Bioinformatics, Volume 26

Volume 26, Number 1, January 2010

Discovery Note - Sequence Analysis

• 
  Andreas S. Richter,Christian Schleberger,Rolf Backofen,Claudia Steglich:
  Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1.1-5

Original Papers - Genome Analysis

• 
  Bart P. P. van Houte,Jaap Heringa:
  Accurate confidence aware clustering of array CGH tumor profiles.6-14
• 
  Shuangge Ma,Yawei Zhang,Jian Huang,Xuesong Han,Theodore Holford,Qing Lan,Nathaniel Rothman,Peter Boyle,Tongzhang Zheng:
  Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method.15-21
• 
  Youngik Yang,Donald Gilbert,Sun Kim:
  Annotation confidence score for genome annotation: a genome comparison approach.22-29
• 
  Xiang Wan,Can Yang,Qiang Yang,Hong Xue,Nelson L. S. Tang,Weichuan Yu:
  Predictive rule inference for epistatic interaction detection in genome-wide association studies.30-37

Sequence Analysis

• 
  Nathan L. Clement,Quinn Snell,Mark J. Clement,Peter C. Hollenhorst,Jahnvi Purwar,Barbara J. Graves,Bradley R. Cairns,W. Evan Johnson:
  The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.38-45

Structural Bioinformatics

• 
  Jian Yu,Yong Zhou,Isao Tanaka,Min Yao:
  Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere.46-52
• 
  Guillaume Bouvier,Nathalie Evrard-Todeschi,Jean-Pierre Girault,Gildas Bertho:
  Automatic clustering of docking poses in virtual screening process using self-organizing map.53-60
• 
  Robert A. Forties,Ralf Bundschuh:
  Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.61-67

Gene Expression

• 
  Mohammadmahdi R. Yousefi,Jianping Hua,Chao Sima,Edward R. Dougherty:
  Reporting bias when using real data sets to analyze classification performance.68-76
• 
  Marc Kirchner,Bernhard Y. Renard,Ullrich Köthe,Darryl J. Pappin,Fred A. Hamprecht,Hanno Steen,Judith A. J. Steen:
  Computational protein profile similarity screening for quantitative mass spectrometry experiments.77-83
• 
  Axel Rasche,Ralf Herwig:
  ARH: predicting splice variants from genome-wide data with modified entropy.84-90

Systems Biology

• 
  Stefano Volinia,Rosa Visone,Marco Galasso,Elda Rossi,Carlo Maria Croce:
  Identification of microRNA activity by Targets' Reverse EXpression.91-97
• 
  Brian Carrillo,Corey Yanofsky,Sylvie Laboissiere,Robert Nadon,Robert E. Kearney:
  Methods for combining peptide intensities to estimate relative protein abundance.98-103
• 
  Tina Toni,Michael P. H. Stumpf:
  Simulation-based model selection for dynamical systems in systems and population biology.104-110

Data and Text Mining

• 
  Yun Niu,David Otasek,Igor Jurisica:
  Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I²D.111-119

Applications Note - Genome Analysis

• 
  Troy Zerr,Gregory M. Cooper,Evan E. Eichler,Deborah A. Nickerson:
  Targeted interrogation of copy number variation using SCIMMkit.120-122

Sequence Analysis

• 
  Anne-Katrin Emde,Marcel Grunert,David Weese,Knut Reinert,Silke R. Sperling:
  MicroRazerS: rapid alignment of small RNA reads.123-124
• 
  Erik Arner,Yoshihide Hayashizaki,Carsten O. Daub:
  NGSView: an extensible open source editor for next-generation sequencing data.125-126
• 
  Ji Qi,Fangqing Zhao,Anne Buboltz,Stephan C. Schuster:
  inGAP: an integrated next-generation genome analysis pipeline.127-129

Phylogenetics

• 
  Abdoulaye Baniré Diallo,Vladimir Makarenkov,Mathieu Blanchette:
  Ancestors 1.0: a web server for ancestral sequence reconstruction.130-131
• 
  Andrew L. Hipp,Marcial Escudero:
  MATICCE: mapping transitions in continuous character evolution.132-133

Gene Expression

• 
  Joshua Buckner,Justin Wilson,Mark Seligman,Brian D. Athey,Stanley J. Watson,Fan Meng:
  The gputools package enables GPU computing in R.134-135
• 
  Likun Wang,Zhixing Feng,Xi Wang,Xiaowo Wang,Xuegong Zhang:
  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.136-138
• 
  Mark D. Robinson,Davis J. McCarthy,Gordon K. Smyth:
  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.139-140

Systems Biology

• 
  Jie Zheng,David Zhang,Pawel F. Przytycki,Rafal Zielinski,Jacek Capala,Teresa M. Przytycka:
  SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks.141-142
• 
  Ben D. MacArthur,Alexander Lachmann,Ihor Lemischka,Avi Ma'ayan:
  GATE: software for the analysis and visualization of high-dimensional time series expression data.143-144

Data and Text Mining

• 
  Wei Yu,Melinda Clyne,Muin J. Khoury,Marta Gwinn:
  Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations.145-146
• 
  Martijn J. Schuemie,Ning Kang,Maarten L. Hekkelman,Jan A. Kors:
  GeneE: Gene and protein query expansion with disambiguation.147-148

Volume 26, Number 2, January 2010

Discovery Note - Sequence Analysis

• 
  Thiago M. Venancio,L. Aravind:
  CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes.149-152

Original Papers - Genome Analysis

• 
  Nancy Ruonan Zhang,Yasin Senbabaoglu,Jun Z. Li:
  Joint estimation of DNA copy number from multiple platforms.153-160
• 
  Raj K. Gaire,James Bailey,Jennifer Bearfoot,Ian G. Campbell,Peter J. Stuckey,Izhak Haviv:
  MIRAGAA - a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer.161-167
• 
  Robert T. Morris,Timothy R. O'Connor,John J. Wyrick:
  Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions inSaccharomyces cerevisiae.168-174

Sequence Analysis

• 
  Fenix W. D. Huang,Jing Qin,Christian M. Reidys,Peter F. Stadler:
  Target prediction and a statistical sampling algorithm for RNA-RNA interaction.175-181

Structural Bioinformatics

• 
  Liam J. McGuffin,Daniel B. Roche:
  Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments.182-188
• 
  Narendra Kumar,Debasisa Mohanty:
  Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials.189-197
• 
  Danzhi Huang,Ting Zhou,Karine Lafleur,Cristina Nevado,Amedeo Caflisch:
  Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.198-204

Gene Expression

• 
  Ramon Xulvi-Brunet,Hongzhe Li:
  Co-expression networks: graph properties and topological comparisons.205-214
• 
  Ai-Jun Yang,Xin-Yuan Song:
  Bayesian variable selection for disease classification using gene expression data.215-222
• 
  William Ritchie,Stephane Flamant,John E. J. Rasko:
  mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets.223-227
• 
  Bin Wang,Xiao-Feng Wang,Paul Howell,Xuemin Qian,Kun Huang,Adam I. Riker,Jingfang Ju,Yaguang Xi:
  A personalized microRNA microarray normalization method using a logistic regression model.228-234

Genetics and Population Analysis

• 
  Runqing Yang,Xin Wang,Zeyuan Wu,Daniel R. Prows,Min Lin:
  Bayesian model selection for characterizing genomic imprinting effects and patterns.235-241
• 
  Benilton S. Carvalho,Thomas A. Louis,Rafael A. Irizarry:
  Quantifying uncertainty in genotype calls.242-249

Systems Biology

• 
  Herbert Pang,Debayan Datta,Hongyu Zhao:
  Pathway analysis using random forests with bivariate node-split for survival outcomes.250-258

Databases and Ontologies

• 
  Eric R. Gamazon,Wei Zhang,Anuar Konkashbaev,Shiwei Duan,Emily O. Kistner,Dan L. Nicolae,M. Eileen Dolan,Nancy J. Cox:
  SCAN: SNP and copy number annotation.259-262

Applications Note - Sequence Analysis

• 
  Jean Muller,Christopher J. Creevey,Julie Dawn Thompson,Detlev Arendt,Peer Bork:
  AQUA: automated quality improvement for multiple sequence alignments.263-265

Phylogenetics

• 
  J. Gregory Caporaso,Kyle Bittinger,Frederic D. Bushman,Todd Z. DeSantis,Gary L. Andersen,Rob Knight:
  PyNAST: a flexible tool for aligning sequences to a template alignment.266-267

Gene Expression

• 
  Shihao Shen,Claude C. Warzecha,Russ P. Carstens,Yi Xing:
  MADS+: discovery of differential splicing events from Affymetrix exon junction array data.268-269

Genetics and Population Analysis

• 
  Kanchana Narayanan,Jing Li:
  MAVEN: a tool for visualization and functional analysis of genome-wide association results.270-272
• 
  Chris Duran,Zoran Boskovic,Michael Imelfort,Jacqueline Batley,Nicholas A. Hamilton,David Edwards:
  CMap3D: a 3D visualization tool for comparative genetic maps.273-274

Systems Biology

• 
  Fei Li,Peng Li,Wenjian Xu,Yuxing Peng,Xiaochen Bo,Shengqi Wang:
  PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.275-277
• 
  Tomás Levitner,Stepán Timr,Dalibor Stys:
  Expertomica Cells: analysis of cell monolayer development.278-279
• 
  Nathaniel Beagley,Kelly G. Stratton,Bobbie-Jo M. Webb-Robertson:
  VIBE 2.0: Visual Integration for Bayesian Evaluation.280-282
• 
  Aaron Ikin,Carlos Riveros,Pablo Moscato,Alexandre Mendes:
  The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis.283-284
• 
  Jesse Paquette,Taku A. Tokuyasu:
  EGAN: exploratory gene association networks.285-286

Databases and Ontologies

• 
  Zhi Xie,Shaohui Hu,Seth Blackshaw,Heng Zhu,Jiang Qian:
  hPDI: a database of experimental human protein-DNA interactions.287-289
• 
  Keiichi Mochida,Takuhiro Yoshida,Tetsuya Sakurai,Kazuko Yamaguchi-Shinozaki,Kazuo Shinozaki,Lam-Son Phan Tran:
  LegumeTFDB: an integrative database ofGlycine max,Lotus japonicus andMedicago truncatula transcription factors.290-291

Corrigendum Databases and Ontologies

• 
  Ronglai Shen,Adam B. Olshen,Marc Ladanyi:
  Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.292-293

Volume 26, Number 3, February 2010

Original Papers - Genome Analysis

• 
  Sean D. Hooper,Daniel Dalevi,Amrita Pati,Konstantinos Mavrommatis,Natalia Ivanova,Nikos Kyrpides:
  Estimating DNA coverage and abundance in metagenomes using a gamma approximation.295-301

Sequence Analysis

• 
  Thanh Le,Tom Altman,Katheleen J. Gardiner:
  HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.302-309

Structural Bioinformatics

• 
  Daniel T. Lavelle,William R. Pearson:
  Globally, unrelated protein sequences appear random.310-318
• 
  N. A. Temiz,Andrew C. Trapp,Oleg A. Prokopyev,Carlos J. Camacho:
  Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.319-325
• 
  Sergiy O. Garbuzynskiy,Michail Yu. Lobanov,Oxana V. Galzitskaya:
  FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence.326-332

Gene Expression

• 
  Shuya Lu,Jia Li,Chi Song,Kui Shen,George C. Tseng:
  Biomarker detection in the integration of multiple multi-class genomic studies.333-340
• 
  Yijing Shen,Wei Sun,Ker-Chau Li:
  Dynamically weighted clustering with noise set.341-347
• 
  Rui Hu,Xing Qiu,Galina V. Glazko:
  A new gene selection procedure based on the covariance distance.348-354
• 
  Steven J. Kiddle,Oliver P. F. Windram,Stuart McHattie,Andrew Meade,Jim Beynon,Vicky Buchanan-Wollaston,Katherine J. Denby,Sach Mukherjee:
  Temporal clustering by affinity propagation reveals transcriptional modules inArabidopsis thaliana.355-362
• 
  Thang V. Pham,Sander R. Piersma,Marc Warmoes,Connie R. Jimenez:
  On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics.363-369
• 
  Theresa Scharl,Bettina Grün,Friedrich Leisch:
  Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects.370-377

Systems Biology

• 
  Monica Chagoyen,Florencio Pazos:
  Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data.378-384
• 
  Suk Hoon Jung,Bo-ra Hyun,Woo-Hyuk Jang,Hee-Young Hur,Dong-Soo Han:
  Protein complex prediction based on simultaneous protein interaction network.385-391

Data and Text Mining

• 
  Thomas Abeel,Thibault Helleputte,Yves Van de Peer,Pierre Dupont,Yvan Saeys:
  Robust biomarker identification for cancer diagnosis with ensemble feature selection methods.392-398

Application Notes - Genome Analysis

• 
  Kousuke Hanada,Kenji Akiyama,Tetsuya Sakurai,Tetsuro Toyoda,Kazuo Shinozaki,Shin-Han Shiu:
  sORF finder: a program package to identify small open reading frames with high coding potential.399-400

Sequence Analysis

• 
  Iain Milne,Micha Bayer,Linda Cardle,Paul D. Shaw,Gordon Stephen,Frank Wright,David F. Marshall:
  Tablet - next generation sequence assembly visualization.401-402
• 
  Emese Meglécz,Caroline Costedoat,Vincent Dubut,André Gilles,Thibaut Malausa,Nicolas Pech,Jean-François Martin:
  QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.403-404
• 
  Hanchang Sun,Yuan Yuan,Yibo Wu,Hui Liu,Jun S. Liu,Hongwei Xie:
  Tmod: toolbox of motif discovery.405-407

Phylogenetics

• 
  Chi Ho Lin,Hao Zhao,Sean Harry Lowcay,Atif Shahab,Guillaume Bourque:
  webMGR: an online tool for the multiple genome rearrangement problem.408-410

Gene Expression

• 
  Nathan S. Watson-Haigh,Haja N. Kadarmideen,Antonio Reverter:
  PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches.411-413
• 
  Keyan Salari,Robert Tibshirani,Jonathan R. Pollack:
  DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.414-416

Genetics and Population Analysis

• 
  Valery Terletskiy,Valentina Tyshchenko,Ilargi Martinez-Ballesteros,Javier Garaizar,Joseba Bikandi:
  Validation of double digest selective label database for sequenced prokaryotic genomes.417-418
• 
  Emmanuel Paradis:
  pegas: an R package for population genetics with an integrated-modular approach.419-420

