October 14, 2004 2004;32(18):5539-5545.Rutledge RG. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucl. Acids Res. %R 10.1093/nar/gnh177. December 15, 2004 2004;32(22):e178-.Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res. %R 10.1093/nar/gkh951. November 23, 2004 2004;32(20):6129-6135.Schatz P, Dietrich D, Schuster M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucl. Acids Res. %R 10.1093/nar/gnh165. December 2, 2004 2004;32(21):e167-.Schmidt KS, Borkowski S, Kurreck J, et al. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucl. Acids Res. %R 10.1093/nar/gkh862. October 27, 2004 2004;32(19):5757-5765.Shen G, Anand MFG, Levicky R. X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides. Nucl. Acids Res. %R 10.1093/nar/gkh932. November 10, 2004 2004;32(20):5973-5980.Shukla LI, Adhikary A, Pazdro R, Becker D, Sevilla MD. Formation of 8-oxo-7,8-dihydroguanine-radicals in {gamma}-irradiated DNA by multiple one-electron oxidations. Nucl. Acids Res. %R 10.1093/nar/gkh989. December 15, 2004 2004;32(22):6565-6574.Sorensen JJ, Nielsen JT, Petersen M. Solution structure of a dsDNA:LNA triplex. Nucl. Acids Res. %R 10.1093/nar/gkh942. November 18, 2004 2004;32(20):6078-6085.Sun Y, Koo S, White N, et al. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucl. Acids Res. %R 10.1093/nar/gnh186. December 22, 2004 2004;32(22):e188-.Takami H, Takaki Y, Chee G-J, et al. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucl. Acids Res. %R 10.1093/nar/gkh970. December 1, 2004 2004;32(21):6292-6303.Tang S, Tan SL, Ramadoss SK, Kumar AP, Tang M-HE, Bajic VB. Computational method for discovery of estrogen responsive genes. Nucl. Acids Res. %R 10.1093/nar/gkh943. December 1, 2004 2004;32(21):6212-6217.Thomas H, Senkel S, Erdmann S, et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line. Nucl. Acids Res. %R 10.1093/nar/gnh144. November 1, 2004 2004;32(19):e150-.Tian W, Arakaki AK, Skolnick J. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucl. Acids Res. %R 10.1093/nar/gkh956. December 1, 2004 2004;32(21):6226-6239.

Ting R, Thomas JM, Lermer L, Perrin DM. Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucl. Acids Res. %R 10.1093/nar/gkh1007. December 29, 2004 2004;32(22):6660-6672.Tomecki R, Dmochowska A, Gewartowski K, Dziembowski A, Stepien PP. Identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase. Nucl. Acids Res. %R 10.1093/nar/gkh923. November 16, 2004 2004;32(20):6001-6014.Wadley LM, Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucl. Acids Res. %R 10.1093/nar/gkh1002. December 17, 2004 2004;32(22):6650-6659.Yamamoto Y, Uehara A, Tomita T, Komiyama M. Site-selective and hydrolytic two-strand scission of double-stranded DNA using Ce(IV)/EDTA and pseudo-complementary PNA. Nucl. Acids Res. %R 10.1093/nar/gnh151. November 1, 2004 2004;32(19):e153-.Yanez J, Arguello M, Osuna J, Soberon X, Gaytan P. Combinatorial codon-based amino acid substitutions. Nucl. Acids Res. %R 10.1093/nar/gnh156. November 10, 2004 2004;32(20):e158-.Yu J, Ha T, Schulten K. Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Nucl. Acids Res. %R 10.1093/nar/gkh1006. December 21, 2004 2004;32(22):6683-6695.Yun S, Lie-A-Cheong C, Porter ACG. Discriminatory suppression of homologous recombination by p53. Nucl. Acids Res. %R 10.1093/nar/gkh986. December 15, 2004 2004;32(22):6479-6489.Zheng Y, Roberts RJ, Kasif S. Identification of genes with fast-evolving regions in microbial genomes. Nucl. Acids Res. %R 10.1093/nar/gkh935. December 2, 2004 2004;32(21):6347-6357.Zhou X, Cai S, Hong A, et al. Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucl. Acids Res. %R 10.1093/nar/gkh879. October 11, 2004 2004;32(18):5409-5417.

Barbe V, Vallenet D, Fonknechten N, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucl. Acids Res. %R 10.1093/nar/gkh910. October 28, 2004 2004;32(19):5766-5779.Bene A, Kurten RC, Chambers TC. Subcellular localization as a limiting factor for utilization of decoy oligonucleotides. Nucl. Acids Res. %R 10.1093/nar/gnh139. October 21, 2004 2004;32(19):e142-.Cardoso J, Molenaar L, de Menezes RX, et al. Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucl. Acids Res. %R 10.1093/nar/gnh142. October 28, 2004 2004;32(19):e146-.Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM. Protein-mediated error correction for de novo DNA synthesis. Nucl. Acids Res. %R 10.1093/nar/gnh160. November 23, 2004 2004;32(20):e162-.Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucl. Acids Res. %R 10.1093/nar/gkh988. December 14, 2004 2004;32(22):6501-6510.Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucl. Acids Res. %R 10.1093/nar/gkh978. December 7, 2004 2004;32(21):6414-6424.D'Anjou H, Chabot C, Chartrand P. Preferential accessibility to specific genomic loci for the repair of double-strand breaks in human cells. Nucl. Acids Res. %R 10.1093/nar/gkh952. November 23, 2004 2004;32(20):6136-6143.Doe CL, Osman F, Dixon J, Whitby MC. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucl. Acids Res. %R 10.1093/nar/gkh853. October 14, 2004 2004;32(18):5570-5581.Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. %R 10.1093/nar/gkh973. December 1, 2004 2004;32(21):6321-6326.Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucl. Acids Res. %R 10.1093/nar/gkh885. October 12, 2004 2004;32(18):5452-5463.Glockner G, Lehmann R, Romualdi A, et al. Comparative analysis of the Borrelia garinii genome. Nucl. Acids Res. %R 10.1093/nar/gkh953. November 16, 2004 2004;32(20):6038-6046.Guglielmi B, van Berkum NL, Klapholz B, et al. A high resolution protein interaction map of the yeast Mediator complex. Nucl. Acids Res. %R 10.1093/nar/gkh878. October 11, 2004 2004;32(18):5379-5391.Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ. Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucl. Acids Res. %R 10.1093/nar/gkh984. December 7, 2004 2004;32(21):6437-6444.Hannoush RN, Min K-L, Damha MJ. Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors. Nucl. Acids Res. %R 10.1093/nar/gkh948. November 29, 2004 2004;32(21):6164-6175.Hartig JS, Kool ET. Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities. Nucl. Acids Res. %R 10.1093/nar/gnh149. November 1, 2004 2004;32(19):e152-.Hashiguchi K, Stuart JA, de Souza-Pinto NC, Bohr VA. The C-terminal {alpha}O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial {beta}-Ogg1 lacks this domain and does not have glycosylase activity. Nucl. Acids Res. %R 10.1093/nar/gkh863. October 19, 2004 2004;32(18):5596-5608.Hodas NO, Aalberts DP. Efficient computation of optimal oligo-RNA binding. Nucl. Acids Res. %R 10.1093/nar/gkh1008. December 17, 2004 2004;32(22):6636-6642.Horisawa K, Tateyama S, Ishizaka M, et al. In vitro selection of Jun-associated proteins using mRNA display. Nucl. Acids Res. %R 10.1093/nar/gnh167. December 2, 2004 2004;32(21):e169-.Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucl. Acids Res. %R 10.1093/nar/gkh828. October 5, 2004 2004;32(17):5260-5279.Jacobs JL, Dinman JD. Systematic analysis of bicistronic reporter assay data. Nucl. Acids Res. %R 10.1093/nar/gnh157. November 23, 2004 2004;32(20):e160-.Janssen CS, Phillips RS, Turner CMR, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucl. Acids Res. %R 10.1093/nar/gkh907. October 26, 2004 2004;32(19):5712-5720.Janzen CJ, Lander F, Dreesen O, Cross GAM. Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei. Nucl. Acids Res. %R 10.1093/nar/gkh991. December 15, 2004 2004;32(22):6575-6584.Jin VX, Leu Y-W, Liyanarachchi S, et al. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucl. Acids Res. %R 10.1093/nar/gkh1005. December 17, 2004 2004;32(22):6627-6635.Kroeger KM, Goodman MF, Greenberg MM. A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh873. October 11, 2004 2004;32(18):5480-5485.Le K, Mitsouras K, Roy M, et al. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucl. Acids Res. %R 10.1093/nar/gnh173. December 14, 2004 2004;32(22):e180-.Le Meur N, Lamirault G, Bihouee A, et al. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucl. Acids Res. %R 10.1093/nar/gkh870. October 8, 2004 2004;32(18):5349-5358.Lindenbaum M, Perkins E, Csonka E, et al. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucl. Acids Res. %R 10.1093/nar/gnh169. December 7, 2004 2004;32(21):e172-.Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh911. October 27, 2004 2004;32(19):5721-5731.Maniura-Weber K, Goffart S, Garstka HL, Montoya J, Wiesner RJ. Transient overexpression of mitochondrial transcription factor A (TFAM) is sufficient to stimulate mitochondrial DNA transcription, but not sufficient to increase mtDNA copy number in cultured cells. Nucl. Acids Res. %R 10.1093/nar/gkh921. November 16, 2004 2004;32(20):6015-6027.Mao Y, Luo C, Deng W, et al. Reversibly switchable DNA nanocompartment on surfaces. Nucl. Acids Res. %R 10.1093/nar/gnh145. October 26, 2004 2004;32(19):e144-.Matsubara M, Tanaka T, Terato H, et al. Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase. Nucl. Acids Res. %R 10.1093/nar/gkh859. October 5, 2004 2004;32(17):5291-5302.May T, Hauser H, Wirth D. Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization. Nucl. Acids Res. %R 10.1093/nar/gkh887. October 14, 2004 2004;32(18):5529-5538.Navarro A-E, Spinelli N, Moustrou C, Chaix C, Mandrand B, Brisset H. Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution. Nucl. Acids Res. %R 10.1093/nar/gkh874. October 5, 2004 2004;32(17):5310-5319.Ohtani N, Yanagawa H, Tomita M, Itaya M. Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucl. Acids Res. %R 10.1093/nar/gkh917. November 1, 2004 2004;32(19):5809-5819.Otsuki K, Hayashi Y, Kato M, Yoshida H, Yamaguchi M. Characterization of dRFX2, a novel RFX family protein in Drosophila. Nucl. Acids Res. %R 10.1093/nar/gkh895. October 19, 2004 2004;32(18):5636-5648.Perez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucl. Acids Res. %R 10.1093/nar/gkh954. November 23, 2004 2004;32(20):6144-6151.Pincas H, Pingle MR, Huang J, et al. High sensitivity EndoV mutation scanning through real-time ligase proofreading. Nucl. Acids Res. %R 10.1093/nar/gnh150. October 28, 2004 2004;32(19):e148-.Qin L-X, Kerr KF, Contributing Members of the Toxicogenomics Research C. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucl. Acids Res. %R 10.1093/nar/gkh866. October 12, 2004 2004;32(18):5471-5479.Quere R, Manchon L, Lejeune M, et al. Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucl. Acids Res. %R 10.1093/nar/gnh161. November 23, 2004 2004;32(20):e163-.Ruepp A, Zollner A, Maier D, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl. Acids Res. %R 10.1093/nar/gkh894. October 14, 2004 2004;32(18):5539-5545.Rutledge RG. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucl. Acids Res. %R 10.1093/nar/gnh177. December 15, 2004 2004;32(22):e178-.Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res. %R 10.1093/nar/gkh951. November 23, 2004 2004;32(20):6129-6135.Schatz P, Dietrich D, Schuster M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucl. Acids Res. %R 10.1093/nar/gnh165. December 2, 2004 2004;32(21):e167-.Schmidt KS, Borkowski S, Kurreck J, et al. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucl. Acids Res. %R 10.1093/nar/gkh862. October 27, 2004 2004;32(19):5757-5765.Shen G, Anand MFG, Levicky R. X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides. Nucl. Acids Res. %R 10.1093/nar/gkh932. November 10, 2004 2004;32(20):5973-5980.Shukla LI, Adhikary A, Pazdro R, Becker D, Sevilla MD. Formation of 8-oxo-7,8-dihydroguanine-radicals in {gamma}-irradiated DNA by multiple one-electron oxidations. Nucl. Acids Res. %R 10.1093/nar/gkh989. December 15, 2004 2004;32(22):6565-6574.Sorensen JJ, Nielsen JT, Petersen M. Solution structure of a dsDNA:LNA triplex. Nucl. Acids Res. %R 10.1093/nar/gkh942. November 18, 2004 2004;32(20):6078-6085.Sun Y, Koo S, White N, et al. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucl. Acids Res. %R 10.1093/nar/gnh186. December 22, 2004 2004;32(22):e188-.Takami H, Takaki Y, Chee G-J, et al. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucl. Acids Res. %R 10.1093/nar/gkh970. December 1, 2004 2004;32(21):6292-6303.Tang S, Tan SL, Ramadoss SK, Kumar AP, Tang M-HE, Bajic VB. Computational method for discovery of estrogen responsive genes. Nucl. Acids Res. %R 10.1093/nar/gkh943. December 1, 2004 2004;32(21):6212-6217.Thomas H, Senkel S, Erdmann S, et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line. Nucl. Acids Res. %R 10.1093/nar/gnh144. November 1, 2004 2004;32(19):e150-.Tian W, Arakaki AK, Skolnick J. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucl. Acids Res. %R 10.1093/nar/gkh956. December 1, 2004 2004;32(21):6226-6239.

