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Bioinformatics VOLUME 28 NUMBER 16 AUGUST 15 2012
DISCOVERY NOTE
Genetics and population analysis
Performance of computational tools inevaluating the functional impact oflaboratory-induced amino acid mutations V.E.Gray, K.R.Kukurba and S.Kumar
ORIGINAL PAPER
Genome analysis
Genomic dark matter: the reliability ofshort read mapping illustrated by thegenome mappability score H.Lee and M.C.Schatz
Associating microbiome composition withenvironmental covariates usinggeneralized UniFrac distances J.Chen, K.Bittinger, E.S.Charlson,C.Hoffmann, J.Lewis, G.D.Wu, R.G.Collman,F.D.Bushman and H.Li
Sequence analysis
Bellerophontes: an RNA-Seq data analysisframework for chimeric transcriptsdiscovery based on accurate fusion model F.Abate, A.Acquaviva, G.Paciello, C.Foti,E.Ficarra, A.Ferrarini, M.Delledonne,I.Iacobucci, S.Soverini, G.Martinelli, andE.Macii
BatMis: a fast algorithm for k-mismatchmapping C.Tennakoon, R.W.Purbojati and W.-K.Sung
Systems biology
RESQUE: Network reduction using semi-Markov random walk scores for efficientquerying of biological networksS.M.E.Sahraeian and B.-J.Yoon
Topology of functional networks predictsphysical binding of proteinsÖ.S.Saraç, V.Pancaldi, J.Bähler and A.Beyer
Identification of feedback loops in neuralnetworks based on multi-step GrangercausalityC.-Y.Dong, D.Shin, S.Joo, Y.Nam and K.-H.Cho
Data and text mining
BioContext: an integrated text miningsystem for large-scale extraction andcontextualization of biomolecular eventsM.Gerner, F.Sarafraz, C.M.Bergman andG.Nenadic
AutoBind: automatic extraction ofprotein–ligand-binding affinity data frombiological literatureD.T.-H.Chang, C.-H.Ke, J.-H.Lin and J.-H.Chiang
Databases and ontologies
Identifying aberrant pathways throughintegrated analysis of knowledge inpharmacogenomicsR.Hoehndorf, M.Dumontier and G.V.Gkoutos
APPLICATIONS NOTE
Genome analysis
gSearch: a fast and flexible general searchtool for whole-genome sequencingT.Song, K.-B.Hwang, M.Hsing, K.Lee,J.Bohn and S.W.Kong
Sequence analysis
SORTALLER: predicting allergens usingsubstantially optimized algorithm onallergen family featured peptidesL.Zhang, Y.Huang, Z.Zou, Y.He, X.Chen andA.Tao
SAAP-RRBS: streamlined analysis andannotation pipeline for reducedrepresentation bisulfite sequencingZ.Sun, S.Baheti, S.Middha, R.Kanwar,Y.Zhang, X.Li, A.S.Beutler, E.Klee,Y.W.Asmann, E.A.Thompson and J.-P.A.Kocher
DySC: software for greedy clustering of16S rRNA readsZ.Zheng, S.Kramer and B.Schmidt
RSeQC: quality control of RNA-seqexperimentsL.Wang, S.Wang and W.Li
Structural bioinformatics
ETAscape: analyzing protein networks topredict enzymatic function and substratesin CytoscapeB.J.Bachman, E.Venner, R.C.Lua, S.Erdinand O.Lichtarge
Bluues server: electrostatic properties ofwild-type and mutated protein structuresI.Walsh, G.Minervini, A.Corazza,G.Esposito, S.C.E.Tosatto and F.Fogolari
Accelerated protein structure comparisonusing TM-score-GPUL.-H.Hung and R.Samudrala
BioinformaticsVOLUME 28 NUMBER 16 AUGUST 15 2012
www.bioinformatics.oxfordjournals.org
ISSN 1367-4803 (PRINT)ISSN 1460-2059 (ONLINE)
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