Systems Biology

• 
  Falko Krause,Jannis Uhlendorf,Timo Lubitz,Marvin Schulz,Edda Klipp,Wolfram Liebermeister:
  Annotation and merging of SBML models with semanticSBML.421-422
• 
  Kendell Clement,Nathaniel Gustafson,Amanda Berbert,Hyrum Carroll,Christopher Merris,Ammon Olsen,Mark J. Clement,Quinn Snell,Jared Allen,Randall J. Roper:
  PathGen: a transitive gene pathway generator.423-425
• 
  Emmet Caulfield,Andreas Hellander:
  CellMC - a multiplatform model compiler for the Cell Broadband Engine and x86.426-428
• 
  Ozgun Babur,Ugur Dogrusöz,Emek Demir,Chris Sander:
  ChiBE: interactive visualization and manipulation of BioPAX pathway models.429-431
• 
  Bart S. Hendriks,Christopher W. Espelin:
  DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.432-433

Databases and Ontologies

• 
  Carson M. Andorf,Carolyn J. Lawrence,Lisa C. Harper,Mary L. Schaeffer,Darwin A. Campbell,Taner Z. Sen:
  The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.434-436

Letters to the Editor - Databases and Ontologies

• 
  Anne-Laure Boulesteix:
  Over-optimism in bioinformatics research.437-439
• 
  Pawel Smialowski,Dmitrij Frishman,Stefan Kramer:
  Pitfalls of supervised feature selection.440-443

Volume 26, Number 4, February 2010

Review Genetics and Population Analysis

• 
  Jason H. Moore,Folkert W. Asselbergs,Scott M. Williams:
  Bioinformatics challenges for genome-wide association studies.445-455

Original Papers - Genome Analysis

• 
  Maureen A. Sartor,Vasudeva Mahavisno,Venkateshwar G. Keshamouni,James D. Cavalcoli,Zach Wright,Alla Karnovsky,Rork Kuick,H. V. Jagadish,Barbara Mirel,Terry E. Weymouth,Brian D. Athey,Gilbert S. Omenn:
  ConceptGen: a gene set enrichment and gene set relation mapping tool.456-463
• 
  Qunyuan Zhang,Li Ding,David E. Larson,Daniel C. Koboldt,Michael D. McLellan,Ken Chen,Xiaoqi Shi,Aldi T. Kraja,Elaine R. Mardis,Richard K. Wilson,Ingrid B. Borecki,Michael A. Province:
  CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data.464-469

Sequence Analysis

• 
  Tuping Zhou,Nanjiang Shu,Sven Hovmöller:
  A novel method for accurate one-dimensional protein structure prediction based on fragment matching.470-477
• 
  Shang-Hong Zhang,Ya-Zhi Huang:
  Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA.478-485

Gene Expression

• 
  Mingoo Kim,Sung-Bum Cho,Ju Han Kim:
  Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data.486-492
• 
  Bo Li,Victor Ruotti,Ron M. Stewart,James A. Thomson,Colin N. Dewey:
  RNA-Seq gene expression estimation with read mapping uncertainty.493-500
• 
  Benhuai Xie,Wei Pan,Xiaotong Shen:
  Penalized mixtures of factor analyzers with application to clustering high-dimensional microarray data.501-508
• 
  Ping-Shi Wu,Hans-Georg Müller:
  Functional embedding for the classification of gene expression profiles.509-517

Genetics and Population Analysis

• 
  Ninad Dewal,Matthew L. Freedman,Thomas LaFramboise,Itsik Pe'er:
  Power to detect selective allelic amplification in genome-wide scans of tumor data.518-528

Systems Biology

• 
  Kelvin Xi Zhang,B. F. Francis Ouellette:
  Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence.529-535
• 
  Naama Tepper,Tomer Shlomi:
  Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways.536-543

Databases and Ontologies

• 
  Kristian Kvilekval,Dmitry V. Fedorov,Boguslaw Obara,Ambuj K. Singh,B. S. Manjunath:
  Bisque: a platform for bioimage analysis and management.544-552
• 
  Victoria Martin-Requena,Javier Ríos,Maximiliano García,Sergio Ramírez,Oswaldo Trelles:
  jORCA: easily integrating bioinformatics Web Services.553-559
• 
  Christine Fong,Dennis C. Ko,Michael Wasnick,Matthew Radey,Samuel I. Miller,Mitchell J. Brittnacher:
  GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.560-564

Applications Note - Genome Analysis

• 
  Jared T. Simpson,Rebecca E. McIntyre,David J. Adams,Richard Durbin:
  Copy number variant detection in inbred strains from short read sequence data.565-567

Sequence Analysis

• 
  Matthew Horton,Natacha Bodenhausen,Joy Bergelson:
  MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.568-569
• 
  Peter Husemann,Jens Stoye:
  r2cat: synteny plots and comparative assembly.570-571
• 
  Elena Yavorska Harris,Nadia Ponts,Aleksandr Levchuk,Karine G. Le Roch,Stefano Lonardi:
  BRAT: bisulfite-treated reads analysis tool.572-573

Structural Bioinformatics

• 
  Karl Frank,Markus Gruber,Manfred J. Sippl:
  COPS Benchmark: interactive analysis of database search methods.574-575

Gene Expression

• 
  Kosaku Shinoda,Masaru Tomita,Yasushi Ishihama:
  emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry.576-577

Genetics and Population Analysis

• 
  William S. Bush,Scott M. Dudek,Marylyn D. Ritchie:
  Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.578-579
• 
  Ming-Huei Chen,Qiong Yang:
  GWAF: an R package for genome-wide association analyses with family data.580-581

Systems Biology

• 
  Cheng-Long Chuang,Jia-Hong Wu,Chi-Sheng Cheng,Grace S. Shieh:
  WebPARE: web-computing for inferring genetic or transcriptional interactions.582-584

Databases and Ontologies

• 
  Tin-Lap Lee,Yunmin Li,Hoi-Hung Cheung,Janek Claus,Sumeeta Singh,Chandan Sastry,Owen M. Rennert,Yun-Fai Chris Lau,Wai-Yee Chan:
  GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development.585-586
• 
  Yanbin Liu,Bin Hu,Chengxin Fu,Xin Chen:
  DCDB: Drug combination database.587-588

Volume 26, Number 5, March 2010

Original Papers - Sequence Analysis

• 
  Heng Li,Richard Durbin:
  Fast and accurate long-read alignment with Burrows-Wheeler transform.589-595
• 
  Martin Madera,Ryan Calmus,Grant Thiltgen,Kevin Karplus,Julian Gough:
  Improving protein secondary structure prediction using a simplek-mer model.596-602
• 
  Ozgur Demir-Kavuk,Henning Riedesel,Ernst-Walter Knapp:
  Exploring classification strategies with the CoEPrA 2006 contest.603-609

Structural Bioinformatics

• 
  Hakim Tafer,Stephanie Kehr,Jana Hertel,Ivo L. Hofacker,Peter F. Stadler:
  RNAsnoop: efficient target prediction for H/ACA snoRNAs.610-616
• 
  Sriram Sankararaman,Fei Sha,Jack F. Kirsch,Michael I. Jordan,Kimmen Sjölander:
  Active site prediction using evolutionary and structural information.617-624
• 
  Christian Schaefer,Avner Schlessinger,Burkhard Rost:
  Protein secondary structure appears to be robust underin silico evolution while protein disorder appears not to be.625-631
• 
  Stefan Janssen,Robert Giegerich:
  Faster computation of exact RNA shape probabilities.632-639

Gene Expression

• 
  Anastasios Markitsis,Yinglei Lai:
  A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes.640-646

Systems Biology

• 
  Royi Itzhack,Yoram Louzoun:
  Random distance dependent attachment as a model for neural network generation in theCaenorhabditis elegans.647-652
• 
  Thomas W. Binsl,David J. C. Alders,Jaap Heringa,A. B. Johan Groeneveld,Johannes H. G. M. van Beek:
  Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.653-660

Data and Text Mining

• 
  Xinglong Wang,Jun'ichi Tsujii,Sophia Ananiadou:
  Disambiguating the species of biomedical named entities using natural language parsers.661-667
• 
  Vanathi Gopalakrishnan,Jonathan L. Lustgarten,Shyam Visweswaran,Gregory F. Cooper:
  Bayesian rule learning for biomedical data mining.668-675

Applications Note - Genome Analysis

• 
  Tim Carver,Ulrike Böhme,Thomas D. Otto,Julian Parkhill,Matthew Berriman:
  BamView: viewing mapped read alignment data in the context of the reference sequence.676-677
• 
  Arnaud Droit,Charles Cheung,Raphael Gottardo:
  rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments.678-679

Sequence Analysis

• 
  Ying Huang,Beifang Niu,Ying Gao,Limin Fu,Weizhong Li:
  CD-HIT Suite: a web server for clustering and comparing biological sequences.680-682
• 
  Sergio Gálvez,David Díaz,Pilar Hernández,Francisco José Esteban,Juan Antonio Caballero,Gabriel Dorado:
  Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.683-686

Structural Bioinformatics

• 
  Shashi Bhushan Pandit,Michal Brylinski,Hongyi Zhou,Mu Gao,Adrian K. Arakaki,Jeffrey Skolnick:
  PSiFR: an integrated resource for prediction of protein structure and function.687-688
• 
  Sidhartha Chaudhury,Sergey Lyskov,Jeffrey J. Gray:
  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.689-691
• 
  Guy Nimrod,Maya Schushan,András Szilágyi,Christina S. Leslie,Nir Ben-Tal:
  iDBPs: a web server for the identification of DNA binding proteins.692-693

Genetics and Population Analysis

• 
  Casey S. Greene,Nicholas A. Sinnott-Armstrong,Daniel S. Himmelstein,Paul J. Park,Jason H. Moore,Brent T. Harris:
  Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.694-695

Systems Biology

• 
  E. Iannuccelli,F. Mompart,Joël Gellin,Yvette Lahbib-Mansais,Martine Yerle,Thomas Boudier:
  NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.696-697

Data and Text Mining

• 
  Gustavo Antônio De Souza,Magnus Ø. Arntzen,Harald G. Wiker:
  MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.698-699

Databases and Ontologies

• 
  Yan Zhang,Vadim N. Gladyshev:
  dbTEU: a protein database of trace element utilization.700-702
• 
  Visotheary Ung,Guillaume Dubus,René Zaragüeta-Bagils,Régine Vignes-Lebbe:
  Xper²: introducinge-taxonomy.703-704
• 
  Thomas D. Otto,Marcos Catanho,Cristian Tristão,Márcia Bezerra,Renan Mathias Fernandes,Guilherme Steinberger Elias,Alexandre Capeletto Scaglia,Bill Bovermann,Viktors Berstis,Sérgio Lifschitz,Antonio Basílio de Miranda,Wim M. Degrave:
  ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.705-707

Volume 26, Number 6, March 2010

Discovery Note - Structural Bioinformatics

• 
  Stephen A. Cammer,Charles W. Carter Jr.:
  Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.709-714

Original Papers - Genome Analysis

• 
  Donovan H. Parks,Robert G. Beiko:
  Identifying biologically relevant differences between metagenomic communities.715-721

Sequence Analysis

• 
  Peter M. Krawitz,Christian Rödelsperger,Marten Jäger,Luke Jostins,Sebastian Bauer,Peter N. Robinson:
  Microindel detection in short-read sequence data.722-729
• 
  Rodrigo Goya,Mark G. F. Sun,Ryan D. Morin,Gillian Leung,Gavin Ha,Kimberley C. Wiegand,Janine Senz,Anamaria Crisan,Marco A. Marra,Martin Hirst,David G. Huntsman,Kevin P. Murphy,Sam Aparicio,Sohrab P. Shah:
  SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.730-736
• 
  Stefan Maetschke,Karin S. Kassahn,Jasmyn A. Dunn,Siew-Ping Han,Eva Z. Curley,Katryn J. Stacey,Mark A. Ragan:
  A visual framework for sequence analysis usingn-grams and spectral rearrangement.737-744

Structural Bioinformatics

• 
  Corin Yeats,Oliver Redfern,Christine A. Orengo:
  A fast and automated solution for accurately resolving protein domain architectures.745-751
• 
  Jiangning Song,Hao Tan,Hong-Bin Shen,Khalid Mahmood,Sarah E. Boyd,Geoffrey I. Webb,Tatsuya Akutsu,James C. Whisstock:
  Cascleave: towards more accurate prediction of caspase substrate cleavage sites.752-760

Gene Expression

• 
  Daniel L. Mace,Nicole Varnado,Weiping Zhang,Erwin Frise,Uwe Ohler:
  Extraction and comparison of gene expression patterns from 2D RNAin situ hybridization images.761-769
• 
  Qiang Liu,Kevin K. Lin,Bogi Andersen,Padhraic Smyth,Alexander Ihler:
  Estimating replicate time shifts using Gaussian process regression.770-776
• 
  Qianxing Mo,Faming Liang:
  A hidden Ising model for ChIP-chip data analysis.777-783
• 
  Daniela Dunkler,Michael Schemper,Georg Heinze:
  Gene selection in microarray survival studies under possibly non-proportional hazards.784-790
• 
  Marc Kirchner,Wiebke Timm,Peying Fong,Philine Wangemann,Hanno Steen:
  Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments.791-797

Genetics and Population Analysis

• 
  Mingyao Li,Muredach P. Reilly,Daniel J. Rader,Li-San Wang:
  Correcting population stratification in genetic association studies using a phylogenetic approach.798-806

Systems Biology

• 
  Chia-Chin Wu,Shahab Asgharzadeh,Timothy Triche,David Z. D'Argenio:
  Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning.807-813

Data and Text Mining

• 
  Jörg Wicker,Kathrin Fenner,Lynda B. M. Ellis,Lawrence P. Wackett,Stefan Kramer:
  Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach.814-821
• 
  Blaise Hanczar,Jianping Hua,Chao Sima,John N. Weinstein,Michael L. Bittner,Edward R. Dougherty:
  Small-sample precision of ROC-related estimates.822-830
• 
  Minghui Wang,Xiang Chen,Heping Zhang:
  Maximal conditional chi-square importance in random forests.831-837

Applications Note - Genome Analysis

• 
  Paul F. O'Reilly,Lachlan J. M. Coin,Clive J. Hoggart:
  invertFREGENE: software for simulating inversions in population genetic data.838-840
• 
  Aaron R. Quinlan,Ira M. Hall:
  BEDTools: a flexible suite of utilities for comparing genomic features.841-842

Sequence Analysis

• 
  Matias Piipari,Thomas A. Down,Harpreet Kaur Saini,Anton J. Enright,Tim J. P. Hubbard:
  iMotifs: an integrated sequence motif visualization and analysis environment.843-844
• 
  Idan Gabdank,Danny Barash,Edward N. Trifonov:
  FineStr: a web server for single-base-resolution nucleosome positioning.845-846
• 
  Paulo C. Carvalho,Xuemei Han,Tao Xu,Daniel Cociorva,Maria da Gloria Carvalho,Valmir Carneiro Barbosa,John R. Yates III:
  XDIA: improving on the label-free data-independent analysis.847-848
• 
  Ariella Sasson,Todd P. Michael:
  Filtering error from SOLiD Output.849-850

Databases and Ontologies

• 
  Anaïs Mottaz,Fabrice P. A. David,Anne-Lise Veuthey,Yum Lina Yip:
  Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar.851-852