Barbe V, Vallenet D, Fonknechten N, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucl. Acids Res. %R 10.1093/nar/gkh910. October 28, 2004 2004;32(19):5766-5779.Bene A, Kurten RC, Chambers TC. Subcellular localization as a limiting factor for utilization of decoy oligonucleotides. Nucl. Acids Res. %R 10.1093/nar/gnh139. October 21, 2004 2004;32(19):e142-.Cardoso J, Molenaar L, de Menezes RX, et al. Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucl. Acids Res. %R 10.1093/nar/gnh142. October 28, 2004 2004;32(19):e146-.Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM. Protein-mediated error correction for de novo DNA synthesis. Nucl. Acids Res. %R 10.1093/nar/gnh160. November 23, 2004 2004;32(20):e162-.Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucl. Acids Res. %R 10.1093/nar/gkh988. December 14, 2004 2004;32(22):6501-6510.Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucl. Acids Res. %R 10.1093/nar/gkh978. December 7, 2004 2004;32(21):6414-6424.D'Anjou H, Chabot C, Chartrand P. Preferential accessibility to specific genomic loci for the repair of double-strand breaks in human cells. Nucl. Acids Res. %R 10.1093/nar/gkh952. November 23, 2004 2004;32(20):6136-6143.Doe CL, Osman F, Dixon J, Whitby MC. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucl. Acids Res. %R 10.1093/nar/gkh853. October 14, 2004 2004;32(18):5570-5581.Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. %R 10.1093/nar/gkh973. December 1, 2004 2004;32(21):6321-6326.Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucl. Acids Res. %R 10.1093/nar/gkh885. October 12, 2004 2004;32(18):5452-5463.

Guglielmi B, van Berkum NL, Klapholz B, et al. A high resolution protein interaction map of the yeast Mediator complex. Nucl. Acids Res. %R 10.1093/nar/gkh878. October 11, 2004 2004;32(18):5379-5391.Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ. Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucl. Acids Res. %R 10.1093/nar/gkh984. December 7, 2004 2004;32(21):6437-6444.Hannoush RN, Min K-L, Damha MJ. Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors. Nucl. Acids Res. %R 10.1093/nar/gkh948. November 29, 2004 2004;32(21):6164-6175.Hartig JS, Kool ET. Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities. Nucl. Acids Res. %R 10.1093/nar/gnh149. November 1, 2004 2004;32(19):e152-.Hashiguchi K, Stuart JA, de Souza-Pinto NC, Bohr VA. The C-terminal {alpha}O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial {beta}-Ogg1 lacks this domain and does not have glycosylase activity. Nucl. Acids Res. %R 10.1093/nar/gkh863. October 19, 2004 2004;32(18):5596-5608.

Horisawa K, Tateyama S, Ishizaka M, et al. In vitro selection of Jun-associated proteins using mRNA display. Nucl. Acids Res. %R 10.1093/nar/gnh167. December 2, 2004 2004;32(21):e169-.Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucl. Acids Res. %R 10.1093/nar/gkh828. October 5, 2004 2004;32(17):5260-5279.

Janssen CS, Phillips RS, Turner CMR, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucl. Acids Res. %R 10.1093/nar/gkh907. October 26, 2004 2004;32(19):5712-5720.Janzen CJ, Lander F, Dreesen O, Cross GAM. Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei. Nucl. Acids Res. %R 10.1093/nar/gkh991. December 15, 2004 2004;32(22):6575-6584.Jin VX, Leu Y-W, Liyanarachchi S, et al. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucl. Acids Res. %R 10.1093/nar/gkh1005. December 17, 2004 2004;32(22):6627-6635.Kroeger KM, Goodman MF, Greenberg MM. A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh873. October 11, 2004 2004;32(18):5480-5485.Le K, Mitsouras K, Roy M, et al. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucl. Acids Res. %R 10.1093/nar/gnh173. December 14, 2004 2004;32(22):e180-.Le Meur N, Lamirault G, Bihouee A, et al. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucl. Acids Res. %R 10.1093/nar/gkh870. October 8, 2004 2004;32(18):5349-5358.Lindenbaum M, Perkins E, Csonka E, et al. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucl. Acids Res. %R 10.1093/nar/gnh169. December 7, 2004 2004;32(21):e172-.Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh911. October 27, 2004 2004;32(19):5721-5731.Maniura-Weber K, Goffart S, Garstka HL, Montoya J, Wiesner RJ. Transient overexpression of mitochondrial transcription factor A (TFAM) is sufficient to stimulate mitochondrial DNA transcription, but not sufficient to increase mtDNA copy number in cultured cells. Nucl. Acids Res. %R 10.1093/nar/gkh921. November 16, 2004 2004;32(20):6015-6027.

