IMG Related Publications 2010 · IMG Related Publications April 21st 2010 BIOLOGY 2005 1. Feil H,...

IMG Related Publications April 21st 2010

SYSTEMS 1. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Ivanova N, Kyrpides

NC. (2005) The Integrated Microbial Genomes (IMG) System, A Case Study in Biological Data Management, Proc. of 31st Int. Conf. on Very Large Data Bases.

2. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Mavromatis K, Ivanova N, Kyrpides NC. (2006) The Integrated Microbial Genomes (IMG) system. Nucleic Acids Research, 34: D344-D348.

3. Markowitz, V.M. and Kyrpides, N. (2007) Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System, book chapter in Comparative Genomics, Vol. 1, Bergman (ed.), Humana Press Inc.

4. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen I-M, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. (2008) The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Research, 36.

5. Angiuoli, S.V., Gusmman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N.C., Madupu, R., Markowitz, V.M., Tatusova, T., Thomson, N., White, O. (2008) Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation, OMICS 12 (2).

6. Hirschman, L., Clark, C., Cohen, B., Mardis, S., Luciano, J., Kottmann, R., Cole, J., Markowitz, V.M., Kyrpides, N.C., Field, D. (2008) Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata, OMICS 12 (2).

7. Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K, Kyrpides NC. (2009) Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Research, 37(7):2096-2104.

8. Markowitz, V.M., Mavromatis, K., Ivanova, N. et al. (2009) ”IMG ER: A System for Microbial Genome Annotation Expert Review and Curation”, Bioinformatics 25(17):2271-2278.

9. Mavromatis, K., Ivanova, N.N. et al. (2009) Standard Operating Procedure for the Annotations of Microbial Genomes by the Production Genomic Facility of the DOE JGI. Standards in Genomic Sciences, 1(1).

10. Mavromatis, K. et al. (2009) Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System, PLoS ONE 4(11): e7979.

11. Markowitz VM, Chen, I.A., Palaniappan K, et al. (2010) The Integrated Microbial Genomes system: an expanding comparative analysis resource. Nucleic Acids Research, 38, Database Issue.


BIOLOGY 2005

1. Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, et al. (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. PNAS, 102(31): 11064-11069.

2. Selmer T, Pierik AJ, Heider J. (2005) New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria. Biol Chem. 386(10):981-8.

3. Ren J, Kotaka M, Lockyer M, Lamb HK, Hawkins AR, Stammers DK. (2005) GTP cyclohydrolase II structure and mechanism. J Biol Chem. 280(44):36912-9

4. Groh JL, Luo Q, Ballard JD, Krumholz LR. (2005) A method adapting microarray technology for signature-tagged mutagenesis of Desulfovibrio desulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments. Appl Environ Microbiol. 71(11):7064-74.

5. Lupa, B., Lyon, D., Gibbs, M.D., Reeves, R.A., Wiegel, J. (2005) Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases, Genomics 86(3), 342-351.


2006 1. Starkenburg SR, Chain PSG, Sayavedra-Soto LA, Hauser L, Land ML, et al.

(2006) Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology, 72 (3): 2050-2063.

2. Mavromatis K, Kuyler DC, Lykidis A, Ivanova N, Francino P, et al. (2006) The genome of obligately intracellular Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Journal of Bacteriology 189:4015-4023.

3. Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, et al. (2006) Free in PMC Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol. 72(9):6299-315.

4. Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, et al. (2006) Free in PMC The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol. 4(12):e383.

5. Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol. 188(4):1473-88.

6. Scott KM, Sievert SM, Abril FN, et al. (2006) The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol. 4 (12): 2196-2212

7. Ashby MK. (2006) Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota. Archaea. 2(1):11-30

8. Ashby MK, Houmard J. (2006) Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev. 70(2):472-509

9. Nichols CE, Sainsbury S, Berrow NS, Alderton D, Saunders NJ, Stammers DK, Owens RJ. (2006) Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 A resolution. Acta Crystallograph Sect F Struct Biol Cryst Commun. 62(Pt 6):494-7

10. Liang C, Zhao F, Wei W, Wen Z, Qin S. (2006) Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics. Int J Biol Sci. 2(4):197-207.

11. Sun S, Gan JH, Paynter JJ, Tucker SJ. (2006) Cloning and functional characterization of a superfamily of microbial inwardly rectifying potassium channels. Physiol Genomics. 26(1):1-7.


12. Lau WW, Armbrust EV. (2006) Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteria. Environ Microbiol. 8(10):1688-702

13. Liang Y, Gardner DR, Miller CD, Chen D, Anderson AJ, Weimer BC, Sims RC. (2006) Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS. Appl Environ Microbiol. 72(12):7821-8

14. Argueta C, Yuksek K, Patel R, Summers ML. (2006) Identification of Nostoc punctiforme akinete-expressed genes using differential display. Mol Microbiol. 61(3):748-57

15. Hensen D, Sperling D, Truper HG, Brune DC, Dahl C. (2006) Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Mol Microbiol. 62(3):794-810.

16. Friedrich U, Lenke J. (2006) mproved enumeration of lactic acid bacteria in mesophilic dairy starter cultures by using multiplex quantitative real-time PCR and flow cytometry-fluorescence in situ hybridization. Appl Environ Microbiol. 72(6):4163-71.

17. Worden AZ, Cuvelier ML & DH Bartlett (2006). In-depth marine microbial community genomics. TRENDS in Microbiology. Vol. 14:331-336.

18. Dyhrman, S.T., Chappell, P.D., Haley, S.T., Moffett, J.W., Orchard, E.D., Waterbury, J.B, Webb, E.A. (2006) Phosphonate utilization by the globally important marine diazotroph Trichodesmium, Nature 439.