Erratum Databases and Ontologies

• 
  Natasa Przulj:
  Biological network comparison using graphlet degree distribution.853-854

Volume 26, Number 7, April 2010

Discovery Note - Genome Analysis

• 
  Liang Chen:
  A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells.855-859

Original Papers - Sequence Analysis

• 
  Fabian A. Buske,Mikael Bodén,Denis C. Bauer,Timothy L. Bailey:
  Assigning roles to DNA regulatory motifs using comparative genomics.860-866
• 
  Supriya Munshaw,Thomas B. Kepler:
  SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements.867-872
• 
  Thomas D. Wu,Serban Nacu:
  Fast and SNP-tolerant detection of complex variants and splicing in short reads.873-881

Structural Bioinformatics

• 
  Zheng Wang,Jesse Eickholt,Jianlin Cheng:
  MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.882-888
• 
  Jinrui Xu,Yang Zhang:
  How significant is a protein structure similarity with TM-score = 0.5?889-895

Gene Expression

• 
  Antonio Reverter,Nicholas J. Hudson,Shivashankar H. Nagaraj,Miguel Pérez-Enciso,Brian P. Dalrymple:
  Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.896-904
• 
  Song Zhang,Jing Cao,Y. Megan Kong,Richard H. Scheuermann:
  GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach.905-911

Systems Biology

• 
  Christoph Lippert,Zoubin Ghahramani,Karsten M. Borgwardt:
  Gene function prediction from synthetic lethality networks via ranking on demand.912-918
• 
  Jing Zhu,Hui Xiao,Xiaopei Shen,Jing Wang,Jinfeng Zou,Lin Zhang,Da Yang,Wencai Ma,Chen Yao,Xue Gong,Min Zhang,Yang Zhang,Zheng Guo:
  Viewing cancer genes from co-evolving gene modules.919-924
• 
  Mike T. Cooling,V. Rouilly,Goksel Misirli,James R. Lawson,Tommy Yu,Jennifer Hallinan,Anil Wipat:
  Standard virtual biological parts: a repository of modular modeling components for synthetic biology.925-931
• 
  Joseph O. Dada,Irena Spasic,Norman W. Paton,Pedro Mendes:
  SBRML: a markup language for associating systems biology data with models.932-938
• 
  Dominik Skanda,Dirk Lebiedz:
  An optimal experimental design approach to model discrimination in dynamic biochemical systems.939-945

Data and Text Mining

• 
  Massimo Natale,Dario Bonino,Paolo Consoli,Tiziana Alberio,Rivka G. Ravid,Mauro Fasano,Enrico M. Bucci:
  A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1.946-952

Databases and Ontologies

• 
  Yiqun Cao,Tao Jiang,Thomas Girke:
  Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing.953-959

Applications Note - Genome Analysis

• 
  Fabian Schreiber,Peter Gumrich,Rolf Daniel,Peter Meinicke:
  Treephyler: fast taxonomic profiling of metagenomes.960-961

Phylogenetics

• 
  Liang Liu,Lili Yu:
  Phybase: an R package for species tree analysis.962-963

Structural Bioinformatics

• 
  Sébastien Loriot,Frédéric Cazals:
  Modeling macro-molecular interfaces withIntervor.964-965

Gene Expression

• 
  Brendan MacLean,Daniela M. Tomazela,Nicholas Shulman,Matthew Chambers,Gregory L. Finney,Barbara Frewen,Randall Kern,David L. Tabb,Daniel C. Liebler,Michael J. MacCoss:
  Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.966-968

Genetics and Population Analysis

• 
  Armin Otto Schmitt,Jens Aßmus,Ralf H. Bortfeldt,Gudrun A. Brockmann:
  CandiSNPer: a web tool for the identification of candidate SNPs for causal variants.969-970

Systems Biology

• 
  Jing Gao,V. Glenn Tarcea,Alla Karnovsky,Barbara R. Mirel,Terry E. Weymouth,Christopher W. Beecher,James D. Cavalcoli,Brian D. Athey,Gilbert S. Omenn,Charles F. Burant,H. V. Jagadish:
  Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.971-973
• 
  Christian Rohr,Wolfgang Marwan,Monika Heiner:
  Snoopy - a unifying Petri net framework to investigate biomolecular networks.974-975
• 
  Guangchuang Yu,Fei Li,Yide Qin,Xiaochen Bo,Yibo Wu,Shengqi Wang:
  GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.976-978

Data and Text Mining

• 
  Grégoire Pau,Florian Fuchs,Oleg Sklyar,Michael Boutros,Wolfgang Huber:
  EBImage - an R package for image processing with applications to cellular phenotypes.979-981
• 
  Dietrich Rebholz-Schuhmann,Silvestras Kavaliauskas,Piotr Pezik:
  PaperMaker: validation of biomedical scientific publications.982-984
• 
  Ricard García-Serna,Oleg Ursu,Tudor I. Oprea,Jordi Mestres:
  iPHACE: integrative navigation in pharmacological space.985-986
• 
  Jens Hollunder,Maik Friedel,Martin Kuiper,Thomas Wilhelm:
  DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.987-989

Volume 26, Number 8, April 2010

Editorial

• 
  Alex Bateman:
  Curators of the world unite: the International Society of Biocuration.991

Discovery Note - Genome Analysis

• 
  David Golan,Carmit Levy,Brad Friedman,Noam Shomron:
  Biased hosting of intronic microRNA genes.992-995
• 
  Inbal Yomtovian,Nuttinee Teerakulkittipong,Byungkook Lee,John Moult,Ron Unger:
  Composition bias and the origin of ORFan genes.996-999

Original Papers - Genome Analysis

• 
  Frank Johannes,René Wardenaar,Maria Colomé-Tatché,Florence Mousson,Petra de Graaf,Michal Mokry,Victor Guryev,H. Th. Marc Timmers,Edwin Cuppen,Ritsert C. Jansen:
  Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.1000-1006
• 
  Gerard Wong,Christopher Leckie,Kylie L. Gorringe,Izhak Haviv,Ian G. Campbell,Adam Kowalczyk:
  Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations.1007-1014

Sequence Analysis

• 
  Eduardo Corel,Florian Pitschi,Burkhard Morgenstern:
  Amin-cut algorithm for the consistency problem in multiple sequence alignment.1015-1021
• 
  Wei-Yao Chou,Wei-I Chou,Tun-Wen Pai,Shu-Chuan Lin,Ting-Ying Jiang,Chuan Yi Tang,Margaret Dah-Tsyr Chang:
  Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules.1022-1028
• 
  Nawar Malhis,Steven J. M. Jones:
  High quality SNP calling using Illumina data at shallow coverage.1029-1035

Structural Bioinformatics

• 
  Hugo Willy,Fushan Song,Zeyar Aung,See-Kiong Ng,Wing-Kin Sung:
  SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank.1036-1042

Gene Expression

• 
  Jennifer Clarke,Pearl Seo,Bertrand S. Clarke:
  Statistical expression deconvolution from mixed tissue samples.1043-1049

Genetics and Population Analysis

• 
  Sonja Zehetmayer,Martin Posch:
  Post hoc power estimation in large-scale multiple testing problems.1050-1056

Systems Biology

• 
  Saket Navlakha,Carl Kingsford:
  The power of protein interaction networks for associating genes with diseases.1057-1063
• 
  Teppei Shimamura,Seiya Imoto,Rui Yamaguchi,Masao Nagasaki,Satoru Miyano:
  Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.1064-1072
• 
  Yuichi Shiraishi,Shuhei Kimura,Mariko Okada:
  Inferring cluster-based networks from differently stimulated multiple time-course gene expression data.1073-1081
• 
  Amin Moghaddas Gholami,Kurt Fellenberg:
  Cross-species common regulatory network inference without requirement for prior gene affiliation.1082-1090

Data and Text Mining

• 
  Lei Qu,Hanchuan Peng:
  A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems.1091-1097
• 
  Daniel Dahlmeier,Hwee Tou Ng:
  Domain adaptation for semantic role labeling in the biomedical domain.1098-1104
• 
  Peng Jiang,Mona Singh:
  SPICi: a fast clustering algorithm for large biological networks.1105-1111

Databases and Ontologies

• 
  James Malone,Ele Holloway,Tomasz Adamusiak,Misha Kapushesky,Jie Zheng,Nikolay Kolesnikov,Anna Zhukova,Alvis Brazma,Helen E. Parkinson:
  Modeling sample variables with an Experimental Factor Ontology.1112-1118

Applications Note - Genome Analysis

• 
  Matthieu Muffato,Alexandra Louis,Charles-Edouard Poisnel,Hugues Roest Crollius:
  Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes.1119-1121
• 
  Chris Hemmerich,Aaron Buechlein,Ram Podicheti,Kashi Vishwanath Revanna,Qunfeng Dong:
  An Ergatis-based prokaryotic genome annotation web server.1122-1124

Phylogenetics

• 
  François Chevenet,Olivier Croce,Maxime Hebrard,Richard Christen,Vincent Berry:
  ScripTree: scripting phylogenetic graphics.1125-1126

Structural Bioinformatics

• 
  Sébastien Loriot,Frédéric Cazals,Julie Bernauer:
  ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.1127-1128

Systems Biology

• 
  Daniela Beisser,Gunnar W. Klau,Thomas Dandekar,Tobias Müller,Marcus T. Dittrich:
  BioNet: an R-Package for the functional analysis of biological networks.1129-1130

Data and Text Mining

• 
  David C. Trudgian,Benjamin Thomas,Simon J. McGowan,Benedikt M. Kessler,Mogjiborahman Salek,Oreste Acuto:
  CPFP: a central proteomics facilities pipeline.1131-1132

Databases and Ontologies

• 
  Nobuhiko Tanaka,Kazunori Waki,Hideki Kaneda,Tomohiro Suzuki,Ikuko Yamada,Tamio Furuse,Kimio Kobayashi,Hiromi Motegi,Hideaki Toki,Maki Inoue,Osamu Minowa,Tetsuo Noda,Keizo Takao,Tsuyoshi Miyakawa,Aki Takahashi,Tsuyoshi Koide,Shigeharu Wakana,Hiroshi Masuya:
  SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses.1133-1134

Volume 26, Number 9, May 2010

Discovery Note - Sequence Analysis

• 
  Andrew D. Fernandes,Gregory B. Gloor:
  Mutual information is critically dependent on prior assumptions: would thecorrect estimate of mutual information please identify itself?1135-1139
• 
  Isabelle Callebaut,Jean Paul Mornon:
  LOTUS, a new domain associated with small RNA pathways in the germline.1140-1144

Original Papers - Genome Analysis

• 
  Manfred G. Grabherr,Pamela H. Russell,Miriah D. Meyer,Evan Mauceli,Jessica Alföldi,Federica Di Palma,Kerstin Lindblad-Toh:
  Genome-wide synteny through highly sensitive sequence alignment:Satsuma.1145-1151

Sequence Analysis

• 
  Vipin Narang,Ankush Mittal,Wing-Kin Sung:
  Localized motif discovery in gene regulatory sequences.1152-1159

Structural Bioinformatics

• 
  Janez Konc,Dusanka Janezic:
  ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment.1160-1168
• 
  Pedro J. Ballester,John B. O. Mitchell:
  A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking.1169-1175
• 
  Degui Zhi,Maxim Shatsky,Steven E. Brenner:
  Alignment-free local structural search by writhe decomposition.1176-1184

Gene Expression

• 
  Salih Tuna,Mahesan Niranjan:
  Reducing the algorithmic variability in transcriptome-based inference.1185-1191
• 
  Kim-Anh Lê Cao,Emmanuelle Meugnier,Geoffrey J. McLachlan:
  Integrative mixture of experts to combine clinical factors and gene markers.1192-1198
• 
  Han Xu,Lusy Handoko,Xueliang Wei,Chaopeng Ye,Jianpeng Sheng,Chia-Lin Wei,Feng Lin,Wing-Kin Sung:
  A signal-noise model for significance analysis of ChIP-seq with negative control.1199-1204

Genetics and Population Analysis

• 
  Joshua C. Denny,Marylyn D. Ritchie,Melissa A. Basford,Jill M. Pulley,Lisa Bastarache,Kristin Brown-Gentry,Deede Wang,Daniel R. Masys,Dan M. Roden,Dana C. Crawford:
  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.1205-1210

Systems Biology

• 
  Karoline Faust,Pierre Dupont,Jérôme Callut,Jacques van Helden:
  Pathway discovery in metabolic networks by subgraph extraction.1211-1218
• 
  Yongjin Li,Jagdish Chandra Patra:
  Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network.1219-1224
• 
  Gunnar Schramm,Stefan Wiesberg,Nicolle Diessl,Anna-Lena Kranz,Vitalia Sagulenko,Marcus Oswald,Gerhard Reinelt,Frank Westermann,Roland Eils,Rainer König:
  PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways.1225-1231
• 
  Sebastian Briesemeister,Jörg Rahnenführer,Oliver Kohlbacher:
  Going from where to why - interpretable prediction of protein subcellular localization.1232-1238
• 
  Riccardo Porreca,Eugenio Cinquemani,John Lygeros,Giancarlo Ferrari-Trecate:
  Identification of genetic network dynamics with unate structure.1239-1245

Data and Text Mining

• 
  Naoaki Okazaki,Sophia Ananiadou,Jun'ichi Tsujii:
  Building a high-quality sense inventory for improved abbreviation disambiguation.1246-1253

Applications Note - Genome Analysis

• 
  Pierre Montalent,Johann Joets:
  EuGène-maize: a web site for maize gene prediction.1254-1255

Phylogenetics

• 
  Jumamurat R. Bayjanov,Roland J. Siezen,Sacha A. F. T. van Hijum:
  PanCGHweb: a web tool for genotype calling in pangenome CGH data.1256-1257

Structural Bioinformatics

• 
  Daron M. Standley,Reiko Yamashita,Akira R. Kinjo,Hiroyuki Toh,Haruki Nakamura:
  SeSAW: balancing sequence and structural information in protein functional mapping.1258-1259
• 
  Asif U. Tamuri,Roman A. Laskowski:
  ArchSchema: a tool for interactive graphing of related Pfam domain architectures.1260-1261

Gene Expression

• 
  Frédéric Boyer,Bruno Besson,Guillaume Baptist,Jérôme Izard,Corinne Pinel,Delphine Ropers,Johannes Geiselmann,Hidde de Jong:
  WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.1262-1263
• 
  Caroline C. Friedel,Stefanie Kaufmann,Lars Dölken,Ralf Zimmer:
  HALO - a Java framework for precise transcript half-life determination.1264-1266
• 
  Yoshiyuki Ogata,Hideyuki Suzuki,Nozomu Sakurai,Daisuke Shibata:
  CoP: a database for characterizing co-expressed gene modules with biological information in plants.1267-1268

Genetics and Population Analysis

• 
  Rick Twee-Hee Ong,Yik-Ying Teo:
  varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.1269-1270