Matsubara M, Tanaka T, Terato H, et al. Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase. Nucl. Acids Res. %R 10.1093/nar/gkh859. October 5, 2004 2004;32(17):5291-5302.May T, Hauser H, Wirth D. Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization. Nucl. Acids Res. %R 10.1093/nar/gkh887. October 14, 2004 2004;32(18):5529-5538.Navarro A-E, Spinelli N, Moustrou C, Chaix C, Mandrand B, Brisset H. Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution. Nucl. Acids Res. %R 10.1093/nar/gkh874. October 5, 2004 2004;32(17):5310-5319.Ohtani N, Yanagawa H, Tomita M, Itaya M. Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucl. Acids Res. %R 10.1093/nar/gkh917. November 1, 2004 2004;32(19):5809-5819.Otsuki K, Hayashi Y, Kato M, Yoshida H, Yamaguchi M. Characterization of dRFX2, a novel RFX family protein in Drosophila. Nucl. Acids Res. %R 10.1093/nar/gkh895. October 19, 2004 2004;32(18):5636-5648.Perez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucl. Acids Res. %R 10.1093/nar/gkh954. November 23, 2004 2004;32(20):6144-6151.Pincas H, Pingle MR, Huang J, et al. High sensitivity EndoV mutation scanning through real-time ligase proofreading. Nucl. Acids Res. %R 10.1093/nar/gnh150. October 28, 2004 2004;32(19):e148-.Qin L-X, Kerr KF, Contributing Members of the Toxicogenomics Research C. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucl. Acids Res. %R 10.1093/nar/gkh866. October 12, 2004 2004;32(18):5471-5479.Quere R, Manchon L, Lejeune M, et al. Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucl. Acids Res. %R 10.1093/nar/gnh161. November 23, 2004 2004;32(20):e163-.Ruepp A, Zollner A, Maier D, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl. Acids Res. %R 10.1093/nar/gkh894. October 14, 2004 2004;32(18):5539-5545.Rutledge RG. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucl. Acids Res. %R 10.1093/nar/gnh177. December 15, 2004 2004;32(22):e178-.Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res. %R 10.1093/nar/gkh951. November 23, 2004 2004;32(20):6129-6135.Schatz P, Dietrich D, Schuster M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucl. Acids Res. %R 10.1093/nar/gnh165. December 2, 2004 2004;32(21):e167-.Schmidt KS, Borkowski S, Kurreck J, et al. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucl. Acids Res. %R 10.1093/nar/gkh862. October 27, 2004 2004;32(19):5757-5765.Shen G, Anand MFG, Levicky R. X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides. Nucl. Acids Res. %R 10.1093/nar/gkh932. November 10, 2004 2004;32(20):5973-5980.Shukla LI, Adhikary A, Pazdro R, Becker D, Sevilla MD. Formation of 8-oxo-7,8-dihydroguanine-radicals in {gamma}-irradiated DNA by multiple one-electron oxidations. Nucl. Acids Res. %R 10.1093/nar/gkh989. December 15, 2004 2004;32(22):6565-6574.

Sun Y, Koo S, White N, et al. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucl. Acids Res. %R 10.1093/nar/gnh186. December 22, 2004 2004;32(22):e188-.Takami H, Takaki Y, Chee G-J, et al. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucl. Acids Res. %R 10.1093/nar/gkh970. December 1, 2004 2004;32(21):6292-6303.Tang S, Tan SL, Ramadoss SK, Kumar AP, Tang M-HE, Bajic VB. Computational method for discovery of estrogen responsive genes. Nucl. Acids Res. %R 10.1093/nar/gkh943. December 1, 2004 2004;32(21):6212-6217.Thomas H, Senkel S, Erdmann S, et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line. Nucl. Acids Res. %R 10.1093/nar/gnh144. November 1, 2004 2004;32(19):e150-.Tian W, Arakaki AK, Skolnick J. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucl. Acids Res. %R 10.1093/nar/gkh956. December 1, 2004 2004;32(21):6226-6239.

Barbe V, Vallenet D, Fonknechten N, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucl. Acids Res. %R 10.1093/nar/gkh910. October 28, 2004 2004;32(19):5766-5779.

Hashiguchi K, Stuart JA, de Souza-Pinto NC, Bohr VA. The C-terminal {alpha}O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial {beta}-Ogg1 lacks this domain and does not have glycosylase activity. Nucl. Acids Res. %R 10.1093/nar/gkh863. October 19, 2004 2004;32(18):5596-5608.

Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucl. Acids Res. %R 10.1093/nar/gkh828. October 5, 2004 2004;32(17):5260-5279.

Jin VX, Leu Y-W, Liyanarachchi S, et al. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucl. Acids Res. %R 10.1093/nar/gkh1005. December 17, 2004 2004;32(22):6627-6635.

Lindenbaum M, Perkins E, Csonka E, et al. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucl. Acids Res. %R 10.1093/nar/gnh169. December 7, 2004 2004;32(21):e172-.Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh911. October 27, 2004 2004;32(19):5721-5731.Maniura-Weber K, Goffart S, Garstka HL, Montoya J, Wiesner RJ. Transient overexpression of mitochondrial transcription factor A (TFAM) is sufficient to stimulate mitochondrial DNA transcription, but not sufficient to increase mtDNA copy number in cultured cells. Nucl. Acids Res. %R 10.1093/nar/gkh921. November 16, 2004 2004;32(20):6015-6027.

Thomas H, Senkel S, Erdmann S, et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line. Nucl. Acids Res. %R 10.1093/nar/gnh144. November 1, 2004 2004;32(19):e150-.

Ting R, Thomas JM, Lermer L, Perrin DM. Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucl. Acids Res. %R 10.1093/nar/gkh1007. December 29, 2004 2004;32(22):6660-6672.

# Live? Journal?1 y y2 y y3 y y4 y y5 y n6 y y7 n y8 y n9 n y

10 n y11 y y12 y y13 y n14 y n15 n y16 n y17 y y18 y n19 n y20 n y21 n y22 y y23 y y24 y y25 n y26 y y27 n y28 y y29 y y30 y n

ReferenceBennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural Genetic Variation Caused by Transposable Elements in Humans. Genetics %R 10.1534/genetics.104.031757. October 1, 2004 2004;168(2):933-951.Laurie CC, Chasalow SD, LeDeaux JR, et al. The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel. Genetics %R 10.1534/genetics.104.029686. December 1, 2004 2004;168(4):2141-2155.Dettman JR, Taylor JW. Mutation and Evolution of Microsatellite Loci in Neurospora. Genetics %R 10.1534/genetics.104.029322. November 1, 2004 2004;168(3):1231-1248.Kato M, Takashima K, Kakutani T. Epigenetic Control of CACTA Transposon Mobility in Arabidopsis thaliana. Genetics %R 10.1534/genetics.104.029637. October 1, 2004 2004;168(2):961-969.Munkvold JD, Greene RA, Bermudez-Kandianis CE, et al. Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1. Genetics %R 10.1534/genetics.104.034819. October 1, 2004 2004;168(2):639-650.Kuittinen H, de Haan AA, Vogl C, et al. Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana. Genetics %R 10.1534/genetics.103.022343. November 1, 2004 2004;168(3):1575-1584.Sandhu D, Gao H, Cianzio S, Bhattacharyya MK. Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics %R 10.1534/genetics.104.032037. December 1, 2004 2004;168(4):2157-2167.Peng JH, Zadeh H, Lazo GR, et al. Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis. Genetics %R 10.1534/genetics.104.034793. October 1, 2004 2004;168(2):609-623.Kiehart DP, Franke JD, Chee MK, et al. Drosophila crinkled, Mutations of Which Disrupt Morphogenesis and Cause Lethality, Encodes Fly Myosin VIIA. Genetics %R 10.1534/genetics.104.026369. November 1, 2004 2004;168(3):1337-1352.Nikoh N, Duty A, Gibson G. Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate. Genetics %R 10.1534/genetics.104.028712. December 1, 2004 2004;168(4):1963-1974.Swanson WJ, Wong A, Wolfner MF, Aquadro CF. Evolutionary Expressed Sequence Tag Analysis of Drosophila Female Reproductive Tracts Identifies Genes Subjected to Positive Selection. Genetics %R 10.1534/genetics.104.030478. November 1, 2004 2004;168(3):1457-1465.Concepcion D, Seburn KL, Wen G, Frankel WN, Hamilton BA. Mutation Rate and Predicted Phenotypic Target Sizes in Ethylnitrosourea-Treated Mice. Genetics %R 10.1534/genetics.104.029843. October 1, 2004 2004;168(2):953-959.Conley EJ, Nduati V, Gonzalez-Hernandez JL, et al. A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034801. October 1, 2004 2004;168(2):625-637.Zhang D, Choi DW, Wanamaker S, et al. Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.). Genetics %R 10.1534/genetics.104.034785. October 1, 2004 2004;168(2):595-608.Adams KL, Percifield R, Wendel JF. Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid. Genetics %R 10.1534/genetics.104.033522. December 1, 2004 2004;168(4):2217-2226.Chardon F, Virlon B, Moreau L, et al. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome. Genetics %R 10.1534/genetics.104.032375. December 1, 2004 2004;168(4):2169-2185.Caetano AR, Johnson RK, Ford JJ, Pomp D. Microarray Profiling for Differential Gene Expression in Ovaries and Ovarian Follicles of Pigs Selected for Increased Ovulation Rate. Genetics %R 10.1534/genetics.104.029595. November 1, 2004 2004;168(3):1529-1537.Linkiewicz AM, Qi LL, Gill BS, et al. A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034835. October 1, 2004 2004;168(2):665-676.Dvorak J, Yang Z-L, You FM, Luo M-C. Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates. Genetics %R 10.1534/genetics.103.024927. November 1, 2004 2004;168(3):1665-1675.Cinar HN, Chisholm AD. Genetic Analysis of the Caenorhabditis elegans pax-6 Locus: Roles of Paired Domain-Containing and Nonpaired Domain-Containing Isoforms. Genetics %R 10.1534/genetics.104.031724. November 1, 2004 2004;168(3):1307-1322.Robertson HM. Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists. Genetics %R 10.1534/genetics.104.029744. October 1, 2004 2004;168(2):1077-1080.Das A, Mohanty S, Stephan W. Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data. Genetics %R 10.1534/genetics.104.031567. December 1, 2004 2004;168(4):1975-1985.Pratt RJ, Lee DW, Aramayo R. DNA Methylation Affects Meiotic trans-sensing, Not Meiotic Silencing, in Neurospora. Genetics %R 10.1534/genetics.104.031526. December 1, 2004 2004;168(4):1925-1935.Brisson JA, Templeton AR, Duncan I. Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha: Evidence for a Role in Abdominal Pigmentation Variation. Genetics %R 10.1534/genetics.104.032078. December 1, 2004 2004;168(4):1999-2010.Anderson JB, Sirjusingh C, Ricker N. Haploidy, Diploidy and Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae. Genetics %R 10.1534/genetics.104.033266. December 1, 2004 2004;168(4):1915-1923.Crepieux S, Lebreton C, Servin B, Charmet G. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data. Genetics %R 10.1534/genetics.104.028993. November 1, 2004 2004;168(3):1737-1749.Stuurman J, Hoballah ME, Broger L, Moore J, Basten C, Kuhlemeier C. Dissection of Floral Pollination Syndromes in Petunia. Genetics %R 10.1534/genetics.104.031138. November 1, 2004 2004;168(3):1585-1599.Wayne ML, Pan YJ, Nuzhdin SV, McIntyre LM. Additivity and trans-acting Effects on Gene Expression in Male Drosophila simulans. Genetics %R 10.1534/genetics.104.030973. November 1, 2004 2004;168(3):1413-1420.Wright SI, Charlesworth B. The HKA Test Revisited: A Maximum-Likelihood-Ratio Test of the Standard Neutral Model. Genetics %R 10.1534/genetics.104.026500. October 1, 2004 2004;168(2):1071-1076.Miftahudin, Ross K, Ma XF, et al. Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4. Genetics %R 10.1534/genetics.104.034827. October 1, 2004 2004;168(2):651-663.

Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural Genetic Variation Caused by Transposable Elements in Humans. Genetics %R 10.1534/genetics.104.031757. October 1, 2004 2004;168(2):933-951.Laurie CC, Chasalow SD, LeDeaux JR, et al. The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel. Genetics %R 10.1534/genetics.104.029686. December 1, 2004 2004;168(4):2141-2155.Dettman JR, Taylor JW. Mutation and Evolution of Microsatellite Loci in Neurospora. Genetics %R 10.1534/genetics.104.029322. November 1, 2004 2004;168(3):1231-1248.Kato M, Takashima K, Kakutani T. Epigenetic Control of CACTA Transposon Mobility in Arabidopsis thaliana. Genetics %R 10.1534/genetics.104.029637. October 1, 2004 2004;168(2):961-969.Munkvold JD, Greene RA, Bermudez-Kandianis CE, et al. Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1. Genetics %R 10.1534/genetics.104.034819. October 1, 2004 2004;168(2):639-650.Kuittinen H, de Haan AA, Vogl C, et al. Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana. Genetics %R 10.1534/genetics.103.022343. November 1, 2004 2004;168(3):1575-1584.Sandhu D, Gao H, Cianzio S, Bhattacharyya MK. Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics %R 10.1534/genetics.104.032037. December 1, 2004 2004;168(4):2157-2167.Peng JH, Zadeh H, Lazo GR, et al. Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis. Genetics %R 10.1534/genetics.104.034793. October 1, 2004 2004;168(2):609-623.Kiehart DP, Franke JD, Chee MK, et al. Drosophila crinkled, Mutations of Which Disrupt Morphogenesis and Cause Lethality, Encodes Fly Myosin VIIA. Genetics %R 10.1534/genetics.104.026369. November 1, 2004 2004;168(3):1337-1352.Nikoh N, Duty A, Gibson G. Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate. Genetics %R 10.1534/genetics.104.028712. December 1, 2004 2004;168(4):1963-1974.Swanson WJ, Wong A, Wolfner MF, Aquadro CF. Evolutionary Expressed Sequence Tag Analysis of Drosophila Female Reproductive Tracts Identifies Genes Subjected to Positive Selection. Genetics %R 10.1534/genetics.104.030478. November 1, 2004 2004;168(3):1457-1465.Concepcion D, Seburn KL, Wen G, Frankel WN, Hamilton BA. Mutation Rate and Predicted Phenotypic Target Sizes in Ethylnitrosourea-Treated Mice. Genetics %R 10.1534/genetics.104.029843. October 1, 2004 2004;168(2):953-959.Conley EJ, Nduati V, Gonzalez-Hernandez JL, et al. A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034801. October 1, 2004 2004;168(2):625-637.Zhang D, Choi DW, Wanamaker S, et al. Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.). Genetics %R 10.1534/genetics.104.034785. October 1, 2004 2004;168(2):595-608.Adams KL, Percifield R, Wendel JF. Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid. Genetics %R 10.1534/genetics.104.033522. December 1, 2004 2004;168(4):2217-2226.Chardon F, Virlon B, Moreau L, et al. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome. Genetics %R 10.1534/genetics.104.032375. December 1, 2004 2004;168(4):2169-2185.Caetano AR, Johnson RK, Ford JJ, Pomp D. Microarray Profiling for Differential Gene Expression in Ovaries and Ovarian Follicles of Pigs Selected for Increased Ovulation Rate. Genetics %R 10.1534/genetics.104.029595. November 1, 2004 2004;168(3):1529-1537.Linkiewicz AM, Qi LL, Gill BS, et al. A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034835. October 1, 2004 2004;168(2):665-676.Dvorak J, Yang Z-L, You FM, Luo M-C. Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates. Genetics %R 10.1534/genetics.103.024927. November 1, 2004 2004;168(3):1665-1675.Cinar HN, Chisholm AD. Genetic Analysis of the Caenorhabditis elegans pax-6 Locus: Roles of Paired Domain-Containing and Nonpaired Domain-Containing Isoforms. Genetics %R 10.1534/genetics.104.031724. November 1, 2004 2004;168(3):1307-1322.Robertson HM. Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists. Genetics %R 10.1534/genetics.104.029744. October 1, 2004 2004;168(2):1077-1080.Das A, Mohanty S, Stephan W. Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data. Genetics %R 10.1534/genetics.104.031567. December 1, 2004 2004;168(4):1975-1985.Pratt RJ, Lee DW, Aramayo R. DNA Methylation Affects Meiotic trans-sensing, Not Meiotic Silencing, in Neurospora. Genetics %R 10.1534/genetics.104.031526. December 1, 2004 2004;168(4):1925-1935.Brisson JA, Templeton AR, Duncan I. Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha: Evidence for a Role in Abdominal Pigmentation Variation. Genetics %R 10.1534/genetics.104.032078. December 1, 2004 2004;168(4):1999-2010.Anderson JB, Sirjusingh C, Ricker N. Haploidy, Diploidy and Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae. Genetics %R 10.1534/genetics.104.033266. December 1, 2004 2004;168(4):1915-1923.Crepieux S, Lebreton C, Servin B, Charmet G. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data. Genetics %R 10.1534/genetics.104.028993. November 1, 2004 2004;168(3):1737-1749.Stuurman J, Hoballah ME, Broger L, Moore J, Basten C, Kuhlemeier C. Dissection of Floral Pollination Syndromes in Petunia. Genetics %R 10.1534/genetics.104.031138. November 1, 2004 2004;168(3):1585-1599.Wayne ML, Pan YJ, Nuzhdin SV, McIntyre LM. Additivity and trans-acting Effects on Gene Expression in Male Drosophila simulans. Genetics %R 10.1534/genetics.104.030973. November 1, 2004 2004;168(3):1413-1420.Wright SI, Charlesworth B. The HKA Test Revisited: A Maximum-Likelihood-Ratio Test of the Standard Neutral Model. Genetics %R 10.1534/genetics.104.026500. October 1, 2004 2004;168(2):1071-1076.Miftahudin, Ross K, Ma XF, et al. Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4. Genetics %R 10.1534/genetics.104.034827. October 1, 2004 2004;168(2):651-663.

Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural Genetic Variation Caused by Transposable Elements in Humans. Genetics %R 10.1534/genetics.104.031757. October 1, 2004 2004;168(2):933-951.Laurie CC, Chasalow SD, LeDeaux JR, et al. The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel. Genetics %R 10.1534/genetics.104.029686. December 1, 2004 2004;168(4):2141-2155.