19. Lu, Y.J., Zhang, Y.M., Grimes, K.D., Qi, J., Lee, R.E., Rock, C.O. (2006) Acyl-Phosphates Initiate Membrane Phospholipid Synthesis in Gram-Positive Pathogens, Molecular Cell 23, 765-772.

20. Chain, P., Denef, V.J., et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility, PNAS 103(42), 15280-15287.

21. Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C. et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum, PNAS 103(48), 18296-18301.

22. Culley, D.E., Kovacik, W.P., Brockman, F.J., Zhang, W. (2006) Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis, Journal of Microbiological Methods 67(1), 36-43.

23. Bryant, D.A., Frigaard, N.U. (2006) Prokaryotic photosynthesis and phototrophy illuminated, Trends in Microbiology 14(11), 488-496.

24. Chew, A.G.M. and Bryant, D.A. (2006) Characterization of Plant-Like Protochloropyllide A Divinyl Reductase in Green Sulfur Bacteria, Journal of Biological Chemistry.


25. Gralnick, J.A., Vali, H., Lies, D.P., Newman, D.K. (2006) Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1, PNAS 103(12), 4669-4674.

26. Wu, Q., Pei, J., Turse, C., Ficht, T.A. (2006) Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival, BMC Microbiology 6:102.


2007 1. Maeder DL, Anderson A, Brettin TS, Bruce DC, Gilna P, et al. (2007) The

Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes. Journal of Bacteriology 188(22): 7922-7931.

2. Morth, J.P., Gosmann, S., Nowak, E., and Tucker, P.A. (2007) A novel two-component system found in Mycobacterium tuberculosis Federation of European Biochemical Societies (FEBS) Letters 579 (19), 4145-4148.

3. Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, et al. (2007) Genome sequence and analysis of soil cellulolytic actinomyceteTthermobifida fusca YX. Journal of Bacteriology, 189(6): 2477-2486.

4. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res. 17(1):7-15.

5. Kerfeld CA, Simons RW (2007) The undergraduate genomics research initiative. PLoS Biol. (5): 980-983 .

6. Normand P, Lapierre P, Tisa LS, et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp strains reflect host range and host plant biogeography. Genome Res. 17 (1): 7-15.

7. Zhao F, Qin S. (2007) Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus. Genetica. 129(3):291-9

8. Kim SJ, Kweon O, Jones RC, Freeman JP, Edmondson RD, Cerniglia CE. (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol. 189(2):464-72.

9. Rodrigues DF, Tiedje JM. (2007) Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost. FEMS Microbiol Ecol. 59(2):489-99

10. Chew AG, Bryant DA. (2007) Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J Biol Chem. 282(5):2967-75

11. Kim HJ, Nam HS, Anderson AJ, Yang KY, Cho BH, Kim YC. (2007) Mutation in the edd gene encoding the 6-phosphogluconate dehydratase of Pseudomonas chlororaphis O6 impairs root colonization and is correlated with reduced induction of systemic resistance. Lett Appl Microbiol. 44(1):56-61.

12. Chen F, Wang K, Stewart J, Belas R. (2007) Free in PMC Induction of multiple prophages from a marine bacterium: a genomic approach. Appl Environ Microbiol. 72(7):4995-5001.

13. Xu Y, Labedan B, Glansdorff N. (2007) Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms. Microbiol Mol Biol Rev. 71(1):36-47.


14. Fischer WW, Pearson A. (2007) Hypotheses for the origin and early evolution of triterpenoid cyclases Geobiology 5(1):19-34.

15. Xie G, Bruce DC, Challacombe JF, Chertkov O, et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appied and Environmental Microbioliogy 73 (11):3536-46.

16. Fuhrer, T., Chen, L., Sauer, U., Vitkup, D. (2007) Computational Prediction and Experimental Verification of the Gene Encoding the NAD+/NADP+-Dependent Succinate Semialdehyde Dehydrogenase in Escherichia coli, Journal of Bacteriology 189(22), 8073-8078.

17. Yu, M., Faan, Y.W., Chung, W.Y.C., Tsang, J.S.H. (2007) Isolation and Characterization of a Novel Haloacid Permease from Burkholderia cepacia MBA4, Applied and Environmental Microbiology, Vol. 73, No. 15, p. 4874-4880.

18. Passel, M.W.J., Smillie, C.S., Ochman, H. (2007) Gene decay in archaea. Archaea 2, 137-143.

19. Achour, A.R., Billard, P.B. (2007) Diversity of arsenite transporter genes from arsenic-resistant soil bacteria. Research in Microbiology 158(2), 128-137.

20. Kehrer D, Ahmed H, Brinkmann H, Siebers B. (2007) Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes. BMC Genomics. 8:301.

21. Simmons SL, Bazylinski DA, Edwards KJ. (2007) Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR. Environmental Microbiology 9(9):2162-74.

22. Gendlina I, Held KG, Bartra SS, Gallis BM, Doneanu CE, Goodlett DR, Plano GV, Collins CM. (2007) Identification and type III-dependent secretion of the Yersinia pestis insecticidal-like proteins. Mol Microbiol. 64(5):1214-27.

23. Frigaard, N.U., and Bryant, D.A. (2007) Genomic and Evolutionary Perspectives on Sulfur Metabolism in Green Sulfur Bacteria. In Microbial Sulfur Metabolism, Springer, 60-76.

24. Galindo, E., Pena, C., Nunez, C., Segura, D., Espin, G. (2007) Molecular and bioengineering strategies to improve alginate and polydydroxyalkanoate production by Azotobacter vinelandii, Microbial Cell Factories 6: 7.

25. Udwary, D.W., Zeigler, L., Asolkar, R.N., Singan, V. et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica, PNAS 104(25), 10376-10381.

26. Schell, M.A., Ulrich, R.L.,. Ribot, W.J., et al. (2007) Type VI secretion is a major virulence determinant in Burkholderia mallei,Molecular Microbiology 64 (6) , 1466–1485.