Systems Biology

• 
  Enrico Glaab,Anaïs Baudot,Natalio Krasnogor,Alfonso Valencia:
  TopoGSA: network topological gene set analysis.1271-1272

Databases and Ontologies

• 
  Sheng-Jian Xiao,Chi Zhang,Quan Zou,Zhi-Liang Ji:
  TiSGeD: a database for tissue-specific genes.1273-1275

Volume 26, Number 10, May 2010

Hitseq Papers - Genome Analysis

• 
  Iman Hajirasouliha,Fereydoun Hormozdiari,Can Alkan,Jeffrey M. Kidd,Inanç Birol,Evan E. Eichler,Süleyman Cenk Sahinalp:
  Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.1277-1283

Sequence Analysis

• 
  Leena Salmela:
  Correction of sequencing errors in a mixed set of reads.1284-1290
• 
  Anna M. Ritz,Ali Bashir,Benjamin J. Raphael:
  Structural variation analysis with strobe reads.1291-1298

Original Papers - Structural Bioinformatics

• 
  Matan Kalman,Nir Ben-Tal:
  Quality assessment of protein model-structures using evolutionary conservation.1299-1307

Gene Expression

• 
  Brigham H. Mecham,Peter S. Nelson,John D. Storey:
  Supervised normalization of microarrays.1308-1315
• 
  Kui Shen,George C. Tseng:
  Meta-analysis for pathway enrichment analysis when combining multiple genomic studies.1316-1323

Systems Biology

• 
  Delali A. Adiamah,Julia Handl,Jean-Marc Schwartz:
  Streamlining the construction of large-scale dynamic models using generic kinetic equations.1324-1331
• 
  Ipsita Banerjee,Spandan Maiti,Natesh Parashurama,Martin L. Yarmush:
  An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells.1332-1339

Data and Text Mining

• 
  André Altmann,Laura Tolosi,Oliver Sander,Thomas Lengauer:
  Permutation importance: a corrected feature importance measure.1340-1347
• 
  Sanjay Joshua Swamidass,Chloé-Agathe Azencott,Kenny Daily,Pierre Baldi:
  A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval.1348-1356
• 
  Annette M. Molinaro,Karen Lostritto,Mark J. van der Laan:
  partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction.1357-1363

Applications Note - Genome Analysis

• 
  Sebastian Fröhler,Christoph Dieterich:
  ACCUSA - accurate SNP calling on draft genomes.1364-1365
• 
  Bart P. P. van Houte,Thomas W. Binsl,Hannes Hettling,Jaap Heringa:
  CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.1366-1367

Sequence Analysis

• 
  Adrianto Wirawan,Chee Keong Kwoh,Bertil Schmidt:
  Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.1368-1369
• 
  David Ochoa,Florencio Pazos:
  Studying the co-evolution of protein families with the Mirrortree web server.1370-1371

Phylogenetics

• 
  Remco R. Bouckaert:
  DensiTree: making sense of sets of phylogenetic trees.1372-1373

Structural Bioinformatics

• 
  Nikita D. Prakhov,Alexander L. Chernorudskiy,Murat R. Gainullin:
  VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.1374-1375

Gene Expression

• 
  Gábor Csárdi,Zoltán Kutalik,Sven Bergmann:
  Modular analysis of gene expression data with R.1376-1377

Systems Biology

• 
  Christoph Müssel,Martin Hopfensitz,Hans A. Kestler:
  BoolNet - an R package for generation, reconstruction and analysis of Boolean networks.1378-1380
• 
  Yukiko Matsuoka,Samik Ghosh,Norihiro Kikuchi,Hiroaki Kitano:
  Payao: a community platform for SBML pathway model curation.1381-1383

Data and Text Mining

• 
  Bo-Yeong Kang,Song Ko,Dae-Won Kim:
  SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology.1384-1385

Letter to the Editor - Genetics and Population Analysis

• 
  Andrew D. Johnson:
  An extended IUPAC nomenclature code for polymorphic nucleic acids.1386-1389

Volume 26, Number 11, June 2010

Discovery Note - Sequence Analysis

• 
  Dijun Chen,Yijun Meng,Xiaoxia Ma,Chuanzao Mao,Youhuang Bai,Junjie Cao,Haibin Gu,Ping Wu,Ming Chen:
  Small RNAs in angiosperms: sequence characteristics, distribution and generation.1391-1394

Original Papers - Genome Analysis

• 
  Sergii Ivakhno,Simon Tavaré:
  CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.1395-1402

Sequence Analysis

• 
  William D. Lees,David S. Moss,Adrian J. Shepherd:
  A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2.1403-1408

Phylogenetics

• 
  Ingo Bulla,Anne-Kathrin Schultz,Fabian Schreiber,Ming Zhang,Thomas Leitner,Bette T. Korber,Burkhard Morgenstern,Mario Stanke:
  HIV classification using the coalescent theory.1409-1415

Gene Expression

• 
  Li Chen,Jianhua Xuan,Rebecca B. Riggins,Yue Joseph Wang,Eric P. Hoffman,Robert Clarke:
  Multilevel support vector regression analysis to identify condition-specific regulatory networks.1416-1422
• 
  Wen-Han Yu,Hedda Høvik,Tsute Chen:
  A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data.1423-1430
• 
  Zhi-Qiang Ling,Yi Wang,Kenichi Mukaisho,Takanori Hattori,Takeshi Tatsuta,Ming-Hua Ge,Li Jin,Wei-Min Mao,Hiroyuki Sugihara:
  Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.1431-1436

Genetics and Population Analysis

• 
  Shu-Yi Su,Julian E. Asher,Marjo-Riitta Järvelin,Philippe Froguel,Alexandra I. F. Blakemore,David J. Balding,Lachlan J. M. Coin:
  Inferring combined CNV/SNP haplotypes from genotype data.1437-1445
• 
  Chuan-Kang Ting,Wei-Ting Lin,Yao-Ting Huang:
  Multi-objective tag SNPs selection using evolutionary algorithms.1446-1452

Data and Text Mining

• 
  Mounir Errami,Zhaohui Sun,Angela C. George,Tara C. Long,Michael A. Skinner,Jonathan D. Wren,Harold R. Garner:
  Identifying duplicate content using statistically improbable phrases.1453-1457

Applications Note - Genome Analysis

• 
  Michael M. Hoffman,Orion J. Buske,William Stafford Noble:
  The Genomedata format for storing large-scale functional genomics data.1458-1459

Sequence Analysis

• 
  Vladimir Shelest,Daniela Albrecht,Ekaterina Shelest:
  DistanceScan: a tool for promoter modeling.1460-1462

Phylogenetics

• 
  Steven W. Kembel,Peter D. Cowan,Matthew R. Helmus,William K. Cornwell,Hélène Morlon,David D. Ackerly,Simon P. Blomberg,Campbell O. Webb:
  Picante: R tools for integrating phylogenies and ecology.1463-1464

Gene Expression

• 
  Ashok Sharma,Jieping Zhao,Robert H. Podolsky,Richard A. McIndoe:
  ParaSAM: a parallelized version of the significance analysis of microarrays algorithm.1465-1467

Genetics and Population Analysis

• 
  Thierry Schüpbach,Ioannis Xenarios,Sven Bergmann,Karen Kapur:
  FastEpistasis: a high performance computing solution for quantitative trait epistasis.1468-1469

Systems Biology

• 
  Alice Villéger,Stephen Pettifer,Douglas B. Kell:
  Arcadia: a visualization tool for metabolic pathways.1470-1471

Volume 26, Number 12, June 2010

ISMB 2010 Conference Proceedings, July 11-13, 2010, Boston, MA, USA Original Papers

• 
  Luís Pedro Coelho,Tao Peng,Robert F. Murphy:
  Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing.7-12
• 
  Steffen Jaensch,Markus Decker,Anthony A. Hyman,Eugene W. Myers:
  Automated tracking and analysis of centrosomes in earlyCaenorhabditis elegans embryos.13-20
• 
  Sinan Kockara,Mutlu Mete,Vincent Yip,Brendan Lee,Kemal Aydin:
  A soft kinetic data structure for lesion border detection.21-28
• 
  Yu-Shi Lin,Chung-Chih Lin,Yuh-Show Tsai,Tien-Chuan Ku,Yi-Hung Huang,Chun-Nan Hsu:
  A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images.29-37
• 
  Hanchuan Peng,Zongcai Ruan,Deniz Atasoy,Scott Sternson:
  Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.38-46
• 
  Kriti Puniyani,Christos Faloutsos,Eric P. Xing:
  SPEX²: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images.47-56
• 
  Stephan Saalfeld,Albert Cardona,Volker Hartenstein,Pavel Tomancak:
  As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.57-63
• 
  Ranga Srinivasan,Qing Li,Xiaobo Zhou,Ju Lu,Jeff Lichtman,Stephen T. C. Wong:
  Reconstruction of the neuromuscular junction connectome.64-70

Databases and Ontologies

• 
  Matthew Holford,Ekta Khurana,Kei-Hoi Cheung,Mark Gerstein:
  Using semantic web rules to reason on an ontology of pseudogenes.71-78
• 
  Adam J. Richards,Brian Muller,Matthew S. Shotwell,L. Ashley Cowart,Bärbel Rohrer,Xinghua Lu:
  Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.79-87
• 
  Thomas Wächter,Michael Schroeder:
  Semi-automated ontology generation within OBO-Edit.88-96

Disease Models and Epidemiology

• 
  Kai Zhang,Joe W. Gray,Bahram Parvin:
  Sparse multitask regression for identifying common mechanism of response to therapeutic targets.97-105
• 
  David Tolliver,Charalampos E. Tsourakakis,Ayshwarya Subramanian,Stanley Shackney,Russell Schwartz:
  Robust unmixing of tumor states in array comparative genomic hybridization data.106-114

Evolution and Comparative genomics

• 
  Vincent Ranwez,Alexis Criscuolo,Emmanuel J. P. Douzery:
  SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics.115-123
• 
  Leo van Iersel,Steven Kelk,Regula Rupp,Daniel H. Huson:
  Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters.124-131
• 
  Alexandros Stamatakis,Nikolaos Alachiotis:
  Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.132-139
• 
  Yufeng Wu:
  Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees.140-148

Gene Regulation and transcriptomics

• 
  Jeroen de Ridder,Alice Gerrits,Jan Bot,Gerald de Haan,Marcel J. T. Reinders,Lodewyk F. A. Wessels:
  Inferring combinatorial association logic networks in multimodal genome-wide screens.149-157
• 
  Richard S. Savage,Zoubin Ghahramani,Jim E. Griffin,Bernard J. de la Cruz,David L. Wild:
  Discovering transcriptional modules by Bayesian data integration.158-167
• 
  Rendong Yang,Zhen Su:
  Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.168-174

Population genomics

• 
  Sivan Bercovici,Christopher Meek,Ydo Wexler,Dan Geiger:
  Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping.175-182
• 
  Dan He,Arthur Choi,Knot Pipatsrisawat,Adnan Darwiche,Eleazar Eskin:
  Optimal algorithms for haplotype assembly from whole-genome sequence data.183-190
• 
  Xin Li,Xiaolin Yin,Jing Li:
  Efficient identification of identical-by-descent status in pedigrees with many untyped individuals.191-198
• 
  Eric Yi Liu,Qi Zhang,Leonard McMillan,Fernando Pardo-Manuel de Villena,Wei Wang:
  Efficient genome ancestry inference in complex pedigrees with inbreeding.199-207
• 
  Kriti Puniyani,Seyoung Kim,Eric P. Xing:
  Multi-population GWA mapping via multi-task regularized regression.208-216
• 
  Xiang Zhang,Shunping Huang,Fei Zou,Wei Wang:
  TEAM: efficient two-locus epistasis tests in human genome-wide association study.217-227

Protein Interactions and Molecular Networks

• 
  Ariel Jaimovich,Ruty Rinott,Maya Schuldiner,Hanah Margalit,Nir Friedman:
  Modularity and directionality in genetic interaction maps.228-236
• 
  Charles J. Vaske,Stephen C. Benz,J. Zachary Sanborn,Dent Earl,Christopher Szeto,Jingchun Zhu,David Haussler,Joshua M. Stuart:
  Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.237-245
• 
  Yoshihiro Yamanishi,Masaaki Kotera,Minoru Kanehisa,Susumu Goto:
  Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.246-254
• 
  Keren Yizhak,Tomer Benyamini,Wolfram Liebermeister,Eytan Ruppin,Tomer Shlomi:
  Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.255-260

Protein Structure and Function

• 
  Shi-Hua Zhang,Daven Vasishtan,Min Xu,Maya Topf,Frank Alber:
  A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.261-268
• 
  Tsung-Han Chiang,David Hsu,Jean-Claude Latombe:
  Markov dynamic models for long-timescale protein motion.269-277
• 
  Feng Lou,Peter Clote:
  Thermodynamics of RNA structures by Wang-Landau sampling.278-286
• 
  Anoop Kumar,Lenore Cowen:
  Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution.287-293
• 
  Jian Peng,Jinbo Xu:
  Low-homology protein threading.294-300
• 
  Mitul Saha,Michael Levitt,Wah Chiu:
  MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.301-309
• 
  Feng Zhao,Jian Peng,Jinbo Xu:
  Fragment-free approach to protein folding using conditional neural fields.310-317

Sequence Analysis

• 
  Vikas Bansal:
  A statistical method for the detection of variants from next-generation resequencing of DNA pools.318-324
• 
  Yoseph Barash,Benjamin J. Blencowe,Brendan J. Frey:
  Model-based detection of alternative splicing signals.325-333
• 
  Xiaoyu Chen,Michael M. Hoffman,Jeff A. Bilmes,Jay R. Hesselberth,William Stafford Noble:
  A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.334-342
• 
  Adrian V. Dalca,Stephen M. Rumble,Samuel Levy,Michael Brudno:
  VARiD: A variation detection framework for color-space and letter-space platforms.343-349
• 
  Fereydoun Hormozdiari,Iman Hajirasouliha,Phuong Dao,Faraz Hach,Deniz Yörükoglu,Can Alkan,Evan E. Eichler,Süleyman Cenk Sahinalp:
  Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.350-357
• 
  Marco Pellegrini,M. Elena Renda,Alessio Vecchio:
  TRStalker: an efficient heuristic for finding fuzzy tandem repeats.358-366
• 
  Jared T. Simpson,Richard Durbin:
  Efficient construction of an assembly string graph using the FM-index.367-373

Text Mining

• 
  Brian Kemper,Takuya Matsuzaki,Yukiko Matsuoka,Yoshimasa Tsuruoka,Hiroaki Kitano,Sophia Ananiadou,Jun'ichi Tsujii:
  PathText: a text mining integrator for biological pathway visualizations.374-381
• 
  Jari Björne,Filip Ginter,Sampo Pyysalo,Jun'ichi Tsujii,Tapio Salakoski:
  Complex event extraction at PubMed scale.382-390