Kato M, Takashima K, Kakutani T. Epigenetic Control of CACTA Transposon Mobility in Arabidopsis thaliana. Genetics %R 10.1534/genetics.104.029637. October 1, 2004 2004;168(2):961-969.Munkvold JD, Greene RA, Bermudez-Kandianis CE, et al. Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1. Genetics %R 10.1534/genetics.104.034819. October 1, 2004 2004;168(2):639-650.Kuittinen H, de Haan AA, Vogl C, et al. Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana. Genetics %R 10.1534/genetics.103.022343. November 1, 2004 2004;168(3):1575-1584.Sandhu D, Gao H, Cianzio S, Bhattacharyya MK. Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics %R 10.1534/genetics.104.032037. December 1, 2004 2004;168(4):2157-2167.Peng JH, Zadeh H, Lazo GR, et al. Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis. Genetics %R 10.1534/genetics.104.034793. October 1, 2004 2004;168(2):609-623.Kiehart DP, Franke JD, Chee MK, et al. Drosophila crinkled, Mutations of Which Disrupt Morphogenesis and Cause Lethality, Encodes Fly Myosin VIIA. Genetics %R 10.1534/genetics.104.026369. November 1, 2004 2004;168(3):1337-1352.Nikoh N, Duty A, Gibson G. Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate. Genetics %R 10.1534/genetics.104.028712. December 1, 2004 2004;168(4):1963-1974.Swanson WJ, Wong A, Wolfner MF, Aquadro CF. Evolutionary Expressed Sequence Tag Analysis of Drosophila Female Reproductive Tracts Identifies Genes Subjected to Positive Selection. Genetics %R 10.1534/genetics.104.030478. November 1, 2004 2004;168(3):1457-1465.Concepcion D, Seburn KL, Wen G, Frankel WN, Hamilton BA. Mutation Rate and Predicted Phenotypic Target Sizes in Ethylnitrosourea-Treated Mice. Genetics %R 10.1534/genetics.104.029843. October 1, 2004 2004;168(2):953-959.Conley EJ, Nduati V, Gonzalez-Hernandez JL, et al. A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034801. October 1, 2004 2004;168(2):625-637.Zhang D, Choi DW, Wanamaker S, et al. Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.). Genetics %R 10.1534/genetics.104.034785. October 1, 2004 2004;168(2):595-608.Adams KL, Percifield R, Wendel JF. Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid. Genetics %R 10.1534/genetics.104.033522. December 1, 2004 2004;168(4):2217-2226.Chardon F, Virlon B, Moreau L, et al. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome. Genetics %R 10.1534/genetics.104.032375. December 1, 2004 2004;168(4):2169-2185.Caetano AR, Johnson RK, Ford JJ, Pomp D. Microarray Profiling for Differential Gene Expression in Ovaries and Ovarian Follicles of Pigs Selected for Increased Ovulation Rate. Genetics %R 10.1534/genetics.104.029595. November 1, 2004 2004;168(3):1529-1537.Linkiewicz AM, Qi LL, Gill BS, et al. A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034835. October 1, 2004 2004;168(2):665-676.Dvorak J, Yang Z-L, You FM, Luo M-C. Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates. Genetics %R 10.1534/genetics.103.024927. November 1, 2004 2004;168(3):1665-1675.Cinar HN, Chisholm AD. Genetic Analysis of the Caenorhabditis elegans pax-6 Locus: Roles of Paired Domain-Containing and Nonpaired Domain-Containing Isoforms. Genetics %R 10.1534/genetics.104.031724. November 1, 2004 2004;168(3):1307-1322.Robertson HM. Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists. Genetics %R 10.1534/genetics.104.029744. October 1, 2004 2004;168(2):1077-1080.Das A, Mohanty S, Stephan W. Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data. Genetics %R 10.1534/genetics.104.031567. December 1, 2004 2004;168(4):1975-1985.Pratt RJ, Lee DW, Aramayo R. DNA Methylation Affects Meiotic trans-sensing, Not Meiotic Silencing, in Neurospora. Genetics %R 10.1534/genetics.104.031526. December 1, 2004 2004;168(4):1925-1935.Brisson JA, Templeton AR, Duncan I. Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha: Evidence for a Role in Abdominal Pigmentation Variation. Genetics %R 10.1534/genetics.104.032078. December 1, 2004 2004;168(4):1999-2010.Anderson JB, Sirjusingh C, Ricker N. Haploidy, Diploidy and Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae. Genetics %R 10.1534/genetics.104.033266. December 1, 2004 2004;168(4):1915-1923.Crepieux S, Lebreton C, Servin B, Charmet G. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data. Genetics %R 10.1534/genetics.104.028993. November 1, 2004 2004;168(3):1737-1749.Stuurman J, Hoballah ME, Broger L, Moore J, Basten C, Kuhlemeier C. Dissection of Floral Pollination Syndromes in Petunia. Genetics %R 10.1534/genetics.104.031138. November 1, 2004 2004;168(3):1585-1599.Wayne ML, Pan YJ, Nuzhdin SV, McIntyre LM. Additivity and trans-acting Effects on Gene Expression in Male Drosophila simulans. Genetics %R 10.1534/genetics.104.030973. November 1, 2004 2004;168(3):1413-1420.Wright SI, Charlesworth B. The HKA Test Revisited: A Maximum-Likelihood-Ratio Test of the Standard Neutral Model. Genetics %R 10.1534/genetics.104.026500. October 1, 2004 2004;168(2):1071-1076.Miftahudin, Ross K, Ma XF, et al. Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4. Genetics %R 10.1534/genetics.104.034827. October 1, 2004 2004;168(2):651-663.

Sandhu D, Gao H, Cianzio S, Bhattacharyya MK. Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics %R 10.1534/genetics.104.032037. December 1, 2004 2004;168(4):2157-2167.

Swanson WJ, Wong A, Wolfner MF, Aquadro CF. Evolutionary Expressed Sequence Tag Analysis of Drosophila Female Reproductive Tracts Identifies Genes Subjected to Positive Selection. Genetics %R 10.1534/genetics.104.030478. November 1, 2004 2004;168(3):1457-1465.

Chardon F, Virlon B, Moreau L, et al. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome. Genetics %R 10.1534/genetics.104.032375. December 1, 2004 2004;168(4):2169-2185.

Brisson JA, Templeton AR, Duncan I. Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha: Evidence for a Role in Abdominal Pigmentation Variation. Genetics %R 10.1534/genetics.104.032078. December 1, 2004 2004;168(4):1999-2010.

Crepieux S, Lebreton C, Servin B, Charmet G. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data. Genetics %R 10.1534/genetics.104.028993. November 1, 2004 2004;168(3):1737-1749.

# Live? Journal?1 n n2 y n3 n n4 y n5 y n6 y n7 n n8 y n9 y n

10 y n11 y n12 y n13 y n14 n n15 y n16 n y17 y n18 y n19 y n20 y n21 y n22 y n23 n y24 y n25 y n26 y n27 y n28 n n29 y n30 y y31 y n32 y n33 y n34 y n35 y n36 y n37 y n38 y n39 y n40 n n41 y n42 y n43 n n44 y n45 n n46 n n47 y n48 y n49 y n50 y n51 y y52 y y

53 y y54 n n55 y n56 y n57 y n58 y n59 y n60 y n61 y n62 n n63 n n64 y n65 y n66 y n67 y n68 y n69 n n70 y n71 y n