27. Grabov A. (2007) Plant KT/KUP/HAK Potassium Transporters: Single Family – Multiple Functions, Annals of Botany 99(6):1035-1041.


28. N. Vermeulen, M.G. Gänzle, R.F. Vogel (2007) Glutamine deamidation by cereal-associated lactic acid bacteria, Journal of Applied Microbiology 103 (4) , 1197–1205.

29. Guan, X., Qin, S., Zhao, F., Zhang, X., Tang, X. (2007) Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution, Int J Biol Sci. 3(7): 434–445.

30. Normand, P., Queiroux, C., Tisa, L.S., et al. (2007) Exploring the genomes of Frankia, Physiologia Plantarum 130 (3) , 331–343.

31. N. Vermeulen, M.G. Gänzle, R.F. Vogel (2007) Glutamine deamidation by cereal-associated lactic acid bacteria, Journal of Applied Microbiology 103 (4) , 1197–1205.

32. Flanagan, J.U., Huber, T. (2007), Structural Evolution of the ABC Transporter Subfamily B, Evolutionary Bioinformatics 3, 309-316.

33. Makarova, K.S., Omelchenko, M.V., Gaidamakova, E.K. et al. (2007) Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks, PLoS ONE 2(9).

34. Arp, D.J., Chain, P.S.G., Klotz, M.G. (2007) The Impact of Genome Analyses on Our Understanding of Ammonia-Oxidizing Bacteria, Annual Review of Microbiology 61, 503-528.

35. Lau, W.W.Y., Keil, R.G., Armbrust, E.V. (2007) Succession and Diel Transcriptional Response of the Glycolate-Utilizing Component of the Bacterial Community during a Spring Phytoplankton Bloom, Applied and Environmental Microbiology 73 (8), 2440-2450.

36. Woodger, F.J., Bryant, D.A., Price, G.D. (2007) Transcriptional Regulation of the CO2-Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR, Journal of Bacteriology 189(9), 3335-3347.

37. Pearson, A., Flood Page, S.R., Jorgenson, T.L., Fischer, W.W., Higgins, M.B. (2007) Novel hopanoid cyclases from the environment Environmental Microbiology 9 (9) , 2175–2188.

38. Meyer, B., Imhoff, J.F., Kuever J. (2007) Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - evolution of the Sox sulfur oxidation enzyme system, Environmental Microbiology 9 (12) , 2957–2977.

39. Cherif-Zahar, B., Durand, A., Schmidt, I. et al. (2007) Evolution and Functional Characterization of the RH50 Gene from the Ammonia-Oxidizing Bacterium Nitrosomonas europaea, Journal of Bacteriology 189 (24), 9090-9100.

40. Zhang, X., Zhao, F., Guan, X., Yang, Y., Liang, C., Qin, S. (2007) Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria, BMC Genomics 8: 395.


41. Fischer, W. W. and Pearson, A. (2007) Hypotheses for the origin and early evolution of triterpenoid cyclases, Geobiology 5 (1) , 19–34.

42. Suen, G, Goldman, B.S., Welch, R.D. (2007) Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis, PLoS ONE 2(8).

43. Tabita, F.R., Hanson, T.E., Li, H. et al. (2007) Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs, Microbiology and Molecular Biology Reviews, 71 (4), 576-599.

44. Granja, A.T., Popescu, A., Marques, A.R., Sa-Correia, I., Fialho, A.M. (2007) Biochemical characterization and phylogenetic analysis of UDP-glucose dehydrogenase from the gellan gum producer Sphingomonas elodea ATCC 31461, Applied Microbiology and Biotechnology 76(6), 1319-1327.

45. Sen, G., Sur, S., Bose, D. et al. (2007) Analysis of Codon Usage Patterns and Predicted Highly Expressed Genes for Six Phytopathogenic Xanthomonas Genomes Shows a High Degree of Conservation, In Silico Biology 7(4-5), 547-558.

46. Stephens, C. Christen, B., et al. (2007) Regulation of D-Xylose Metabolism in Caulobacter crescentus by a LacI-Type Repressor, Journal of Bacteriology, 189(24), 8828-8834.

47. Kirkland, P.A., Reuter, C.J., and Maupin-Furlow, J.A. (2007) Effect of proteasome inhibitor clasto-lactacystin-β-lactone on the proteome of the haloarchaeon Haloferax volcanii, Microbiology 153, 2271-2280.

48. T. de Vrije, A. E. Mars, M. A. W. Budde, M. H. Lai, C. Dijkema, P. de Waard and P. A. M. Claassen (2007) Glycolytic pathway and hydrogen yield studies of the extreme thermophile Caldicellulosiruptor saccharolyticus, Applied Microbiology and Biotechnology 74(6), 1358-1367.

49. Meyer, B., and Kuever, J. (2007) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway, Microbiology 153, 2026-2044.

50. Meyer, B., and Kuever, J. (2007) Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5'-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes, Microbiology 153, 3478-3498.

51. Vigneuz, F., Zumbihl, R., Jubelin, G. et al. (2007) The xaxAB Genes Encoding a New Apoptotic Toxin from the Insect Pathogen Xenorhabdus nematophila Are Present in Plant and Human Pathogens, J. Biol. Chem. 282 (13), 9571-9580.

52. Beck, L.L., Smith, T.G., Hoover, T.R. (2007) Look, no hands! Unconventional transcriptional activators in bacteria, Trends in Microbiology 15(12), 530-537.

53. Paz-Yepes, J., Herrero, A., and Flores, E. (2007) The NtcA-Regulated amtB Gene Is Necessary for Full Methylammonium Uptake Activity in the Cyanobacterium Synechococcus elongates, Journal of Bacteriology, 189(21) , 7791-7798.