Other Bioinformatics Applications

• 
  Ilkka Huopaniemi,Tommi Suvitaival,Janne Nikkilä,Matej Oresic,Samuel Kaski:
  Multivariate multi-way analysis of multi-source data.391-398
• 
  Ding Ye,Yan Fu,Ruixiang Sun,Haipeng Wang,Zuofei Yuan,Hao Chi,Si-Min He:
  Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate.399-406

Discovery Note - Sequence Analysis

• 
  Daria V. Dibrova,Michael Y. Galperin,Armen Y. Mulkidjanian:
  Characterization of the N-ATPase, a distinct, laterally transferred Na⁺-translocating form of the bacterial F-type membrane ATPase.1473-1476
• 
  Robson Francisco de Souza,L. Aravind:
  UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes.1477-1480

Original Papers - Genome Analysis

• 
  David M. Kristensen,Lavanya Kannan,Michael K. Coleman,Yuri I. Wolf,Alexander Sorokin,Eugene V. Koonin,Arcady R. Mushegian:
  A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.1481-1487

Sequence Analysis

• 
  Joshua Orvis,Jonathan Crabtree,Kevin Galens,Aaron Gussman,Jason M. Inman,Eduardo Lee,Sreenath Nampally,David R. Riley,Jaideep P. Sundaram,Victor Felix,Brett Whitty,Anup Mahurkar,Jennifer R. Wortman,Owen White,Samuel V. Angiuoli:
  Ergatis: a web interface and scalable software system for bioinformatics workflows.1488-1492

Structural Bioinformatics

• 
  Kota Kasahara,Kengo Kinoshita,Toshihisa Takagi:
  Ligand-binding site prediction of proteins based on known fragment-fragment interactions.1493-1499

Gene Expression

• 
  Douglas W. Bryant Jr.,Rongkun Shen,Henry D. Priest,Weng-Keen Wong,Todd C. Mockler:
  Supersplat - spliced RNA-seq alignment.1500-1505
• 
  Inho Park,Kwang H. Lee,Doheon Lee:
  Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.1506-1512
• 
  Natthakan Iam-on,Tossapon Boongoen,Simon M. Garrett:
  LCE: a link-based cluster ensemble method for improved gene expression data analysis.1513-1519
• 
  Sepp Hochreiter,Ulrich Bodenhofer,Martin Heusel,Andreas Mayr,Andreas Mitterecker,Adetayo Kasim,Tatsiana Khamiakova,Suzy Van Sanden,Dan Lin,Willem Talloen,Luc Bijnens,Hinrich W. H. Göhlmann,Ziv Shkedy,Djork-Arné Clevert:
  FABIA: factor analysis for bicluster acquisition.1520-1527

Systems Biology

• 
  Wolfram Liebermeister,Jannis Uhlendorf,Edda Klipp:
  Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.1528-1534
• 
  Xinghua Lou,Marc Kirchner,Bernhard Y. Renard,Ullrich Köthe,Sebastian Boppel,Christian Graf,Chung-Tien Lee,Judith A. J. Steen,Hanno Steen,Matthias P. Mayer,Fred A. Hamprecht:
  Deuteration distribution estimation with improved sequence coverage for HX/MS experiments.1535-1541
• 
  Sabine Pérès,Liza Figueredo Felicori,Stéphanie Rialle,Elodie Jobard,Franck Molina:
  Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.1542-1547
• 
  Allison P. Heath,George N. Bennett,Lydia E. Kavraki:
  Finding metabolic pathways using atom tracking.1548-1555
• 
  Noushin Ghaffari,Ivan Ivanov,Xiaoning Qian,Edward R. Dougherty:
  A CoD-based reduction algorithm for designing stationary control policies on Boolean networks.1556-1563

Applications Note Sequence Analysis

• 
  Bong-Hyun Kim,Qian Cong,Nick V. Grishin:
  HangOut: generating clean PSI-BLAST profiles for domains with long insertions.1564-1565
• 
  Eric Bonnet,Ying He,Kenny Billiau,Yves Van de Peer:
  TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.1566-1568

Phylogenetics

• 
  Jeet Sukumaran,Mark T. Holder:
  DendroPy: a Python library for phylogenetic computing.1569-1571

Gene Expression

• 
  Matthew D. Wilkerson,D. Neil Hayes:
  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.1572-1573
• 
  N. L. Heinecke,B. S. Pratt,Tomas Vaisar,L. Becker:
  PepC: proteomics software for identifying differentially expressed proteins based on spectral counting.1574-1575

Systems Biology

• 
  Aloke Phatak,Harri T. Kiiveri,Line Harder Clemmensen,William J. Wilson:
  NetRaVE: constructing dependency networks using sparse linear regression.1576-1577

Volume 26, Number 13, July 2010

Original Papers - Genome Analysis

• 
  Hiram A. Firpi,Duygu Ucar,Kai Tan:
  Discover regulatory DNA elements using chromatin signatures and artificial neural network.1579-1586
• 
  Chunfang Zheng:
  Pathgroups, a dynamic data structure for genome reconstruction problems.1587-1594

Sequence Analysis

• 
  Henrik Stranneheim,Max Käller,Tobias Allander,Björn Andersson,Lars Arvestad,Joakim Lundeberg:
  Classification of DNA sequences using Bloom filters.1595-1600
• 
  Anuj R. Shah,Khushbu Agarwal,Erin S. Baker,Mudita Singhal,Anoop M. Mayampurath,Yehia M. Ibrahim,Lars J. Kangas,Matthew E. Monroe,Rui Zhao,Mikhail E. Belov,Gordon A. Anderson,Richard D. Smith:
  Machine learning based prediction for peptide drift times in ion mobility spectrometry.1601-1607
• 
  Nancy Y. Yu,James R. Wagner,Matthew R. Laird,Gabor Melli,Sébastien Rey,Raymond Lo,Phuong Dao,Süleyman Cenk Sahinalp,Martin Ester,Leonard J. Foster,Fiona S. L. Brinkman:
  PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.1608-1615

Structural Bioinformatics

• 
  Zhi-Ping Liu,Ling-Yun Wu,Yong Wang,Xiang-Sun Zhang,Luonan Chen:
  Prediction of protein-RNA binding sites by a random forest method with combined features.1616-1622

Gene Expression

• 
  Manfred Opper,Guido Sanguinetti:
  Learning combinatorial transcriptional dynamics from gene expression data.1623-1629

Systems Biology

• 
  Yanhua Hu,Elvira Osuna-Highley,Juchang Hua,Theodore Scott Nowicki,Robert Stolz,Camille McKayle,Robert F. Murphy:
  Automated analysis of protein subcellular location in time series images.1630-1636
• 
  Alan Veliz-Cuba,Abdul Salam Jarrah,Reinhard C. Laubenbacher:
  Polynomial algebra of discrete models in systems biology.1637-1643

Data and Text Mining

• 
  Dong Wang,Juan Wang,Ming Lu,Fei Song,Qinghua Cui:
  Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases.1644-1650

Databases and Ontologies

• 
  Michael Baitaluk,Julia V. Ponomarenko:
  Semantic integration of data on transcriptional regulation.1651-1661

Applications Note - Genome Analysis

• 
  Aaron L. Statham,Dario Strbenac,Marcel W. Coolen,Clare Stirzaker,Susan J. Clark,Mark D. Robinson:
  Repitools: an R package for the analysis of enrichment-based epigenomic data.1662-1663

Sequence Analysis

• 
  Ignacio L. Ibarra,Francisco Melo:
  Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.1664-1665
• 
  Florian Gnad,Shubin Ren,Chunaram Choudhary,Jürgen Cox,Matthias Mann:
  Predicting post-translational lysine acetylation using support vector machines.1666-1668

Phylogenetics

• 
  Thomas Junier,Evgeny M. Zdobnov:
  The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.1669-1670

Structural Bioinformatics

• 
  Christian Schudoma,Patrick May,Dirk Walther:
  Modeling RNA loops using sequence homology and geometric constraints.1671-1672
• 
  Reda Rawi,Lee Whitmore,Maya Topf:
  CHOYCE: a web server for constrained homology modelling with cryoEM maps.1673-1674

Systems Biology

• 
  Maria Rodriguez-Fernandez,Julio R. Banga:
  SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.1675-1676

Corrigendum - Systems Biology

• 
  Bobbie-Jo M. Webb-Robertson,William R. Cannon,Christopher S. Oehmen,Anuj R. Shah,Vidhya Gurumoorthi,Mary S. Lipton,Katrina M. Waters:
  A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.1677-1683

Volume 26, Number 14, July 2010

Discovery Note - Sequence Analysis

• 
  Emanuele Raineri,Paolo Ribeca,Luis Serrano,Tobias Maier:
  A more precise characterization of chaperonin substrates.1685-1689

Original Papers - Genome Analysis

• 
  Stacy S. Hung,James Wasmuth,Christopher Sanford,John Parkinson:
  DETECT - a Density Estimation Tool for Enzyme ClassificaTion and its application toPlasmodium falciparum.1690-1698
• 
  James K. Bonfield,Andrew Whitwham:
  Gap5 - editing the billion fragment sequence assembly.1699-1703
• 
  Thomas D. Otto,Mandy Sanders,Matthew Berriman,Chris Newbold:
  Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.1704-1707

Sequence Analysis

• 
  Hyrum D. Carroll,Maricel G. Kann,Sergey Sheetlin,John L. Spouge:
  Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics.1708-1713

Structural Bioinformatics

• 
  David T. Barkan,Daniel R. Hostetter,Sami Mahrus,Ursula Pieper,James A. Wells,Charles S. Craik,Andrej Sali:
  Prediction of protease substrates using sequence and structure features.1714-1722

Gene Expression

• 
  Changsik Kim,Jiwon Choi,Hyunjin Park,Yunsun Park,Jungsun Park,Taesung Park,Kwanghui Cho,Young Yang,Sukjoon Yoon:
  Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity.1723-1730

Genetics and Population Analysis

• 
  Monnat Pongpanich,Patrick F. Sullivan,Jung-Ying Tzeng:
  A quality control algorithm for filtering SNPs in genome-wide association studies.1731-1737

Systems Biology

• 
  Gökmen Altay,Frank Emmert-Streib:
  Revealing differences in gene network inference algorithms on the network level by ensemble methods.1738-1744

Data and Text Mining

• 
  Christian Baumgartner,Gregory D. Lewis,Michael Netzer,Bernhard Pfeifer,Robert E. Gerszten:
  A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury.1745-1751
• 
  Daniel F. Schwarz,Inke R. König,Andreas Ziegler:
  On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data.1752-1758
• 
  Sara Mostafavi,Quaid Morris:
  Fast integration of heterogeneous data sources for predicting gene function with limited annotation.1759-1765

Databases and Ontologies

• 
  Gilles Parmentier,Frederic B. Bastian,Marc Robinson-Rechavi:
  Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.1766-1771
• 
  Anmol M. Kiran,Pavel V. Baranov:
  DARNED: a DAtabase of RNa EDiting in humans.1772-1776

Applications Note Genome Analysis

• 
  Giuseppe Maccari,Federica Gemignani,Stefano Landi:
  COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes.1777-1778
• 
  Aris Floratos,Kenneth Smith,Zhou Ji,John Watkinson,Andrea Califano:
  geWorkbench: an open source platform for integrative genomics.1779-1780
• 
  Hui Jiang,Fan Wang,Nigel P. Dyer,Wing Hung Wong:
  CisGenome Browser: a flexible tool for genomic data visualization.1781-1782

Sequence Analysis

• 
  Daniel J. Blankenberg,Assaf Gordon,Gregory Von Kuster,Nathan Coraor,James Taylor,Anton Nekrutenko:
  Manipulation of FASTQ data with Galaxy.1783-1785

Genetics and Population Analysis

• 
  James A. Morris,Joshua C. Randall,Julian B. Maller,Jeffrey C. Barrett:
  Evoker: a visualization tool for genotype intensity data.1786-1787

Systems Biology

• 
  Florian Centler,Christoph Kaleta,Pietro Speroni di Fenizio,Peter Dittrich:
  A parallel algorithm to compute chemical organizations in biological networks.1788-1789
• 
  Michal Wozniak,Jerzy Tiuryn,Janusz Dutkowski:
  MODEVO: exploring modularity and evolution of protein interaction networks.1790-1791
• 
  Serdar Bozdag,Aiguo Li,Stefan Wuchty,Howard A. Fine:
  FastMEDUSA: a parallelized tool to infer gene regulatory networks.1792-1793
• 
  Chuan Hock Koh,Masao Nagasaki,Ayumu Saito,Limsoon Wong,Satoru Miyano:
  DA 1.0: parameter estimation of biological pathways using data assimilation approach.1794-1796
• 
  Juliane Liepe,Chris P. Barnes,Erika Cule,Kamil Erguler,Paul D. W. Kirk,Tina Toni,Michael P. H. Stumpf:
  ABC-SysBio - approximate Bayesian computation in Python with GPU support.1797-1799

Data and Text Mining

• 
  Christophe Roeder,Clément Jonquet,Nigam H. Shah,William A. Baumgartner Jr.,Karin Verspoor,Lawrence Hunter:
  A UIMA wrapper for the NCBO annotator.1800-1801
• 
  Marko Laakso,Sampsa Hautaniemi:
  Integrative platform to translate gene sets to networks.1802-1803

Databases and Ontologies

• 
  George Khelashvili,Kevin C. Dorff,Jufang Shan,Marta Camacho-Artacho,Lucy Skrabanek,Bas Vroling,Michel Bouvier,Lakshmi Devi,Susan R. George,Jonathan A. Javitch,Martin J. Lohse,Graeme Milligan,Richard R. Neubig,Krzysztof Palczewski,Marc Parmentier,Jean-Philippe Pin,Gerrit Vriend,Fabien Campagne,Marta Filizola:
  GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.1804-1805
• 
  John E. Beaver,Murat Tasan,Francis D. Gibbons,Weidong Tian,Timothy R. Hughes,Frederick P. Roth:
  FuncBase : a resource for quantitative gene function annotation.1806-1807
• 
  Thea Van Rossum,Ben W. Tripp,Denise Daley:
  SLIMS - a user-friendly sample operations and inventory management system for genotyping labs.1808-1810

Volume 26, Number 15, August 2010

Original Papers - Genome Analysis

• 
  Helena Brunel,Joan-Josep Gallardo-Chacón,Alfonso Buil,Montserrat Vallverdú,José Manuel Soria,Pere Caminal,Alexandre Perera:
  MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis.1811-1818
• 
  Andrey Kislyuk,Lee S. Katz,Sonia Agrawal,Matthew S. Hagen,Andrew B. Conley,Pushkala Jayaraman,Viswateja Nelakuditi,Jay C. Humphrey,Scott A. Sammons,Dhwani Govil,Raydel D. Mair,Kathleen M. Tatti,Maria L. Tondella,Brian H. Harcourt,Leonard W. Mayer,I. King Jordan:
  A computational genomics pipeline for prokaryotic sequencing projects.1819-1826
• 
  Maria Ortiz-Estevez,Henrik Bengtsson,Angel Rubio:
  ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.1827-1833
• 
  Norman J. MacDonald,Robert G. Beiko:
  Efficient learning of microbial genotype-phenotype association rules.1834-1840