ReferenceAdryan B, Schuh R. Gene-Ontology-based clustering of gene expression data. Bioinformatics %R 10.1093/bioinformatics/bth289. November 1, 2004 2004;20(16):2851-2852.Alexandridis R, Lin S, Irwin M. Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach. Bioinformatics %R 10.1093/bioinformatics/bth281. November 1, 2004 2004;20(16):2545-2552.Almeida LGP, Paixao R, Souza RC, et al. A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics %R 10.1093/bioinformatics/bth273. November 1, 2004 2004;20(16):2832-2833.Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics %R 10.1093/bioinformatics/bth272. November 1, 2004 2004;20(16):2513-2520.Bae K, Mallick BK. Gene selection using a two-level hierarchical Bayesian model. Bioinformatics %R 10.1093/bioinformatics/bth419. December 12, 2004 2004;20(18):3423-3430.Bahlo M, Xing L, Wilkinson CR. HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers. Bioinformatics %R 10.1093/bioinformatics/bth375. November 22, 2004 2004;20(17):3280-3283.Bhattacharjee M, Pritchard CC, Nelson PS, Arjas E. Bayesian integrated functional analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth338. November 22, 2004 2004;20(17):2943-2953.Bidaut G, Ochs MF. ClutrFree: cluster tree visualization and interpretation. Bioinformatics %R 10.1093/bioinformatics/bth307. November 1, 2004 2004;20(16):2869-2871.Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics %R 10.1093/bioinformatics/bth374. November 22, 2004 2004;20(17):2911-2917.Catherinot V, Labesse G. ViTO: tool for refinement of protein sequence-structure alignments. Bioinformatics %R 10.1093/bioinformatics/bth429. December 12, 2004 2004;20(18):3694-3696.Catic A, Collins C, Church GM, Ploegh HL. Preferred in vivo ubiquitination sites. Bioinformatics %R 10.1093/bioinformatics/bth407. December 12, 2004 2004;20(18):3302-3307.Chen C-Y, Oyang Y-J, Juan H-F. Incremental generation of summarized clustering hierarchy for protein family analysis. Bioinformatics %R 10.1093/bioinformatics/bth290. November 1, 2004 2004;20(16):2586-2596.Chou H-H, Hsia A-P, Mooney DL, Schnable PS. Picky: oligo microarray design for large genomes. Bioinformatics %R 10.1093/bioinformatics/bth347. November 22, 2004 2004;20(17):2893-2902.de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics %R 10.1093/bioinformatics/bth445. December 12, 2004 2004;20(18):3565-3574.Delgrange O, Rivals E. STAR: an algorithm to Search for Tandem Approximate Repeats. Bioinformatics %R 10.1093/bioinformatics/bth335. November 1, 2004 2004;20(16):2812-2820.Dettling M. BagBoosting for tumor classification with gene expression data. Bioinformatics %R 10.1093/bioinformatics/bth447. December 12, 2004 2004;20(18):3583-3593.Dou Y, Baisnee P-F, Pollastri G, Pecout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by {beta}-sheet formation. Bioinformatics %R 10.1093/bioinformatics/bth326. November 1, 2004 2004;20(16):2767-2777.Fernandez JM, Valencia A. YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics %R 10.1093/bioinformatics/bth243. October 12, 2004 2004;20(15):2455-2457.Finocchiaro G, Parise P, Minardi SP, Alcalay M, Muller H. GenePicker: replicate analysis of Affymetrix gene expression microarrays. Bioinformatics %R 10.1093/bioinformatics/bth416. December 12, 2004 2004;20(18):3670-3672.Fofanov Y, Luo Y, Katili C, et al. How independent are the appearances of n-mers in different genomes? Bioinformatics %R 10.1093/bioinformatics/bth266. October 12, 2004 2004;20(15):2421-2428.Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics %R 10.1093/bioinformatics/bth320. November 1, 2004 2004;20(16):2738-2750.Grubb SC, Churchill GA, Bogue MA. A collaborative database of inbred mouse strain characteristics. Bioinformatics %R 10.1093/bioinformatics/bth299. November 1, 2004 2004;20(16):2857-2859.Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics %R 10.1093/bioinformatics/bth288. November 1, 2004 2004;20(16):2579-2585.Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics %R 10.1093/bioinformatics/bth423. December 12, 2004 2004;20(18):3682-3686.Han K, Park B, Kim H, Hong J, Park J. HPID: The Human Protein Interaction Database. Bioinformatics %R 10.1093/bioinformatics/bth253. October 12, 2004 2004;20(15):2466-2470.Hitte C, Derrien T, Andre C, Ostrander EA, Galibert F. CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. Bioinformatics %R 10.1093/bioinformatics/bth411. December 12, 2004 2004;20(18):3665-3667.Ji L, Tan K-L. Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics %R 10.1093/bioinformatics/bth312. November 1, 2004 2004;20(16):2711-2718.Kaluszka A, Gibas C. Interactive gene-order comparison for multiple small genomes. Bioinformatics %R 10.1093/bioinformatics/bth406. December 12, 2004 2004;20(18):3662-3664.Kim JH, Lee J, Oh B, Kimm K, Koh I. Prediction of phosphorylation sites using SVMs. Bioinformatics %R 10.1093/bioinformatics/bth382. November 22, 2004 2004;20(17):3179-3184.King AD, Przulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics %R 10.1093/bioinformatics/bth351. November 22, 2004 2004;20(17):3013-3020.Kinjo AR, Nishikawa K. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. Bioinformatics %R 10.1093/bioinformatics/bth297. November 1, 2004 2004;20(16):2504-2508.Krishnan A, Tang F. Exhaustive whole-genome tandem repeats search. Bioinformatics %R 10.1093/bioinformatics/bth311. November 1, 2004 2004;20(16):2702-2710.Kyoda K, Baba K, Onami S, Kitano H. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics %R 10.1093/bioinformatics/bth306. November 1, 2004 2004;20(16):2662-2675.Lanckriet GRG, De Bie T, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics %R 10.1093/bioinformatics/bth294. November 1, 2004 2004;20(16):2626-2635.Laval G, Excoffier L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics %R 10.1093/bioinformatics/bth264. October 12, 2004 2004;20(15):2485-2487.Li L, Li H. Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics %R 10.1093/bioinformatics/bth415. December 12, 2004 2004;20(18):3406-3412.Liao B-Y, Chang Y-J, Ho J-M, Hwang M-J. The UniMarker (UM) method for synteny mapping of large genomes. Bioinformatics %R 10.1093/bioinformatics/bth380. November 22, 2004 2004;20(17):3156-3165.Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R. BacTregulators: a database of transcriptional regulators in bacteria and archaea. Bioinformatics %R 10.1093/bioinformatics/bth330. November 1, 2004 2004;20(16):2787-2791.O'Donoghue SI, Meyer JEW, Schafferhans A, Fries K. The SRS 3D module: integrating structures, sequences and features. Bioinformatics %R 10.1093/bioinformatics/bth260. October 12, 2004 2004;20(15):2476-2478.Pandey N, Ganapathi M, Kumar K, Dasgupta D, Das Sutar SK, Dash D. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins. Bioinformatics %R 10.1093/bioinformatics/bth344. November 22, 2004 2004;20(17):2904-2910.Parr CS, Lee B, Campbell D, Bederson BB. Visualizations for taxonomic and phylogenetic trees. Bioinformatics %R 10.1093/bioinformatics/bth345. November 22, 2004 2004;20(17):2997-3004.Pasquier C, Girardot F, Jevardat de Fombelle K, Christen R. THEA: ontology-driven analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth295. November 1, 2004 2004;20(16):2636-2643.Pochet N, De Smet F, Suykens JAK, De Moor BLR. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics %R 10.1093/bioinformatics/bth383. November 22, 2004 2004;20(17):3185-3195.Pons JL, Malliavin TE, Tramesel D, Delsuc MA. NMRb: a web-site repository for raw NMR datasets. Bioinformatics %R 10.1093/bioinformatics/bth450. December 12, 2004 2004;20(18):3707-3709.Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. CoPS: Comprehensive Peptide Signature Database. Bioinformatics %R 10.1093/bioinformatics/bth325. November 1, 2004 2004;20(16):2886-2888.Przulj N, Corneil DG, Jurisica I. Modeling interactome: scale-free or geometric? Bioinformatics %R 10.1093/bioinformatics/bth436. December 12, 2004 2004;20(18):3508-3515.Qi Y, Grishin NV. PCOAT: positional correlation analysis using multiple methods. Bioinformatics %R 10.1093/bioinformatics/bth431. December 12, 2004 2004;20(18):3697-3699.Rainey JK, Goh MC. An interactive triple-helical collagen builder. Bioinformatics %R 10.1093/bioinformatics/bth247. October 12, 2004 2004;20(15):2458-2459.Robles JR, van den Oord EJCG. lga972: a cross-platform application for optimizing LD studies using a genetic algorithm. Bioinformatics %R 10.1093/bioinformatics/bth348. November 22, 2004 2004;20(17):3244-3245.Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics %R 10.1093/bioinformatics/bth427. December 12, 2004 2004;20(18):3462-3465.Samuelsson J, Dalevi D, Levander F, Rognvaldsson T. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics %R 10.1093/bioinformatics/bth460. December 12, 2004 2004;20(18):3628-3635.Satten GA, Datta S, Moura H, et al. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics %R 10.1093/bioinformatics/bth372. November 22, 2004 2004;20(17):3128-3136.

Saunders NFW, Curmi PMG, Cavicchioli R. An online database for the detection of novel archaeal sequences in human ESTs. Bioinformatics %R 10.1093/bioinformatics/bth249. October 12, 2004 2004;20(15):2361-2362.Sese J, Kurokawa Y, Monden M, Kato K, Morishita S. Constrained clusters of gene expression profiles with pathological features. Bioinformatics %R 10.1093/bioinformatics/bth373. November 22, 2004 2004;20(17):3137-3145.Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics %R 10.1093/bioinformatics/bth271. November 1, 2004 2004;20(16):2829-2831.Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE. Effects of pooling mRNA in microarray class comparisons. Bioinformatics %R 10.1093/bioinformatics/bth391. December 12, 2004 2004;20(18):3318-3325.Simonis N, Wodak SJ, Cohen GN, van Helden J. Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics %R 10.1093/bioinformatics/bth252. October 12, 2004 2004;20(15):2370-2379.Smid M, Dorssers LCJ. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics %R 10.1093/bioinformatics/bth293. November 1, 2004 2004;20(16):2618-2625.Spencer CCA, Coop G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics %R 10.1093/bioinformatics/bth417. December 12, 2004 2004;20(18):3673-3675.Tessier D, Bardiaux B, Larre C, Popineau Y. Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor. Bioinformatics %R 10.1093/bioinformatics/bth332. November 1, 2004 2004;20(16):2509-2512.Tibshirani R, Hastie T, Narasimhan B, et al. Sample classification from protein mass spectrometry, by 'peak probability contrasts'. Bioinformatics %R 10.1093/bioinformatics/bth357. November 22, 2004 2004;20(17):3034-3044.Tusnady GE, Dosztanyi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics %R 10.1093/bioinformatics/bth340. November 22, 2004 2004;20(17):2964-2972.van Bakel H, Huynen M, Wijmenga C. Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway. Bioinformatics %R 10.1093/bioinformatics/bth298. November 1, 2004 2004;20(16):2644-2655.Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics %R 10.1093/bioinformatics/bth381. November 22, 2004 2004;20(17):3166-3178.Wang J-PZ, Lindsay BG, Leebens-Mack J, et al. EST clustering error evaluation and correction. Bioinformatics %R 10.1093/bioinformatics/bth342. November 22, 2004 2004;20(17):2973-2984.Wu C-C, Huang H-C, Juan H-F, Chen S-T. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics %R 10.1093/bioinformatics/bth428. December 12, 2004 2004;20(18):3691-3693.Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics %R 10.1093/bioinformatics/bth352. November 22, 2004 2004;20(17):3252-3255.Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics %R 10.1093/bioinformatics/bth448. December 12, 2004 2004;20(18):3594-3603.Zhang S-D, Gant TW. A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics %R 10.1093/bioinformatics/bth336. November 1, 2004 2004;20(16):2821-2828.Zhang Y, Eberhard DA, Frantz GD, et al. GEPIS--quantitative gene expression profiling in normal and cancer tissues. Bioinformatics %R 10.1093/bioinformatics/bth256. October 12, 2004 2004;20(15):2390-2398.Zhou X, Wang X, Pal R, Ivanov I, Bittner M, Dougherty ER. A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics %R 10.1093/bioinformatics/bth318. November 22, 2004 2004;20(17):2918-2927.