54. Campbell, E.L., Summers, M.L., Christman, H., Martin, M.E., Meeks, J.C. (2007) Global Gene Expression Patterns of Nostoc punctiforme in Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia, Journal of Bacteriology 189(14), 5247-5256.

55. Mikucki, J.A., and Priscu, J.C. (2007) Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica, Applied and Environmental Microbiology 73(12), 4029-4039.

56. Hau, H.H., and Gralnick, J.A. (2007) Ecology and Biotechnology of the Genus Shewanella, Annual Review of Microbiology 61, 237-258.

57. Kapteyn, J., Qualley, A.V., Xie, Z., Fridman, E., Dudareva, N., and Gang, D.R. (2007) Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate, The Plant Cell 19, 3212-3229.

58. Mavrodi, D.V., Paulsen, I.T., Ren, Q., Loper, J.E. (2007) Genomics of Pseudomonas fluorescens Pf-5, in Pseudomonas, Springer, 3-30.

59. Yang Y, Qin S, et al. (2007) Comparison of envelope-related genes in unicellular and filamentous cyanobacteria. Comp Funct Genomics 2007: 25751.

60. Jin H, Retallack DM, et al. (2007) Characterization of the SOS response of Pseudomonas fluorescens strain DC206 using whole-genome transcript analysis. FEMS Microbiol Lett 269(2): 256-264.


2008 1. Badger, M.R. and Bek, E.J. (2008) Multiple Rubisco forms in proteobacteria:

their functional significance in relation to CO2 acquisition by the CBB cycle, Journal of Experimental Botany.

2. Brinkhoff, T. Giebel, H.A., and Simon, M. (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Archives of Microbiology 189(6), 531-539.

3. Chen, D.E., Podell, S., Sauer, J.D., Swanson, M.S., and Saier, M.H. (2008) The phagosomal nutrient transporter (Pht) family, Microbiology 154, 42-53.

4. Suarez, G., Sierra, J.C., Sha, J. et al. (2008) Molecular characterization of a functional type VI secretion system from a clinical isolate of Aeromonas hydrophila. Microbial Pathogenesis 44(4), 344-361.

5. Mastronunzio, J.E., Tisa, L.S., Normand, P., and Benson, D.R. (2008) Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts, BMC Genomics 9: 47.

6. Norton, J.M., Klotz, M.G., Stein, L.Y., et al. (2008) Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment, Appl. Environ. Microbiol. 74(11): 3559-3572,

7. El Sheikh, A., Poret-Peterson, A.T., and Klotz, M.G. (2008) Characterization of Two New Genes, amoR and amoD, in the amo Operon of the Marine Ammonia Oxidizer Nitrosococcus oceani ATCC 19707, Applied and Environmental Microbiology, 74(1), 312-318.

8. Elizaquível, P., Chenoll, E., Aznar, R. (2008) A TaqMan-based real-time PCR assay for the specific detection and quantification of Leuconostoc mesenteroides in meat products, FEMS Microbiology Letters 278 (1) , 62–71

9. Shen, G., Schluchter, W.M., Bryant, D.A. (2008) Biogenesis of Phycobiliproteins. I. cpcS-I and cpcU Mutants of the Cyanobacterium Synechococcus SP. PCC 7002 Define a Heterodimeric Phyococyanobilin Lyase Specific for β-Phyocacyanin and Allophycocyanin Subunits. Journal of Biological Chemistry 238(12), 7503-7512.

10. Lapidus, A., Goltsman, E. Auger, S. et al. (2008) Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity, Chemico-Biological Interactions 171(2), 236-249.

11. Kilian, O., Steunou, A.S.,. Grossman, A.R., and Bhaya D. (2008) A Novel Two Domain-Fusion Protein in Cyanobacteria with Similarity to the CAB/ELIP/HLIP Superfamily: Evolutionary Implications and Regulation, Molecular Plant 1(1):155-166.

12. Pinchuk, G.E., Ammons, C., Culley, D.E. et al. (2008) Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction, Applied and Environmental Microbiology, 74(4), 1198-1208.


13. Naponelli, V., Noiriel, A., Ziemak, M.J. et al. (2008) Phylogenomic and Functional Analysis of Pterin-4a-Carbinolamine Dehydratase Family (COG2154) Proteins in Plants and Microorganisms, Plant Physiology 146:1515-1527.

14. Sen, A., Sur, S. Bothra, A.K. et al. (2008) The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes, Antonie van Leeuwenhoek 93(4), 335-346.

15. Shell, M.A., Lipscomb, L., and DeShazer, D. (2008), Comparative Genomics and an Insect Model Rapidly Identify Novel Virulence Genes of Burkholderia mallei, Jpurnal of Bacteriology, 190(7), 2306-2313.

16. Sutcliffe, I.C., Black, G.W., and Harrington, D.J. (2008) Bioinformatic insights into the biosynthesis of the Group B carbohydrate in Streptococcus agalactiae, Microbiology 154 (2008), 1354-1363.

17. Crabbé, A., De Boever, P., Van Houdt, R., Moors, H., Mergeay, M., Cornelis, P. (2008) Use of the rotating wall vessel technology to study the effect of shear stress on growth behaviour of Pseudomonas aeruginosa PA01, Environmental Microbiology.

18. Vinatzer, B., Yan, S. (2008) Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence, Molecular Plant Pathology 9(1) , 105–118.

19. Gao, H., Wang, X., Yang, Z.K., Palzkill, T., and Zhou, J. (2008) Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses, BMC Genomics 9:42.

20. Chan, L.K., Weber, T.S., Morgan-Kiss, R.M., Hanson, T.E. (2008) A genomic region required for phototrophic thiosulfate oxidation in the green sulfur bacterium Chlorobium tepidum (syn. Chlorobaculum tepidum), Microbiology 154, 818-829.