Sequence Analysis

• 
  Yoichi Murakami,Kenji Mizuguchi:
  Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.1841-1848

Structural Bioinformatics

• 
  Braddon K. Lance,Charlotte M. Deane,Graham R. Wood:
  Exploring the potential of template-based modelling.1849-1856
• 
  Huiying Zhao,Yuedong Yang,Yaoqi Zhou:
  Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.1857-1863

Gene Expression

• 
  Hao Wu,Hongkai Ji:
  JAMIE: joint analysis of multiple ChIP-chip experiments.1864-1870

Genetics and Population Analysis

• 
  Xing Hua,Han Zhang,Hong Zhang,Yaning Yang,Anthony Y. C. Kuk:
  Testing multiple gene interactions by the ordered combinatorial partitioning method in case-control studies.1871-1878

Systems Biology

• 
  Ahrim Youn,David J. Reiss,Werner Stuetzle:
  Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.1879-1886

Data and Text Mining

• 
  Vincenzo Lagani,Ioannis Tsamardinos:
  Structure-based variable selection for survival data.1887-1894

Applications Note - Genome Analysis

• 
  Bruno Zeitouni,Valentina Boeva,Isabelle Janoueix-Lerosey,Sophie Loeillet,Patricia Legoix-né,Alain Nicolas,Olivier Delattre,Emmanuel Barillot:
  SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.1895-1896
• 
  Christian Baudet,Claire Lemaitre,Zanoni Dias,Christian Gautier,Eric Tannier,Marie-France Sagot:
  Cassis: detection of genomic rearrangement breakpoints.1897-1898

Sequence Analysis

• 
  Kazutaka Katoh,Hiroyuki Toh:
  Parallelization of the MAFFT multiple sequence alignment program.1899-1900
• 
  Brian D. Ondov,Charles Cochran,Mark Landers,Gavin D. Meredith,Miroslav Dudas,Nicholas H. Bergman:
  An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.1901-1902
• 
  Paolo Di Tommaso,Miquel Orobitg,Fernando Guirado,Fernando Cores,Toni Espinosa,Cédric Notredame:
  Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.1903-1904
• 
  Mindaugas Margelevicius,Mindaugas Laganeckas,Ceslovas Venclovas:
  COMA server for protein distant homology search.1905-1906

Phylogenetics

• 
  Thibaut Jombart,François Balloux,Stéphane Dray:
  adephylo: new tools for investigating the phylogenetic signal in biological traits.1907-1909
• 
  Miklós Csuös:
  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.1910-1912

Structural Bioinformatics

• 
  Sourav Das,Michael P. Krein,Curt M. Breneman:
  PESDserv: a server for high-throughput comparison of protein binding site surfaces.1913-1914
• 
  Christopher D. Lau,Marshall J. Levesque,Shu Chien,Susumu Date,Jason H. Haga:
  ViewDock TDW: high-throughput visualization of virtual screening results.1915-1917

Gene Expression

• 
  Zhang Zhang,Francesc López-Giráldez,Jeffrey P. Townsend:
  LOX: inferring Level Of eXpression from diverse methods of census sequencing.1918-1919

Systems Biology

• 
  Yitzhak Friedman,Guy Naamati,Michal Linial:
  MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets.1920-1921

Data and Text Mining

• 
  Sven Schuierer,Léon-Charles Tranchevent,Uwe Dengler,Yves Moreau:
  Large-scale benchmark of Endeavour using MetaCore maps.1922-1923
• 
  Philip Groth,Ivan Kalev,Ivaylo Kirov,Borislav Traikov,Ulf Leser,Bertram Weiss:
  Phenoclustering: online mining of cross-species phenotypes.1924-1925

Volume 26, Number 16, August 2010

Discovery Note - Sequence Analysis

• 
  Klaus O. Kopec,Vikram Alva,Andrei N. Lupas:
  Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria.1927-1931

Original Papers - Genome Analysis

• 
  Mark E. T. Horn,Peter M. Waterhouse:
  Rapid match-searching for gene silencing assessment.1932-1937
• 
  Marc Fiume,Vanessa Williams,Andrew Brook,Michael Brudno:
  Savant: genome browser for high-throughput sequencing data.1938-1944
• 
  Ari B. Kahn,Barry Zeeberg,Michael C. Ryan,D. Curtis Jamison,David M. Rockoff,Yves Pommier,John N. Weinstein:
  Ontogenomic study of the relationship between number of gene splice variants and GO categorization.1945-1949

Sequence Analysis

• 
  Yin Hu,Kai Wang,Xiaping He,Derek Y. Chiang,Jan F. Prins,Jinze Liu:
  A probabilistic framework for aligning paired-end RNA-seq data.1950-1957
• 
  Yongchao Liu,Bertil Schmidt,Douglas L. Maskell:
  MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.1958-1964

Structural Bioinformatics

• 
  Thomas C. Freeman Jr.,William C. Wimley:
  A highly accurate statistical approach for the prediction of transmembrane beta-barrels.1965-1974
• 
  Fuxiao Xin,Steven A. Myers,Yong Fuga Li,David N. Cooper,Sean D. Mooney,Predrag Radivojac:
  Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.1975-1982

Gene Expression

• 
  Xinping Cui,Na You,Thomas Girke,Richard Michelmore,Allen Van Deynze:
  Single feature polymorphism detection using recombinant inbred line microarray expression data.1983-1989
• 
  Monika Jelizarow,Vincent Guillemot,Arthur Tenenhaus,Korbinian Strimmer,Anne-Laure Boulesteix:
  Over-optimism in bioinformatics: an illustration.1990-1998

Genetics and Population Analysis

• 
  Taane G. Clark,Susana G. Campino,Elisa Anastasi,Sarah Auburn,Yik Y. Teo,Kerrin S. Small,Kirk A. Rockett,Dominic Kwiatkowski,Christopher C. Holmes:
  A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.1999-2003

Systems Biology

• 
  John M. O. Ranola,Sangtae Ahn,Mary E. Sehl,Desmond J. Smith,Kenneth Lange:
  A Poisson model for random multigraphs.2004-2011
• 
  Pablo Carbonell,Jean-Loup Faulon:
  Molecular signatures-based prediction of enzyme promiscuity.2012-2019
• 
  Tong Zhou,Ya-Li Wang:
  Causal relationship inference for a large-scale cellular network.2020-2028
• 
  Kresimir Letinic,Rafael Sebastián,Andrew Barthel,Derek Toomre:
  Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networks.2029-2036
• 
  Yi Ming Zou:
  Modeling and analyzing complex biological networks incooperating experimental information on both network topology and stable states.2037-2041

Databases and Ontologies

• 
  Tamás Korcsmáros,Illés J. Farkas,Mate S. Szalay,Petra Rovó,Dávid Fazekas,Zoltán Spiró,Csaba Böde,Katalin Lenti,Tibor Vellai,Peter Csermely:
  Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery.2042-2050

Applications Note - Genome Analysis

• 
  Fengfeng Zhou,Ying Xu:
  cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.2051-2052

Sequence Analysis

• 
  Eduardo Gorrón,Fausto Rodríguez,Diana Bernal,Luis Miguel Rodriguez-Rojas,Adriana Bernal,Silvia Restrepo,Joe Tohme:
  A new method for designing degenerate primers and its use in the identification of sequences inBrachiaria showing similarity to apomixis-associated genes.2053-2054
• 
  Alexey S. Kondrashov,Raquel Assis:
  Bridges: a tool for identifying local similarities in long sequences.2055-2056

Structural Bioinformatics

• 
  Fabrice Jossinet,Thomas E. Ludwig,Eric Westhof:
  Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.2057-2059

Gene Expression

• 
  Jose M. G. Vilar,Leonor Saiz:
  CplexA: aMathematica package to study macromolecular-assembly control of gene expression.2060-2061
• 
  Andreas Lüscher,Gábor Csárdi,Aitana Morton de Lachapelle,Zoltán Kutalik,Bastian Peter,Sven Bergmann:
  ExpressionView - an interactive viewer for modules identified in gene expression data.2062-2063

Genetics and Population Analysis

• 
  Gregory Ewing,Joachim Hermisson:
  MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus.2064-2065

Systems Biology

• 
  Ivan Dimitrov,Panayot Garnev,Darren R. Flower,Irini A. Doytchinova:
  EpiTOP - a proteochemometric tool for MHC class II binding prediction.2066-2068

Databases and Ontologies

• 
  William M. McLaren,Bethan Pritchard,Daniel Rios,Yuan Chen,Paul Flicek,Fiona Cunningham:
  Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.2069-2070

Volume 26, Number 17, September 2010

Discovery Note - Genome Analysis

• 
  Stephen A. Ramsey,Theo A. Knijnenburg,Kathleen A. Kennedy,Daniel E. Zak,Mark Gilchrist,Elizabeth S. Gold,Carrie D. Johnson,Aaron E. Lampano,Vladimir Litvak,Garnet Navarro,Tetyana Stolyar,Alan Aderem,Ilya Shmulevich:
  Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.2071-2075

Original Papers - Genome Analysis

• 
  Khalid Mahmood,Arun Siddharth Konagurthu,Jiangning Song,Ashley M. Buckle,Geoffrey I. Webb,James C. Whisstock:
  EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes.2076-2084
• 
  Jasmina Bogojeska,Steffen Bickel,André Altmann,Thomas Lengauer:
  Dealing with sparse data in predicting outcomes of HIV combination therapies.2085-2092
• 
  Roman Pahl,Helmut Schäfer:
  PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing.2093-2100

Sequence Analysis

• 
  Jirí Macas,Pavel Neumann,Petr Novák,Jiming Jiang:
  Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data.2101-2108
• 
  Arunachalam Manonmani,Karthik Jayasurya,Pavel Tomancak,Uwe Ohler:
  An alignment-free method to identify candidate orthologous enhancers in multipleDrosophila genomes.2109-2115
• 
  Rahul Satija,Jotun Hein,Gerton Lunter:
  Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.2116-2120

Structural Bioinformatics

• 
  Liang-Tsung Huang,M. Michael Gromiha:
  First insight into the prediction of protein folding rate change upon point mutation.2121-2127

Gene Expression

• 
  Timothy Hancock,Ichigaku Takigawa,Hiroshi Mamitsuka:
  Mining metabolic pathways through gene expression.2128-2135
• 
  Marc Johannes,Jan C. Brase,Holger Fröhlich,Stephan Gade,Mathias C. Gehrmann,Maria Fälth,Holger Sültmann,Tim Beißbarth:
  Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients.2136-2144

Genetics and Population Analysis

• 
  William Rowe,David C. Wedge,Mark Platt,Douglas B. Kell,Joshua D. Knowles:
  Predictive models for population performance on real biological fitness landscapes.2145-2152

Systems Biology

• 
  David M. A. Martin,Isabelle R. E. Nett,Franck Vandermoere,Jonathan D. Barber,Nicholas A. Morrice,Michael A. J. Ferguson:
  Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry.2153-2159
• 
  Steffen Klamt,Robert J. Flassig,Kai Sundmacher:
  TRANSWESD: inferring cellular networks with transitive reduction.2160-2168
• 
  Jungsoo Gim,Ho-Shik Kim,Junil Kim,Minsoo Choi,Jeong-Rae Kim,Yeun-Jun Chung,Kwang-Hyun Cho:
  A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway.2169-2175
• 
  Di Wu,Elgene Lim,François Vaillant,Marie-Liesse Asselin-Labat,Jane E. Visvader,Gordon K. Smyth:
  ROAST: rotation gene set tests for complex microarray experiments.2176-2182

Data and Text Mining

• 
  Bethany J. Wolf,Elizabeth G. Hill,Elizabeth H. Slate:
  Logic Forest: an ensemble classifier for discovering logical combinations of binary markers.2183-2189

Applications Note Genome Analysis

• 
  Cristen J. Willer,Yun Li,Gonçalo R. Abecasis:
  METAL: fast and efficient meta-analysis of genomewide association scans.2190-2191

Sequence Analysis

• 
  Waibhav Tembe,James Lowey,Edward Suh:
  G-SQZ: compact encoding of genomic sequence and quality data.2192-2194
• 
  Kjetil Klepper,Finn Drabløs:
  PriorsEditor: a tool for the creation and use of positional priors in motif discovery.2195-2197

Genetics and Population Analysis

• 
  Malu Luz Calle,Víctor Urrea,Núria Malats,Kristel Van Steen:
  mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits.2198-2199
• 
  Brendan O'Fallon:
  TreesimJ: a flexible, forward time population genetic simulator.2200-2201

Systems Biology

• 
  Heiko A. Mannsperger,Stephan Gade,Frauke Henjes,Tim Beißbarth,Ulrike Korf:
  RPPanalyzer: Analysis of reverse-phase protein array data.2202-2203

Data and Text Mining

• 
  W. James Kent,Ann S. Zweig,Galt P. Barber,Angie S. Hinrichs,Donna Karolchik:
  BigWig and BigBed: enabling browsing of large distributed datasets.2204-2207
• 
  Michael Wittig,Ingo Helbig,Stefan Schreiber,Andre Franke:
  CNVineta: a data mining tool for large case-control copy number variation datasets.2208-2209

Databases and Ontologies

• 
  Sylvain Brohée,Roland Barriot,Yves Moreau:
  Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.2210-2211
• 
  Meng-Pin Weng,Ben-Yang Liao:
  MamPhEA: a web tool for mammalian phenotype enrichment analysis.2212-2213

Letters to the Editor Gene Expression

• 
  Phillip Good:
  Exchangeable random variables.2214
• 
  Violeta Calian,Jason C. Hsu:
  Response to Letter to the Editor by Philip Good on To Permute or Not to Permute.2215

Volume 26, Number 18, September 2010

ECCB 2010 Conference Proceedings, September 26 to September 29, 2010, Ghent, Belgium