Adryan B, Schuh R. Gene-Ontology-based clustering of gene expression data. Bioinformatics %R 10.1093/bioinformatics/bth289. November 1, 2004 2004;20(16):2851-2852.Alexandridis R, Lin S, Irwin M. Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach. Bioinformatics %R 10.1093/bioinformatics/bth281. November 1, 2004 2004;20(16):2545-2552.Almeida LGP, Paixao R, Souza RC, et al. A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics %R 10.1093/bioinformatics/bth273. November 1, 2004 2004;20(16):2832-2833.Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics %R 10.1093/bioinformatics/bth272. November 1, 2004 2004;20(16):2513-2520.Bae K, Mallick BK. Gene selection using a two-level hierarchical Bayesian model. Bioinformatics %R 10.1093/bioinformatics/bth419. December 12, 2004 2004;20(18):3423-3430.Bahlo M, Xing L, Wilkinson CR. HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers. Bioinformatics %R 10.1093/bioinformatics/bth375. November 22, 2004 2004;20(17):3280-3283.Bhattacharjee M, Pritchard CC, Nelson PS, Arjas E. Bayesian integrated functional analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth338. November 22, 2004 2004;20(17):2943-2953.Bidaut G, Ochs MF. ClutrFree: cluster tree visualization and interpretation. Bioinformatics %R 10.1093/bioinformatics/bth307. November 1, 2004 2004;20(16):2869-2871.Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics %R 10.1093/bioinformatics/bth374. November 22, 2004 2004;20(17):2911-2917.Catherinot V, Labesse G. ViTO: tool for refinement of protein sequence-structure alignments. Bioinformatics %R 10.1093/bioinformatics/bth429. December 12, 2004 2004;20(18):3694-3696.Catic A, Collins C, Church GM, Ploegh HL. Preferred in vivo ubiquitination sites. Bioinformatics %R 10.1093/bioinformatics/bth407. December 12, 2004 2004;20(18):3302-3307.Chen C-Y, Oyang Y-J, Juan H-F. Incremental generation of summarized clustering hierarchy for protein family analysis. Bioinformatics %R 10.1093/bioinformatics/bth290. November 1, 2004 2004;20(16):2586-2596.Chou H-H, Hsia A-P, Mooney DL, Schnable PS. Picky: oligo microarray design for large genomes. Bioinformatics %R 10.1093/bioinformatics/bth347. November 22, 2004 2004;20(17):2893-2902.de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics %R 10.1093/bioinformatics/bth445. December 12, 2004 2004;20(18):3565-3574.Delgrange O, Rivals E. STAR: an algorithm to Search for Tandem Approximate Repeats. Bioinformatics %R 10.1093/bioinformatics/bth335. November 1, 2004 2004;20(16):2812-2820.Dettling M. BagBoosting for tumor classification with gene expression data. Bioinformatics %R 10.1093/bioinformatics/bth447. December 12, 2004 2004;20(18):3583-3593.Dou Y, Baisnee P-F, Pollastri G, Pecout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by {beta}-sheet formation. Bioinformatics %R 10.1093/bioinformatics/bth326. November 1, 2004 2004;20(16):2767-2777.Fernandez JM, Valencia A. YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics %R 10.1093/bioinformatics/bth243. October 12, 2004 2004;20(15):2455-2457.Finocchiaro G, Parise P, Minardi SP, Alcalay M, Muller H. GenePicker: replicate analysis of Affymetrix gene expression microarrays. Bioinformatics %R 10.1093/bioinformatics/bth416. December 12, 2004 2004;20(18):3670-3672.Fofanov Y, Luo Y, Katili C, et al. How independent are the appearances of n-mers in different genomes? Bioinformatics %R 10.1093/bioinformatics/bth266. October 12, 2004 2004;20(15):2421-2428.Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics %R 10.1093/bioinformatics/bth320. November 1, 2004 2004;20(16):2738-2750.Grubb SC, Churchill GA, Bogue MA. A collaborative database of inbred mouse strain characteristics. Bioinformatics %R 10.1093/bioinformatics/bth299. November 1, 2004 2004;20(16):2857-2859.Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics %R 10.1093/bioinformatics/bth288. November 1, 2004 2004;20(16):2579-2585.Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics %R 10.1093/bioinformatics/bth423. December 12, 2004 2004;20(18):3682-3686.Han K, Park B, Kim H, Hong J, Park J. HPID: The Human Protein Interaction Database. Bioinformatics %R 10.1093/bioinformatics/bth253. October 12, 2004 2004;20(15):2466-2470.Hitte C, Derrien T, Andre C, Ostrander EA, Galibert F. CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. Bioinformatics %R 10.1093/bioinformatics/bth411. December 12, 2004 2004;20(18):3665-3667.Ji L, Tan K-L. Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics %R 10.1093/bioinformatics/bth312. November 1, 2004 2004;20(16):2711-2718.Kaluszka A, Gibas C. Interactive gene-order comparison for multiple small genomes. Bioinformatics %R 10.1093/bioinformatics/bth406. December 12, 2004 2004;20(18):3662-3664.Kim JH, Lee J, Oh B, Kimm K, Koh I. Prediction of phosphorylation sites using SVMs. Bioinformatics %R 10.1093/bioinformatics/bth382. November 22, 2004 2004;20(17):3179-3184.King AD, Przulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics %R 10.1093/bioinformatics/bth351. November 22, 2004 2004;20(17):3013-3020.Kinjo AR, Nishikawa K. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. Bioinformatics %R 10.1093/bioinformatics/bth297. November 1, 2004 2004;20(16):2504-2508.Krishnan A, Tang F. Exhaustive whole-genome tandem repeats search. Bioinformatics %R 10.1093/bioinformatics/bth311. November 1, 2004 2004;20(16):2702-2710.Kyoda K, Baba K, Onami S, Kitano H. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics %R 10.1093/bioinformatics/bth306. November 1, 2004 2004;20(16):2662-2675.Lanckriet GRG, De Bie T, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics %R 10.1093/bioinformatics/bth294. November 1, 2004 2004;20(16):2626-2635.Laval G, Excoffier L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics %R 10.1093/bioinformatics/bth264. October 12, 2004 2004;20(15):2485-2487.Li L, Li H. Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics %R 10.1093/bioinformatics/bth415. December 12, 2004 2004;20(18):3406-3412.Liao B-Y, Chang Y-J, Ho J-M, Hwang M-J. The UniMarker (UM) method for synteny mapping of large genomes. Bioinformatics %R 10.1093/bioinformatics/bth380. November 22, 2004 2004;20(17):3156-3165.Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R. BacTregulators: a database of transcriptional regulators in bacteria and archaea. Bioinformatics %R 10.1093/bioinformatics/bth330. November 1, 2004 2004;20(16):2787-2791.O'Donoghue SI, Meyer JEW, Schafferhans A, Fries K. The SRS 3D module: integrating structures, sequences and features. Bioinformatics %R 10.1093/bioinformatics/bth260. October 12, 2004 2004;20(15):2476-2478.Pandey N, Ganapathi M, Kumar K, Dasgupta D, Das Sutar SK, Dash D. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins. Bioinformatics %R 10.1093/bioinformatics/bth344. November 22, 2004 2004;20(17):2904-2910.Parr CS, Lee B, Campbell D, Bederson BB. Visualizations for taxonomic and phylogenetic trees. Bioinformatics %R 10.1093/bioinformatics/bth345. November 22, 2004 2004;20(17):2997-3004.Pasquier C, Girardot F, Jevardat de Fombelle K, Christen R. THEA: ontology-driven analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth295. November 1, 2004 2004;20(16):2636-2643.Pochet N, De Smet F, Suykens JAK, De Moor BLR. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics %R 10.1093/bioinformatics/bth383. November 22, 2004 2004;20(17):3185-3195.Pons JL, Malliavin TE, Tramesel D, Delsuc MA. NMRb: a web-site repository for raw NMR datasets. Bioinformatics %R 10.1093/bioinformatics/bth450. December 12, 2004 2004;20(18):3707-3709.Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. CoPS: Comprehensive Peptide Signature Database. Bioinformatics %R 10.1093/bioinformatics/bth325. November 1, 2004 2004;20(16):2886-2888.Przulj N, Corneil DG, Jurisica I. Modeling interactome: scale-free or geometric? Bioinformatics %R 10.1093/bioinformatics/bth436. December 12, 2004 2004;20(18):3508-3515.Qi Y, Grishin NV. PCOAT: positional correlation analysis using multiple methods. Bioinformatics %R 10.1093/bioinformatics/bth431. December 12, 2004 2004;20(18):3697-3699.Rainey JK, Goh MC. An interactive triple-helical collagen builder. Bioinformatics %R 10.1093/bioinformatics/bth247. October 12, 2004 2004;20(15):2458-2459.Robles JR, van den Oord EJCG. lga972: a cross-platform application for optimizing LD studies using a genetic algorithm. Bioinformatics %R 10.1093/bioinformatics/bth348. November 22, 2004 2004;20(17):3244-3245.Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics %R 10.1093/bioinformatics/bth427. December 12, 2004 2004;20(18):3462-3465.Samuelsson J, Dalevi D, Levander F, Rognvaldsson T. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics %R 10.1093/bioinformatics/bth460. December 12, 2004 2004;20(18):3628-3635.Satten GA, Datta S, Moura H, et al. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics %R 10.1093/bioinformatics/bth372. November 22, 2004 2004;20(17):3128-3136.