21. Haverkamp, T., Acinas, S.G., Doeleman, M., Stomp, M., Huisman, J., Stal L.J. (2008) Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons, Environmental Microbiology 10 (1) , 174–188.

22. Ettema, T.J.G., Ahmed, H., Geerling, A.C.M., der Oost, J., Siebers, B. (2008) The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus : a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway, Extremophiles 12(1), 75-88.

23. Caffrey, S.M., Park, H.S., Been, J., Gordon, P, Sensen, C.W., Voordouw, G. (2008). Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions, Applied and Environmental Microbiology, 74(8), 2404-2413.

24. Zhao, J.S., Manno, D., and Hawari, J. (2008) Regulation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) metabolism in Shewanella halifaxensis HAW-EB4 by terminal electron acceptor and involvement of c-type cytochrome, Microbiology 154, 1026-1037.


25. Talbot, G., Topp, E., Palin, M.F., Masse, D.I. (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in

26. Elkins, G.J., Podar, M. et al (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. Proc PNAS 105(23):8102-7.

27. Grzymski, J.J., Murray, A.E. et al. (2008) Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility, PNAS 105 (45):17516-17521.

28. Podar, M., Anderson, I., Makarova, K.S., Elkins, J.G. et al. (2008) A genomic analysis of the archaeal system Ignicoccus hospitalis: Nanoarchaeum equitans. Genome Biology 9(11).

29. Thomas T, Evans FF, et al. (2008) Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS ONE 3(9): e3252.

30. van de Werken HJ, Verhaart MR, et al. (2008) Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 74(21): 6720-6729.

31. Chen DE, Podell S, et al. (2008) The phagosomal nutrient transporter (Pht) family. Microbiology 154: 42-53.

32. Anderson MT and Armstrong SK. (2008) Norepinephrine mediates acquisition of transferrin-iron in Bordetella bronchiseptica. J Bacteriol. 190 (11):3940-3947.

33. Reysenbach AL and Flores GE. (2008) Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei. Geobiology 6(3): 331-336.

34. Chan LK, Weber TS et al. (2008) A genomic region required for phototrophic thiosulfate oxidation in the green sulfur bacterium Chlorobium tepidum (syn. Chlorobaculum tepidum). Microbiology 154: 818-829.

35. Tamura M and D’haeseleer P. (2008) Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics 24(13): 1523-1529.

36. Matz C, Webb JS, Schupp PJ, et al. (2008) Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense , PLoS ONE 3(7): e2744.

37. Rodrigues DF, Ivanova N, He A, Huebner M, et al. (2008) Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 9(1):547.

38. Mondal UK, Sur S, Bothra AK, Sen A (2008) Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes. Indian Journal of Medical Microbiology 26(4): 313-321.

39. Plugge CM et al. (2008) Effect of tungsten and molybdenum on growth of a syntrophic coculture of Syntrophobacter fumaroxidans and Methanospirillum hungatei. Archives of Microbiology.


40. Karl DM et al. (2008) Aerobic production of methane in the sea. Nature Geosciences 1:473-478.

41. Hesse H et al. (2008) Metabolism of Methionine in Plants and Phototrophic Bacteria. Sulfur Metabolism in Phototropic Organisms, Advances in Photosynthesis and Respiration vol. 27, Springer.

42. Chi X et al. (2008) Comparative analysis of fatty acid desturases in cyanobacterial genomes. Comparative and Functional Genomics, Hindawi Publishing Corporoation.

43. West KA et al. (2008) Comparative Genomics of "Dehalococcoides ethenogenes" 195 and an Enrichment Culture Containing Unsequenced "Dehalococcoides" Strains. Applied and Environmental Microbiology 74(11): 3533-3540.

44. Leon R and Espin G (2008) flhDC, but not fleQ, regulates flagella biogenesis in Azotobacter vinelandii, and is under AlgU and CydR negative control. Microbiology 154: 1719-1728.

45. Atlas et al. (2008) Archaeal genomes. Encyclopedia of Life Sciences. John Wiley & Sons.

46. Riley M et al. (2008) Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9:210.

47. Mastronunzio JE et al. (2008) Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts. BMC Genomics 9:47.

48. Lopez-Sanchez et al. (2008) Blattabacteria, the endosymbionts of cockroaches, have small genome sizes and high genome copy numbers. Environmental Microbiology 10(12): 3417-3422.

49. Burghardt T et al. (2008) Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis : the major cytosolic and membrane proteins. Archives of Microbiology 190(3): 379-394.

50. Gabor K et al. (2008) Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression. Microbiology 154: 3686-3696.

51. Maresca JA et al. (2008) Isorenieratene Biosynthesis in Green Sulfur Bacteria Requires the Cooperative Actions of Two Carotenoid Cyclases, Journal of Bacteriology 190(19): 6384-6391.

52. Huber H et al. (2008) A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. PNAS 105(22): 7851-7856.

53. Wu J et al. (2008) Lineage-Specific Domain Fusion in the Evolution of Purine Nucleotide Cyclases in Cyanobacteria. Journal of Molecular Evolution 67(1): 85-94.


54. Kouril T et al. (2008) A novel trehalose synthesizing pathway in the hyperthermophilic Crenarchaeon Thermoproteus tenax : the unidirectional TreT pathway. Archives of Microbiology 190(3): 355-369.

55. Kim SJ et al. (2008) Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19(6): 859-881.

56. Dufour YS et al. (2008) Organization and Evolution of the Biological Response to Singlet Oxygen Stress. Journal of Molecular Biology 383(3): 713-730.

57. Sutcliffe IA et al. (2008) Bioinformatic insights into the biosynthesis of the Group B carbohydrate in Streptococcus agalactiae Microbiology 154: 1354-1363.