• 
  Abhilash Srikantha,Ajit S. Bopardikar,Kalyan Kumar Kaipa,Parthasarathy Venkataraman,Kyusang Lee,TaeJin Ahn,Rangavittal Narayanan:
  A fast algorithm for exact sequence search in biological sequences using polyphase decomposition.
• 
  Susanne Balzer,Ketil Malde,Anders Lanzén,Animesh Sharma,Inge Jonassen:
  Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim.
• 
  Florian Erhard,Ralf Zimmer:
  Classification of ncRNAs using position and size information in deep sequencing data.
• 
  Jurgen F. Nijkamp,Wynand Winterbach,Marcel van den Broek,Jean-Marc Daran,Marcel J. T. Reinders,Dick de Ridder:
  Integrating genome assemblies with MAIA.
• 
  Osnat Ravid-Amir,Saharon Rosset:
  Maximum likelihood estimation of locus-specific mutation rates in Y-chromosome short tandem repeats.
• 
  Crystal L. Kahn,Borislav H. Hristov,Benjamin J. Raphael:
  Parsimony and likelihood reconstruction of human segmental duplications.
• 
  Christian Höner zu Siederdissen,Ivo L. Hofacker:
  Discriminatory power of RNA family models.
• 
  Yuki Kato,Kengo Sato,Michiaki Hamada,Yoshihide Watanabe,Kiyoshi Asai,Tatsuya Akutsu:
  RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
• 
  An P. N. Vo,Nha Nguyen,Heng Huang:
  Solenoid and non-solenoid protein recognition using stationary wavelet packet transform.
• 
  Gergely Csaba,Ralf Zimmer:
  Vorescore - fold recognition improved by rescoring of protein structure models.
• 
  Guy Naamati,Manor Askenazi,Michal Linial:
  A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes.
• 
  Marcin J. Mizianty,Wojciech Stach,Ke Chen,Kanaka Durga Kedarisetti,Fatemeh Miri Disfani,Lukasz A. Kurgan:
  Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources.
• 
  Alexander Goncearenco,Igor N. Berezovsky:
  Prototypes of elementary functional loops unravel evolutionary connections between protein functions.
• 
  Kuan-Bei Chen,Yu Zhang:
  A varying threshold method for ChIP peak-calling using multiple sources of information.
• 
  Dougu Nam:
  De-correlating expression in gene-set analysis.
• 
  Ali Shojaie,George Michailidis:
  Discovering graphical Granger causality using the truncating lasso penalty.
• 
  Geoff MacIntyre,James Bailey,Izhak Haviv,Adam Kowalczyk:
  is-rSNP: a novel technique forin silico regulatory SNP detection.
• 
  Carlo Vittorio Cannistraci,Timothy Ravasi,Franco Maria Montevecchi,Trey Ideker,Massimo Alessio:
  Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.
• 
  Matús Kalas,Pål Puntervoll,Alexandre Joseph,Edita Bartaseviciute,Armin Töpfer,Prabakar Venkataraman,Steve Pettifer,Jan Christian Bryne,Jon C. Ison,Christophe Blanchet,Kristoffer Rapacki,Inge Jonassen:
  BioXSD: the common data-exchange format for everyday bioinformatics web services.
• 
  Luis Tari,Saadat Anwar,Shanshan Liang,James Cai,Chitta Baral:
  Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism.
• 
  Sofie Van Landeghem,Thomas Abeel,Yvan Saeys,Yves Van de Peer:
  Discriminative and informative features for biomolecular text mining with ensemble feature selection.
• 
  Andreas Schlicker,Thomas Lengauer,Mario Albrecht:
  Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
• 
  Terri K. Attwood,Douglas B. Kell,Philip McDermott,James Marsh,Stephen Pettifer,David Thorne:
  Utopia documents: linking scholarly literature with research data.
• 
  Steven Gay,Sylvain Soliman,François Fages:
  A graphical method for reducing and relating models in systems biology.
• 
  Max Sajitz-Hermstein,Zoran Nikoloski:
  A novel approach for determining environment-specific protein costs: the case ofArabidopsis thaliana.
• 
  Ryo Yoshida,Masaya M. Saito,Hiromichi Nagao,Tomoyuki Higuchi:
  Bayesian experts in exploring reaction kinetics of transcription circuits.
• 
  Christian Bender,Frauke Henjes,Holger Fröhlich,Stefan Wiemann,Ulrike Korf,Tim Beißbarth:
  Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data.
• 
  Grégory Batt,Michel Page,Irene Cantone,Gregor Goessler,Pedro T. Monteiro,Hidde de Jong:
  Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.
• 
  Tiago Rito,Zi Wang,Charlotte M. Deane,Gesine Reinert:
  How threshold behaviour affects the use of subgraphs for network comparison.
• 
  Rosario Michael Piro,Ivan Molineris,Ugo Ala,Paolo Provero,Ferdinando Di Cunto:
  Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR.
• 
  Phuong Dao,Recep Colak,Raheleh Salari,Flavia Moser,Elai Davicioni,Alexander Schönhuth,Martin Ester:
  Inferring cancer subnetwork markers using density-constrained biclustering.
• 
  Edwin Villanueva,Carlos Dias Maciel:
  Modeling associations between genetic markers using Bayesian networks.
• 
  Eric Bonnet,Tom Michoel,Yves Van de Peer:
  Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data.
• 
  Yanjun Qi,Öznur Tastan,Jaime G. Carbonell,Judith Klein-Seetharaman,Jason Weston:
  Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins.
• 
  Apichat Suratanee,Ilka Rebhan,Petr Matula,Anil Kumar,Lars Kaderali,Karl Rohr,Ralf Bartenschlager,Roland Eils,Rainer König:
  Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images.
• 
  Nha Nguyen,Heng Huang,Soontorn Oraintara,An P. N. Vo:
  Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet.

Review - Sequence Analysis

• 
  Filippo Geraci:
  A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.2217-2225

Original Papers - Genome Analysis

• 
  Anthony Mathelier,Alessandra Carbone:
  MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.2226-2234

Sequence Analysis

• 
  Rao M. Kotamarti,Michael Hahsler,Douglas Raiford,Monnie McGee,Margaret H. Dunham:
  Analyzing taxonomic classification using extensible Markov models.2235-2241
• 
  Penghao Wang,Pengyi Yang,Jonathan Arthur,Jean Yee Hwa Yang:
  A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data.2242-2249

Structural Bioinformatics

• 
  Pietro di Lena,Piero Fariselli,Luciano Margara,Marco Vassura,Rita Casadio:
  Fast overlapping of protein contact maps by alignment of eigenvectors.2250-2258
• 
  Mu Gao,Jeffrey Skolnick:
  iAlign: a method for the structural comparison of protein-protein interfaces.2259-2265
• 
  Menachem Fromer,Michal Linial:
  Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design.2266-2272
• 
  Inken Wohlers,Francisco S. Domingues,Gunnar W. Klau:
  Towards optimal alignment of protein structure distance matrices.2273-2280

Gene Expression

• 
  Numanul Subhani,Luis Rueda,Alioune Ngom,Conrad J. Burden:
  Multiple gene expression profile alignment for microarray time-series data clustering.2281-2288

Systems Biology

• 
  Jianfei Hu,Jun Wan,Laszlo Hackler Jr.,Donald J. Zack,Jiang Qian:
  Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.2289-2297
• 
  Stéphanie Rialle,Liza Figueredo Felicori,Camila Dias-Lopes,Sabine Pérès,Sanaâ El Atia,Alain R. Thierry,Patrick Amar,Franck Molina:
  BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.2298-2304
• 
  Edward R. Morrissey,Miguel A. Juárez,Katherine J. Denby,Nigel J. Burroughs:
  On reverse engineering of gene interaction networks using time course data with repeated measurements.2305-2312
• 
  Ze Tian,Rui Kuang:
  Integrative classification and analysis of multiple arrayCGH datasets with probe alignment.2313-2320

Data and Text Mining

• 
  Jiannan Wang,Inci Cetindil,Shengyue Ji,Chen Li,Xiaohui Xie,Guoliang Li,Jianhua Feng:
  Interactive and fuzzy search: a dynamic way to explore MEDLINE.2321-2327

Databases and Ontologies

• 
  Pascal Gellert,Katharina Jenniches,Thomas Braun,Shizuka Uchida:
  C-It: a knowledge database for tissue-enriched genes.2328-2333

Applications Note - Genome Analysis

• 
  Lionel Guy,Jens Roat Kultima,Siv G. E. Andersson:
  genoPlotR: comparative gene and genome visualization in R.2334-2335
• 
  Randall J. Pruim,Ryan P. Welch,Serena Sanna,Tanya M. Teslovich,Peter S. Chines,Terry P. Gliedt,Michael Boehnke,Gonçalo R. Abecasis,Cristen J. Willer:
  LocusZoom: regional visualization of genome-wide association scan results.2336-2337

Systems Biology

• 
  San-Yuan Wang,Tsung-Jung Ho,Ching-Hua Kuo,Yufeng J. Tseng:
  Chromaligner: a web server for chromatogram alignment.2338-2339
• 
  Tobias Czauderna,Christian Klukas,Falk Schreiber:
  Editing, validating and translating of SBGN maps.2340-2341
• 
  Jianguo Xia,David S. Wishart:
  MetPA: a web-based metabolomics tool for pathway analysis and visualization.2342-2344
• 
  John L. Van Hemert,Julie A. Dickerson:
  PathwayAccess: CellDesigner plugins for pathway databases.2345-2346
• 
  Christian Tannus Lopes,Max Franz,Farzana Kazi,Sylva L. Donaldson,Quaid Morris,Gary D. Bader:
  Cytoscape Web: an interactive web-based network browser.2347-2348
• 
  André Fujita,Kaname Kojima,Alexandre Galvão Patriota,João Ricardo Sato,Patricia Severino,Satoru Miyano:
  A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets.2349-2351
• 
  Thomas Forth,Glenn A. McConkey,David R. Westhead:
  MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.2352-2353

Databases and Ontologies

• 
  Philippe Rocca-Serra,Marco Brandizi,Eamonn Maguire,Nataliya Sklyar,Chris F. Taylor,Kimberly Begley,Dawn Field,Stephen C. Harris,Winston Hide,Oliver Hofmann,Steffen Neumann,Peter Sterk,Weida Tong,Susanna-Assunta Sansone:
  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.2354-2356
• 
  Edward A. Kawas,Mark D. Wilkinson:
  OWL2Perl: creating Perl modules from OWL class definitions.2357-2358
• 
  Hyunchul Jang,Jinhyun Kim,Sang-Kyun Kim,Chul Kim,Soon-Hee Bae,Anna Kim,Dong-Myung Eom,Mi-Young Song:
  Ontology for medicinal materials based on traditional Korean medicine.2359-2360
• 
  Mileidy W. Gonzalez,William R. Pearson:
  RefProtDom: a protein database with improved domain boundaries and homology relationships.2361-2362

Volume 26, Number 19, October 2010

Original Papers - Genome Analysis

• 
  Benilton S. Carvalho,Rafael A. Irizarry:
  A framework for oligonucleotide microarray preprocessing.2363-2367
• 
  Nikolas Askitis,Ranjan Sinha:
  RepMaestro: scalable repeat detection on disk-based genome sequences.2368-2374
• 
  Hua Zhou,Mary E. Sehl,Janet S. Sinsheimer,Kenneth Lange:
  Association screening of common and rare genetic variants by penalized regression.2375-2382

Sequence Analysis

• 
  Akito Taneda:
  Multi-objective pairwise RNA sequence alignment.2383-2390
• 
  Hashem Koohy,Nigel P. Dyer,John E. Reid,Georgy Koentges,Sascha Ott:
  An alignment-free model for comparison of regulatory sequences.2391-2397

Structural Bioinformatics

• 
  David W. Ritchie,Vishwesh Venkatraman:
  Ultra-fast FFT protein docking on graphics processors.2398-2405
• 
  Navdeep Jaitly,Marcus A. Brubaker,John L. Rubinstein,Ryan H. Lilien:
  A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy.2406-2415

Gene Expression

• 
  Hai-Son Le,Zoltán N. Oltvai,Ziv Bar-Joseph:
  Cross-species queries of large gene expression databases.2416-2423

Systems Biology

• 
  Oleh Dzyubachyk,Jeroen Essers,Wiggert A. van Cappellen,Céline Baldeyron,Akiko Inagaki,Wiro J. Niessen,Erik Meijering:
  Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci.2424-2430
• 
  Philip M. R. Tedder,James R. Bradford,Chris J. Needham,Glenn A. McConkey,Andrew J. Bulpitt,David R. Westhead:
  Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasitePlasmodium falciparum.2431-2437
• 
  Alexander Lachmann,Huilei Xu,Jayanth Krishnan,Seth I. Berger,Amin R. Mazloom,Avi Ma'ayan:
  ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.2438-2444

Databases and Ontologies

• 
  Bo Jin,Xinghua Lu:
  Identifying informative subsets of the Gene Ontology with information bottleneck methods.2445-2451

Applications Note - Genome Analysis

• 
  Nikos Darzentas,Alexandros Bousios,V. Apostolidou,Athanasios Tsaftaris:
  MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences.2452-2454

Sequence Analysis

• 
  Wayne Delport,Art F. Y. Poon,Simon D. W. Frost,Sergei L. Kosakovsky Pond:
  Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.2455-2457
• 
  Thomas A. Peterson,Asa Adadey,Ivette Santana-Cruz,Yanan Sun,Andrew Winder,Maricel G. Kann:
  DMDM: domain mapping of disease mutations.2458-2459
• 
  Robert C. Edgar:
  Search and clustering orders of magnitude faster than BLAST.2460-2461
• 
  Darren P. Martin,Philippe Lemey,Martin Lott,Vincent Moulton,David Posada,Pierre Lefeuvre:
  RDP3: a flexible and fast computer program for analyzing recombination.2462-2463
• 
  Wen-Chi Chou,Yanbin Yin,Ying Xu:
  GolgiP: prediction of Golgi-resident proteins in plants.2464-2465

Structural Bioinformatics

• 
  Menachem Fromer,Chen Yanover,Amir Harel,Ori Shachar,Yair Weiss,Michal Linial:
  SPRINT: side-chain prediction inference toolbox for multistate protein design.2466-2467

Gene Expression

• 
  Adeline Simon,Eric Biot:
  ANAIS: Analysis of NimbleGen Arrays Interface.2468-2469
• 
  Ravi Shankar,Helen E. Parkinson,Tony Burdett,Emma Hastings,Junmin Liu,Michael Miller,Rashmi Srinivasa,Joseph White,Alvis Brazma,Gavin Sherlock,Christian J. Stoeckert Jr.,Catherine A. Ball:
  Annotare - a tool for annotating high-throughput biomedical investigations and resulting data.2470-2471
• 
  Kevin C. Dorff,Nyasha Chambwe,Marko Srdanovic,Fabien Campagne:
  BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets.2472-2473

Genetics and Population Analysis

• 
  Tsun-Po Yang,Claude Beazley,Stephen B. Montgomery,Antigone S. Dimas,Maria Gutierrez-Arcelus,Barbara E. Stranger,Panos Deloukas,Emmanouil T. Dermitzakis:
  Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.2474-2476

Systems Biology

• 
  Thai Quang Tung,Doheon Lee:
  PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics.2477-2479
• 
  Anika Jöcker,Johanna Sonntag,Frauke Henjes,Frank Götschel,Achim Tresch,Tim Beißbarth,Stefan Wiemann,Ulrike Korf:
  QuantProReloaded: quantitative analysis of microspot immunoassays.2480-2481

Data and Text Mining

• 
  Arnold Kuzniar,Somdutta Dhir,Harm Nijveen,Sándor Pongor,Jack A. M. Leunissen:
  Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.2482-2483
• 
  Phoenix Kwan,Amanda Birmingham:
  NoiseMaker: simulated screens for statistical assessment.2484-2485
• 
  Yoshinobu Kano,Paul D. Dobson,Mio Nakanishi,Jun'ichi Tsujii,Sophia Ananiadou:
  Text mining meets workflow: linking U-Compare with Taverna.2486-2487
• 
  H. Paul Benton,Elizabeth J. Want,Timothy M. D. Ebbels:
  Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data.2488-2489