Alexandridis R, Lin S, Irwin M. Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach. Bioinformatics %R 10.1093/bioinformatics/bth281. November 1, 2004 2004;20(16):2545-2552.Almeida LGP, Paixao R, Souza RC, et al. A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics %R 10.1093/bioinformatics/bth273. November 1, 2004 2004;20(16):2832-2833.Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics %R 10.1093/bioinformatics/bth272. November 1, 2004 2004;20(16):2513-2520.

Bahlo M, Xing L, Wilkinson CR. HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers. Bioinformatics %R 10.1093/bioinformatics/bth375. November 22, 2004 2004;20(17):3280-3283.Bhattacharjee M, Pritchard CC, Nelson PS, Arjas E. Bayesian integrated functional analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth338. November 22, 2004 2004;20(17):2943-2953.

Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics %R 10.1093/bioinformatics/bth374. November 22, 2004 2004;20(17):2911-2917.Catherinot V, Labesse G. ViTO: tool for refinement of protein sequence-structure alignments. Bioinformatics %R 10.1093/bioinformatics/bth429. December 12, 2004 2004;20(18):3694-3696.

Chen C-Y, Oyang Y-J, Juan H-F. Incremental generation of summarized clustering hierarchy for protein family analysis. Bioinformatics %R 10.1093/bioinformatics/bth290. November 1, 2004 2004;20(16):2586-2596.Chou H-H, Hsia A-P, Mooney DL, Schnable PS. Picky: oligo microarray design for large genomes. Bioinformatics %R 10.1093/bioinformatics/bth347. November 22, 2004 2004;20(17):2893-2902.de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics %R 10.1093/bioinformatics/bth445. December 12, 2004 2004;20(18):3565-3574.

Dou Y, Baisnee P-F, Pollastri G, Pecout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by {beta}-sheet formation. Bioinformatics %R 10.1093/bioinformatics/bth326. November 1, 2004 2004;20(16):2767-2777.Fernandez JM, Valencia A. YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics %R 10.1093/bioinformatics/bth243. October 12, 2004 2004;20(15):2455-2457.Finocchiaro G, Parise P, Minardi SP, Alcalay M, Muller H. GenePicker: replicate analysis of Affymetrix gene expression microarrays. Bioinformatics %R 10.1093/bioinformatics/bth416. December 12, 2004 2004;20(18):3670-3672.Fofanov Y, Luo Y, Katili C, et al. How independent are the appearances of n-mers in different genomes? Bioinformatics %R 10.1093/bioinformatics/bth266. October 12, 2004 2004;20(15):2421-2428.Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics %R 10.1093/bioinformatics/bth320. November 1, 2004 2004;20(16):2738-2750.Grubb SC, Churchill GA, Bogue MA. A collaborative database of inbred mouse strain characteristics. Bioinformatics %R 10.1093/bioinformatics/bth299. November 1, 2004 2004;20(16):2857-2859.Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics %R 10.1093/bioinformatics/bth288. November 1, 2004 2004;20(16):2579-2585.Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics %R 10.1093/bioinformatics/bth423. December 12, 2004 2004;20(18):3682-3686.

Hitte C, Derrien T, Andre C, Ostrander EA, Galibert F. CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. Bioinformatics %R 10.1093/bioinformatics/bth411. December 12, 2004 2004;20(18):3665-3667.Ji L, Tan K-L. Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics %R 10.1093/bioinformatics/bth312. November 1, 2004 2004;20(16):2711-2718.

Kinjo AR, Nishikawa K. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. Bioinformatics %R 10.1093/bioinformatics/bth297. November 1, 2004 2004;20(16):2504-2508.

Kyoda K, Baba K, Onami S, Kitano H. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics %R 10.1093/bioinformatics/bth306. November 1, 2004 2004;20(16):2662-2675.Lanckriet GRG, De Bie T, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics %R 10.1093/bioinformatics/bth294. November 1, 2004 2004;20(16):2626-2635.Laval G, Excoffier L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics %R 10.1093/bioinformatics/bth264. October 12, 2004 2004;20(15):2485-2487.Li L, Li H. Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics %R 10.1093/bioinformatics/bth415. December 12, 2004 2004;20(18):3406-3412.Liao B-Y, Chang Y-J, Ho J-M, Hwang M-J. The UniMarker (UM) method for synteny mapping of large genomes. Bioinformatics %R 10.1093/bioinformatics/bth380. November 22, 2004 2004;20(17):3156-3165.Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R. BacTregulators: a database of transcriptional regulators in bacteria and archaea. Bioinformatics %R 10.1093/bioinformatics/bth330. November 1, 2004 2004;20(16):2787-2791.O'Donoghue SI, Meyer JEW, Schafferhans A, Fries K. The SRS 3D module: integrating structures, sequences and features. Bioinformatics %R 10.1093/bioinformatics/bth260. October 12, 2004 2004;20(15):2476-2478.Pandey N, Ganapathi M, Kumar K, Dasgupta D, Das Sutar SK, Dash D. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins. Bioinformatics %R 10.1093/bioinformatics/bth344. November 22, 2004 2004;20(17):2904-2910.Parr CS, Lee B, Campbell D, Bederson BB. Visualizations for taxonomic and phylogenetic trees. Bioinformatics %R 10.1093/bioinformatics/bth345. November 22, 2004 2004;20(17):2997-3004.Pasquier C, Girardot F, Jevardat de Fombelle K, Christen R. THEA: ontology-driven analysis of microarray data. Bioinformatics %R 10.1093/bioinformatics/bth295. November 1, 2004 2004;20(16):2636-2643.Pochet N, De Smet F, Suykens JAK, De Moor BLR. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics %R 10.1093/bioinformatics/bth383. November 22, 2004 2004;20(17):3185-3195.Pons JL, Malliavin TE, Tramesel D, Delsuc MA. NMRb: a web-site repository for raw NMR datasets. Bioinformatics %R 10.1093/bioinformatics/bth450. December 12, 2004 2004;20(18):3707-3709.Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. CoPS: Comprehensive Peptide Signature Database. Bioinformatics %R 10.1093/bioinformatics/bth325. November 1, 2004 2004;20(16):2886-2888.

Robles JR, van den Oord EJCG. lga972: a cross-platform application for optimizing LD studies using a genetic algorithm. Bioinformatics %R 10.1093/bioinformatics/bth348. November 22, 2004 2004;20(17):3244-3245.Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics %R 10.1093/bioinformatics/bth427. December 12, 2004 2004;20(18):3462-3465.Samuelsson J, Dalevi D, Levander F, Rognvaldsson T. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics %R 10.1093/bioinformatics/bth460. December 12, 2004 2004;20(18):3628-3635.Satten GA, Datta S, Moura H, et al. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics %R 10.1093/bioinformatics/bth372. November 22, 2004 2004;20(17):3128-3136.

Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics %R 10.1093/bioinformatics/bth320. November 1, 2004 2004;20(16):2738-2750.

Kyoda K, Baba K, Onami S, Kitano H. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics %R 10.1093/bioinformatics/bth306. November 1, 2004 2004;20(16):2662-2675.

Pandey N, Ganapathi M, Kumar K, Dasgupta D, Das Sutar SK, Dash D. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins. Bioinformatics %R 10.1093/bioinformatics/bth344. November 22, 2004 2004;20(17):2904-2910.

Pochet N, De Smet F, Suykens JAK, De Moor BLR. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics %R 10.1093/bioinformatics/bth383. November 22, 2004 2004;20(17):3185-3195.

Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics %R 10.1093/bioinformatics/bth381. November 22, 2004 2004;20(17):3166-3178.

link.springer.com1… · XLS file · Web view · 2014-03-18Wright SI, Charlesworth B. The HKA...

Documents

Transcript of link.springer.com1… · XLS file · Web view · 2014-03-18Wright SI, Charlesworth B. The HKA...