58. Bernardelli CE et al. (2008) Symbiotic phenotype of a membrane-bound glucose dehydrogenase mutant of Sinorhizobium meliloti. Plant and Soil.

59. Schell MA et al. (2008) Comparative Genomics and an Insect Model Rapidly Identify Novel Virulence Genes of Burkholderia mallei. Journal of Bacteriology 190 (7):2306-2313.

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2009

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2. Ward NL et al. (2009) Three genomes from the phylum Acidobacteria provide insight into their lifestyles of these microorganisms in soils. Appl Environ Microbiol. 75(7): 2046-2056.

3. Unden G and Zaunmuller T (2009) Metabolism of Sugars and Organic Acids by Lactic Acid Bacteria from Wine and Must. Book chapter in Biology of Microorganisms on Grapes, in Must and in Wine. Springer.

4. Hunter N, Daldal F, Thurnauer MC, and Beatty JT (2009) Dissimilatory and Assimilatory Nitrate Reduction in the Purple Photosynthetic Bacteria. Advances in Photosynthesis and Respiration vol. 28, Springer, pp. 623-642.

5. Choudhary M et al. (2009) Purple Bacterial Genomics. Advances in Photosynthesis and Respiration vol. 28, Springer, pp. 691-706.

6. Mavromatis K et al. (2009) Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii. PLoS ONE 4(1):e4192.

7. Herlemann DPR et al. (2009) Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1). Applied and Environmental Microbiology.

8. Núñez et al. (2009) The Na+-translocating NADH : ubiquinone oxidoreductase of Azotobacter vinelandii negatively regulates alginate synthesis. Microbiology 155: 249-256.

9. Garcia-Migura L et al. (2009) Presence of pRI1: A Small Cryptic Mobilizable Plasmid Isolated from Enterococcus faecium of Human and Animal Origin. Current Microbiology, Springer.

10. Taghavi S et al. (2009) Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees. Applied and Environmental Microbiology 75(3): 748-757.

11. Passalacqua KD et al. (2009) Comparative Transcriptional Profiling of Bacillus cereus Sensu Lato Strains during Growth in CO2-Bicarbonate and Aerobic Atmospheres. PLoS ONE. 4(3): e4904.

12. Henne KL et al. (2009) Global Proteomic Analysis of the Chromate Response in Arthrobacter sp. Strain FB24. Journal of Proteome Research.

13. Lin S et al. (2009) Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyceae): Remarkable sequence divergence and possible functional diversification. Journal of Experimental Marine Biology and Ecology 371(1): 93-101.

14. Sankar TS et al. (2009) Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli. PLoS Genet. 5(3): e1000405.


15. Biers EJ et al. (2009) Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton. Applied and Environmental Microbiology 74(10): 2933-2939.

16. Fonknechten N et al. (2009) A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine. Journal of Bacteriology 191 (9): 3162-3167.

17. Collado-Vides J et al. (2009) Bioinformatics Resources for the Study of Gene Regulation in Bacteria. Journal of Bacteriology 191(1): 23-31.

18. Hudek L et al. (2009) Bioinformatic and Expression Analyses of Genes Mediating Zinc Homeostasis in Nostoc punctiforme. Applied and Environmental Microbiology 75(3): 784-791.

19. Durot M et al. (2009) Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiology Reviews 33(1): 164-190.

20. Lönn-Stensrud J et al. (2009) Furanones, potential agents for preventing Staphylococcus epidermidis biofilm infections? Journal of Antimicrobial Chemotherapy 63(2):309-316

21. Sharma, K.K. and Kuhad, R.C. (2009) An evidence of laccases in archaea. Indian Journal of Microbiology 49(2): 142-150.

22. Shapleigh, P.J. (2009) Dissimilarity and Assimilatory Nitrate Reduction in the Purple Photosynthetic Bacteria, The Purple Phototropic Bacteria, Springer: 623-642.

23. Woyke, T., Xie, G., Copeland, A. et al. (2009) Assembling the Marine Metagenome, Once Cell at a Time. PLoS One 4(4): e5299.

24. Johnson, D.R., Nemir, A., Andersen, G.L. et al. (2009) Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiology Letters 294(2): 198-206.

25. Hooper, S.D., Mavaromatis, K., and Kyrpides, N.C. (2009) Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biology 10(4).

26. Feng, X., Mouttaki, H., Lin, L. et al. (2009) Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. X514 via Isotopomer-Assisted Metabolite Analysis. Applied and Environmental Microbiology.

27. Klassen, J.L., McKay, R., and Foght, J.M. (2009) 2′-Methyl and 1′-xylosyl derivatives of 2′-hydroxyflexixanthin are major carotenoids of Hymenobacter species. Tetrahedron Letters 50(22): 2656-2660.

28. Yagi, J.M., Sims, D., Brettin, T., Bruce, D. and Madsen, E.L. (2009) The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer. Environmental Microbiology.


29. Richey, C., Chovanec, P., Hoeft, S.E., et al. (2009) Respiratory arsenate reductase as a bidirectional enzyme. Biochemical and Biophysical Research Communications 382(2): 298-302.

30. Bosch, G., Wang, T., Latypova, E., et al (2009) Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis, Microbiology 155: 1103-1110.

31. O’Flaherty S., Goh, Y.J., and Klaenhammer, T.R. (2009) Genomics of Probiotic Bacteria, Prebiotics and Probiotics Science and Technology, Springer: 681-723.

32. Alen, M.A., Lauro, F.M., Williams, T.J., Burg, D. et al. (2009) The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME Journal, doi: 10.1038/ismej.2009.45.

33. Schubbe, S., Williams, T.J., Xie, G. et al. (2009) Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1. Applied and Environmental Microbiology, doi:10.1128/AEM.02874-08.

34. Barabote, R.D., Xie, G., Normand, P., et al. (2009) Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations, Genome Research 19: 1033-1043.

35. Martinez, I., Wallace, G., Zhang, C., et al. (2009) Diet-Induced Metabolic Improvements in a Hamster Model of Hypercholesterolemia Are Strongly Linked to Alterations of the Gut Microbiota, Applied and Environmental Microbiology 75(12): 4175-4184.

36. Vissa, V.D., Sakamuri, R.M., Li, W., and Brennan, P.J. (2009) Defining mycobacteria: Shared and specific genome features for different lifestyles. Indian Journal of Microbiology 49(1): 11-47.

37. Zhang, J.Y., Chen, W.L., and Zhang, C.C. (2009) hetR and patS, two genes necessary for heterocyst pattern formation, are widespread in filamentous nonheterocyst-forming cyanobacteria, Microbiology 155: 1418-1426.

38. Lecher, J., Pittelkow, M., Zobel, S., et al. (2009) The Crystal Structure of UehA in Complex with Ectoine—A Comparison with Other TRAP-T Binding Proteins, Journal of Molecular Biology 389(1): 58-73.

39. Ardley, J.K., O’Hara, G.W., Reeve, W.G. et al. (2009) Root nodule bacteria isolated from South African Lotononis bainesii, L. listii and L. solitudinis are species of Methylobacterium that are unable to utilize methanol, Archives of Microbiology (4): 311-318.

40. Pearson, A., Leavitt, W.D., Saenz, J.P., et al. (2009) Diversity of hopanoids and squalene-hopene cyclases across a tropical land-sea gradient. Environmental Microbiology 11(5): 1208-1223.

41. Graham, J.E. and Bryant, D.A. (2009) The Biosynthetic Pathway for Myxol-2' Fucoside (Myxoxanthophyll) in the Cyanobacterium Synechococcus sp. Strain PCC 7002, Journal of Bacteriology 191(10): 3292-3300.


42. Gan, H.M., Buckley, L., Szegedi, E., et al. (2009) Identification of an rsh Gene from a Novosphingobium sp. Necessary for Quorum-Sensing Signal Accumulation, Journal of Bacteriology 191(8): 2551-2560.

43. Kolsto, A.B. (2009) What Sets Bacillus anthracis Apart from Other Bacillus Species? Annual Review of Microbiology 63.

44. Chistoserdova, L., Kalyuzhnaya, M.G., and Lidstrom, M.E. (2009) The Expanding World of Methylotrophic Metabolism, Annual Review of Microbiology 63.

45. Anderson, I., Dharmarajan, L., Rodriguez, J. et al. (2009) The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota, BMC Genomics 10:145doi:10.1186/1471-2164-10-145

46. Campbell, B.J., Smith, J.L., Hanson, T.E. et al. (2009) Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola, PLoS Genetics 5(2): e1000362. doi:10.1371/journal.pgen.1000362.

47. Sankar, T.S., Neelakanta, G., Sangal, V. et al. (2009) Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli, PLoS Genetics 5(3): e1000405. doi:10.1371/journal.pgen.1000405.

48. Slater, S.C., Goldman, B.S., Goodner, B. et al. (2009) Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria, Journal of Bacteriology 191(8): 2501-2511.

49. Wilkins, M.J., VerBerkmoes, N.C., Williams, K.H. et al. (2009) Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation, Applied and Environmental Microbiology 75(20): 6591-6599.

50. Unell, M., Abraham, P.E., Shah, M. et al. (2009) Impact of Phenolic Substrate and Growth Temperature on the Arthrobacter chlorophenolicus Proteome. Journal of Proteome Research 8(4): 1953-1964.

51. Hou, Y. and Lin, S. (2009) Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes. PLoS One 4(9): e6978.

52. Henne KL et al. (2009) High-level chromate resistance in Arthrobacter sp. Strain FB24 requires previously uncharacterized accessory genes. BMC Microbiology, 9:199.

53. McMurdie, P.J., Behrens, S.F., Muller, J.A. et al. (2009) Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides, PLoS Genetics 5(11): e1000714.

54. Hooper, S.D., Mavromatis, K., and Kyrpides, N.C. (2009) Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biology 10: R45.

55. Freilich S., Goldovsky, L., Gottlieb, A. et al. (2009) Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics, 10:355.


56. Grana, M., Bellinzoni, M. et al. (2009) Structure of Mycobacterium tuberculosis Rv2714, a representative of a duplicated gene family in Actinobacteria, Acta Crystallographica Section F 65: 972-977.

57. Feist, A.M., Herrgard, M.J., Thiele, I., et al. (2009) Reconstruction of biochemical networks in microorganisms, Nature Reviews, Microbiology, 7: 129-143.

58. Thomas, H., Huang, L., et al. (2009) Evolution of plant senescence. BMC Evolutionary Biology 9:163.

59. Slightom, R.N. and Buchan, A. (2009) Surface Colonization by Marine Roseobacters: Integrating Genotype and Phenotype, Applied and Environmental Microbiology, 75(19): 6027-6037.

60. Van der Oost, J. Jore, M.M., Westra, E.R. et al. (2009) CRISPR-based adaptive and heritable immunity in prokaryotes, Trends in Biochemical Sciences 34(8): 401-407.

61. Coats, V., Schwintzer, C.R. et al. (2009) Truncated hemoglobins in Frankia CcI3: effects of nitrogen source, oxygen concentration, and nitric oxide, Canadian Journal of Microbiology 55(7): 867-873.

62. Guo, Y.B., Li, J., et al. (2009) Mutations that disrupt either the pqq or gdh genes abolish the production of the antibacterial substance by Rahnella aquatilis and cause reduced biological control of grapevine crown gall, Appl. Environ. Microbiol. doi:10.1128/AEM.00902-09.

63. Twine, S.M., Reid, C.W., Aubry, A. et al. (2009) Motility and Flagellar Glycosylation in Clostridium difficile, Journal of Bacteriology, 191(22): 7050-7062.

64. Wang Q, Yang M, Xiao J, Wu H, Wang X, et al. (2009) Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches. PLoS ONE 4(10): e7646.

65. McBride, M.J., Xie, G., Martens, E.C., Lapidus, A., et al. (2009) Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis, Applied and Environmental Microbiology, 75(21): 6864-6875.

66. Cai, H., Thompson, R. et al. (2009) Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution, Genome Biology and Evolution.

67. Graham J.E. and Bryant D.A. (2009) The Biosynthetic Pathway for Myxol-2' Fucoside (Myxoxanthophyll) in the Cyanobacterium Synechococcus sp. Strain PCC 7002, Journal of Bacteriology, 191(10): 3292-3300.

68. Satapathy, S.S., Dutta, M., et al. (2009) Variable correlation of genome GC% with transfer RNA number as well as with transfer RNA diversity among bacterial groups: α-Proteobacteria and Tenericutes exhibit strong positive correlation, Microbiological Research.


69. Marta V. Rodrigues, M.V., Nuno Borges, N., Carla P. Almeida, C.P. et al. (2009) A Unique β-1,2-Mannosyltransferase of Thermotoga maritima That Uses Di-myo-Inositol Phosphate as the Mannosyl Acceptor, Journal of Bacteriology, 191(19): 6105-6115.

70. Wu D et al., (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea", Nature 462: 1056-1060.

71. Mavromatis K et al., (2009) Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System, PLoS One. 4(11): e7979.

72. Bodaker, I., et al. (2009) Comparative community genomics in the Dead Sea: an increasingly extreme environment", The ISME Journal 4: 399-407.

73. Xue, F., Yan, J., and Picardeau, M. (2009) Evolution and pathogenesis of Leptospira spp.: lessons learned from the genomes, Microbes and Infection 11(3): 328-333.

74. Sen A et al., (2009) Homology modelling of the Frankia nitrogenase iron protein, Symbiosis, Springer Netherlands, 37-44.

Short Genome Reports (Standards in Genomic Sciences) 75. Lapidus et al. (2009) Complete genome sequence of Brachybacterium faecium

type strain (Schefferle 6-10T), Standards in Genomic Sciences, 1(1).

76. Sims, et al. (2009) Complete genome sequence of Kytococcus sedentarius type strain (strain 541T), Standards in Genomic Sciences, 1(1).

77. Land, et al. (2009) Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T), Standards in Genomic Sciences, 1(1).

78. Copeland et al. (2009) Complete genome sequence of Desulfomicrobium baculatum type strain (X), Standards in Genomic Sciences, 1(1).

79. Clum et al. (2009) Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT), Standards in Genomic Sciences, 1(1).

80. Land et al. (2009) Complete genome sequence of Actinosynnema mirum type strain (101T), Standards in Genomic Sciences, 1(1).

81. Ham et al. (2009) Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

82. Mavrommatis, K. et al. (2009) Complete genome sequence of Cryptobacterium curtum type strain (12-3T), Standards in Genomic Sciences, 1(2).

83. Mavrommatis et al. (2009) Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T), Standards in Genomic Sciences, 1(2).

84. Ivanova, et al. (2009) Complete genome sequence of Sanguibacter keddieii type strain (ST-74T), Standards in Genomic Sciences, 1(2).

85. Copeland et al. (2009) Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T), Standards in Genomic Sciences, 1(2).

86. Ivanova, et al. (2009) Complete genome sequence of Leptotrichia buccalis type strain C-1013-bT), Standards in Genomic Sciences, 1(2).


87. Lang et al. (2009) Complete genome sequence of Dyadobacter fermentans type strain (NS114T), Standards in Genomic Sciences, 1(2).

88. Pati et al. (2009) Complete genome sequence of Saccharomonospora viridis type strain (P101T), Standards in Genomic Sciences, 1(2).

89. Malfatti, et al. (2009) Complete genome sequence of Halogeometricum borinquense type strain (PR3T), Standards in Genomic Sciences, 1(2).

90. Labutti, et al. (2009) Complete genome sequence of Anaerococcus prevotii type strain (PC1T), Standards in Genomic Sciences, 1(2).

91. Saunders, et al. (2009) Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T), Standards in Genomic Sciences, 1(2).

92. Copeland, et al. (2009) Complete genome sequence of Atopobium parvulum type strain (IPP 1246T), Standards in Genomic Sciences, 1(2).


2010 1. Woyke T et al., (2010) Metagenomic Analysis of Microbial Symbionts in a

Gutless Worm, eScholarship, Lawrence Berkeley National Laboratory. 2. Thrash J.C. et al., (2010) Genome Sequence of Lentisphaera araneosa

HTCC2155T, the 1 type species of the 2 order Lentisphaerales in the phylum Lentisphaerae", J. Bacteriol.

3. Denger K and Cook A. M. (2010) Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase", Microbiology 156: 967-974.

4. Bielen A.A.M. et al (2010) Pyrophosphate as a central energy carrier in the hydrogen-producing extremely thermophilic Caldicellulosiruptor saccharolyticus", FEMS Microbiology Letters.

5. Jiang Q., Qin S., and Wu Q. (2010) Genome-wide comparative analysis of metacaspases in unicellular and filamentous cyanobacteria", BMC Genomics 2010, 11:198.

6. Santarella-Mellwig R et al (2010) The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins", PLoS Biol. 8(1): e1000281.

7. Scott D. Hamilton-Brehm S.D. et al (2010) Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park, Applied and Environmental Microbiology 76(4): 1014-1020.

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IMG Related Publications 2010 · IMG Related Publications April 21st 2010 BIOLOGY 2005 1. Feil H,...

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