Databases and Ontologies

• 
  Georgios N. Tsaousis,Konstantinos D. Tsirigos,Xanthi D. Andrianou,Theodore D. Liakopoulos,Pantelis G. Bagos,Stavros J. Hamodrakas:
  ExTopoDB: a database of experimentally derived topological models of transmembrane proteins.2490-2492
• 
  Jie Bai,Junrong Wang,Feng Xue,Jingsong Li,Lijing Bu,Junming Hu,Gang Xu,Qiyu Bao,Guoping Zhao,Xiaoming Ding,Jie Yan,Jinyu Wu:
  proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors.2493-2495
• 
  Julia D. Fischer,Gemma L. Holliday,Janet M. Thornton:
  The CoFactor database: organic cofactors in enzyme catalysis.2496-2497

Letter to the Editor - Databases and Ontologies

• 
  Anna Marabotti,Angelo M. Facchiano:
  The misuse of terms in scientific literature.2498

Corrigenda - Databases and Ontologies

• 
  Elena Yavorska Harris,Nadia Ponts,Aleksandr Levchuk,Karine G. Le Roch,Stefano Lonardi:
  BRAT: bisulfite-treated reads analysis tool.2499
• 
  Andrew D. Fernandes,Gregory B. Gloor:
  Mutual information is critically dependent on prior assumptions: would thecorrect estimate of mutual information please identify itself?2500

Volume 26, Number 20, October 2010

Original Paper - Genome Analysis

• 
  Jianrong Wang,Ahsan Huda,Victoria V. Lunyak,I. King Jordan:
  A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.2501-2508
• 
  Son K. Pham,Pavel A. Pevzner:
  DRIMM-Synteny: decomposing genomes into evolutionary conserved segments.2509-2516
• 
  Xiang Wan,Can Yang,Qiang Yang,Hong Xue,Nelson L. S. Tang,Weichuan Yu:
  Detecting two-locus associations allowing for interactions in genome-wide association studies.2517-2525

Sequence Analysis

• 
  Xiao Yang,Karin S. Dorman,Srinivas Aluru:
  Reptile: representative tiling for short read error correction.2526-2533
• 
  Guillaume Rizk,Dominique Lavenier:
  GASSST: global alignment short sequence search tool.2534-2540

Structural Bioinformatics

• 
  Weiqiang Zhou,Hong Yan:
  A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.2541-2548
• 
  Wissam Mehio,Graham J. L. Kemp,Paul Taylor,Malcolm D. Walkinshaw:
  Identification of protein binding surfaces using surface triplet propensities.2549-2555
• 
  Anthony Y. C. Kuk,Jinfeng Xu,Yaning Yang:
  A study of the efficiency of pooling in haplotype estimation.2556-2563
• 
  Zohar Itzhaki,Eyal Akiva,Hanah Margalit:
  Preferential use of protein domain pairs as interaction mediators: order and transitivity.2564-2570

Gene Expression

• 
  Timo Erkkilä,Saara Lehmusvaara,Pekka Ruusuvuori,Tapio Visakorpi,Ilya Shmulevich,Harri Lähdesmäki:
  Probabilistic analysis of gene expression measurements from heterogeneous tissues.2571-2577
• 
  Devin C. Koestler,Carmen J. Marsit,Brock C. Christensen,Margaret R. Karagas,Raphael Bueno,David J. Sugarbaker,Karl T. Kelsey,Eugene Andres Houseman:
  Semi-supervised recursively partitioned mixture models for identifying cancer subtypes.2578-2585
• 
  Zhibao Mi,Kui Shen,Nan Song,Chunrong Cheng,Chi Song,Naftali Kaminski,George C. Tseng:
  Module-based prediction approach for robust inter-study predictions in microarray data.2586-2593
• 
  Cesim Erten,Melih Sözdinler:
  Improving performances of suboptimal greedy iterative biclustering heuristics via localization.2594-2600

Systems Biology

• 
  Rick A. Fasani,Michael A. Savageau:
  Automated construction and analysis of the design space for biochemical systems.2601-2609
• 
  Jiantao Yu,Maozu Guo,Chris J. Needham,Yangchao Huang,Lu Cai,David R. Westhead:
  Simple sequence-based kernels do not predict protein-protein interactions.2610-2614

Applications Note - Genome Analysis

• 
  Roy Ronen,Ido Gan,Shira Modai,Alona Sukacheov,Gideon Dror,Eran Halperin,Noam Shomron:
  miRNAkey: a software for microRNA deep sequencing analysis.2615-2616

Sequence Analysis

• 
  Naohisa Goto,Pjotr Prins,Mitsuteru Nakao,Raoul Jean Pierre Bonnal,Jan Aerts,Toshiaki Katayama:
  BioRuby: bioinformatics software for the Ruby programming language.2617-2619
• 
  Nikos Darzentas:
  Circoletto: visualizing sequence similarity with Circos.2620-2621
• 
  Ivan V. Kulakovskiy,Valentina Boeva,Alexander V. Favorov,Vsevolod J. Makeev:
  Deep and wide digging for binding motifs in ChIP-Seq data.2622-2623

Structural Bioinformatics

• 
  D. P. Klose,B. A. Wallace,Robert W. Janes:
  2Struc: the secondary structure server.2624-2625
• 
  Marco Biasini,Valerio Mariani,Jürgen Haas,Stefan Scheuber,Andreas D. Schenk,Torsten Schwede,Ansgar Philippsen:
  OpenStructure: a flexible software framework for computational structural biology.2626-2628
• 
  Minghua Wang,Man Wai Mok,Hong Harper,Wen Hwa Lee,Jinrong Min,Stefan Knapp,Udo C. T. Oppermann,Brian D. Marsden,Matthieu Schapira:
  Structural genomics of histone tail recognition.2629-2630

Database and Ontologies

• 
  Johannes Goll,Douglas B. Rusch,David M. Tanenbaum,Mathangi Thiagarajan,Kelvin Li,Barbara A. Methé,Shibu Yooseph:
  METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics.2631-2632

Gene Expression

• 
  Dokyun Na,Doheon Lee:
  RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.2633-2634
• 
  Hafiz Muhammad Shahzad Asif,Matthew D. Rolfe,Jeffrey Green,Neil D. Lawrence,Magnus Rattray,Guido Sanguinetti:
  TFInfer: a tool for probabilistic inference of transcription factor activities.2635-2636
• 
  Bao-Hong Liu,Hui Yu,Kang Tu,Chun Li,Yi-Xue Li,Yuan-Yuan Li:
  DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data.2637-2638

Systems Biology

• 
  Ambarish Biswas,Kalyan C. Mynampati,Shivshankar Umashankar,Sheela Reuben,Gauri Parab,Raghuraj Rao,Velayutham S. Kannan,Sanjay Swarup:
  MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation.2639-2640
• 
  Stefan Hoehme,Dirk Drasdo:
  A cell-based simulation software for multi-cellular systems.2641-2642

Data and Text Mining

• 
  Haiying Wang,Huiru Zheng,Francisco Azuaje:
  Ontology- and graph-based similarity assessment in biological networks.2643-2644
• 
  Selim Mimaroglu,Ertunc Erdil:
  Obtaining better quality final clustering by merging a collection of clusterings.2645-2646

Databases and Ontologies

• 
  Gert Wohlgemuth,Pradeep Kumar Haldiya,Egon L. Willighagen,Tobias Kind,Oliver Fiehn:
  The Chemical Translation Service - a web-based tool to improve standardization of metabolomic reports.2647-2648
• 
  Xinyu Zhang,Lin Shi,Yan Liu,Feng Tian,Haitao Zhao,Xiaoping Miao,Ming-lie Huang,Xiao-yan Zhu:
  ICPS: an integrative cancer profiler system.2649-2650

Volume 26, Number 21, November 2010

Discovery Note - Sequence Analysis

• 
  A. Robbins-Pianka,Michael D. Rice,Michael P. Weir:
  The mRNA landscape at yeast translation initiation sites.2651-2655

Genome Analysis

• 
  Marco Mariotti,Roderic Guigó:
  Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.2656-2663
• 
  Daniel Chubb,Benjamin R. Jefferys,Michael J. E. Sternberg,Lawrence A. Kelley:
  Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe.2664-2671

Sequence Analysis

• 
  Gurmukh Sahota,Gary D. Stormo:
  Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.2672-2677
• 
  Bo Liao,Benyou Liao,Xingming Sun,Qingguang Zeng:
  A Novel method for similarity analysis and protein sub-cellular localization prediction.2678-2683
• 
  Haley J. Abel,Eric J. Duncavage,Nils Becker,Jon R. Armstrong,Vincent J. Magrini,John D. Pfeifer:
  SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.2684-2688

Structural Bioinformatics

• 
  Ryan R. Rahrig,Neocles Leontis,Craig L. Zirbel:
  R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.2689-2697
• 
  Tsuyoshi Kato,Nozomi Nagano:
  Metric learning for enzyme active-site search.2698-2704

Gene Expression

• 
  Paul David McNicholas,Thomas Brendan Murphy:
  Model-based clustering of microarray expression data via latent Gaussian mixture models.2705-2712
• 
  Leo Lahti,Juha E. A. Knuuttila,Samuel Kaski:
  Global modeling of transcriptional responses in interaction networks.2713-2720
• 
  Stefano Moretti,Vito Fragnelli,Fioravante Patrone,Stefano Bonassi:
  Using coalitional games on biological networks to measure centrality and power of genes.2721-2730
• 
  Ilya Papatsenko,Mike Levine,Dmitri A. Papatsenko:
  Temporal waves of coherent gene expression duringDrosophila embryogenesis.2731-2736

Systems Biology

• 
  Iziah Edwin Sama,Martijn A. Huynen:
  Measuring the physical cohesiveness of proteins using physical interaction enrichment.2737-2743
• 
  Zhuhong You,Ying-Ke Lei,Jie Gui,De-Shuang Huang,Xiaobo Zhou:
  Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data.2744-2751
• 
  Aleksandar Stojmirovic,Yi-Kuo Yu:
  Robust and accurate data enrichment statistics via distribution function of sum of weights.2752-2759
• 
  Thora Pommerencke,Kathi Westphal,Claudia Ernst,Kai Safferling,Hartmut Dickhaus,Thorsten Steinberg,Pascal Tomakidi,Niels Grabe:
  Spatial quantification and classification of skin response following perturbation using organotypic skin cultures.2760-2766

Data and Text Mining

• 
  Rezarta Islamaj Dogan,Zhiyong Lu:
  Click-words: learning to predict document keywords from a user perspective.2767-2775

Applications Note - Genome Analysis

• 
  Sebastian Zöllner:
  CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.2776-2777
• 
  Leo Goodstadt:
  Ruffus: a lightweight Python library for computational pipelines.2778-2779

Sequence Analysis

• 
  Damon P. Little:
  A unified index of sequence quality and contig overlap for DNA barcoding.2780-2781
• 
  Paul R. Staab,Jörg Walossek,David Nellessen,Raik Grünberg,Katja M. Arndt,Kristian M. Müller:
  SynBioWave - a real-time communication platform for molecular and synthetic biology.2782-2783

Structural Bioinformatics

• 
  Manuel Rueda,Vsevolod Katritch,Eugene Raush,Ruben Abagyan:
  SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.2784-2785
• 
  Jose-Roman Bilbao-Castro,Carlos Oscar Sánchez Sorzano,Inmaculada García,José-Jesús Fernández:
  XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography.2786-2787

Gene Expression

• 
  James Long,Chris Hartman:
  ODES: an overlapping dense sub-graph algorithm.2788-2789

Genetics and Population Analysis

• 
  Rosemarie Plaetke,Federico Balbi:
  PedMerge: merging pedigrees to facilitate family-based genetic statistical analyses.2790-2791

Systems Biology

• 
  Elana J. Fertig,Jie Ding,Alexander V. Favorov,Giovanni Parmigiani,Michael F. Ochs:
  CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.2792-2793
• 
  Si Yuan Shen,Frank T. Bergmann,Herbert M. Sauro:
  SBML2TikZ: supporting the SBML render extension in LaTeX.2794-2795

Databases and Ontologies

• 
  Konstantin Pentchev,Keiichiro Ono,Ralf Herwig,Trey Ideker,Atanas Kamburov:
  Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.2796-2797
• 
  Catherine Voegele,Lucile Alteyrac,Elodie Caboux,M. Smans,Fabienne Lesueur,Florence Le Calvez-Kelm,Pierre Hainaut:
  A sample storage management system for biobanks.2798-2800
• 
  Miguel García-Remesal,Alejandro Cuevas,David Pérez-Rey,Luis Martín,Alberto Anguita,Diana de la Iglesia,Guillermo de la Calle,José Crespo,Victor Maojo:
  PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.2801-2802

Volume 26, Number 22, November 2010

Original Papers - Sequence Analysis

• 
  Eden R. Martin,D. D. Kinnamon,Michael A. Schmidt,E. H. Powell,Stephan Züchner,R. W. Morris:
  SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.2803-2810
• 
  Pantelis G. Bagos,Elisanthi P. Nikolaou,Theodore D. Liakopoulos,Konstantinos D. Tsirigos:
  Combined prediction of Tat and Sec signal peptides with hidden Markov models.2811-2817
• 
  Saheli Datta,Raquel Prado,Abel Rodríguez,Ananías A. Escalante:
  Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties.2818-2825
• 
  Mike J. Mason,Kathrin Plath,Qing Zhou:
  Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data.2826-2832

Structural Bioinformatics

• 
  Sebastian Kelm,Jiye Shi,Charlotte M. Deane:
  MEDELLER: homology-based coordinate generation for membrane proteins.2833-2840

Gene Expression

• 
  Veit Schwämmle,Ole Nørregaard Jensen:
  A simple and fast method to determine the parameters for fuzzy c-means cluster analysis.2841-2848
• 
  Pei Fen Kuan,Sijian Wang,Xin Zhou,Haitao Chu:
  A statistical framework for Illumina DNA methylation arrays.2849-2855

Genetics and Population Analysis

• 
  Dumitru Brinza,Matthew Schultz,Glenn Tesler,Vineet Bafna:
  RAPID detection of gene-gene interactions in genome-wide association studies.2856-2862
• 
  Tianjiao Chu,Kimberly Bunce,W. Allen Hogge,David G. Peters:
  Statistical considerations for digital approaches to non-invasive fetal genotyping.2863-2866
• 
  Ani Manichaikul,Josyf Mychaleckyj,Stephen S. Rich,Kathy Daly,Michèle Sale,Wei-Min Chen:
  Robust relationship inference in genome-wide association studies.2867-2873

Systems Biology

• 
  Nicole Radde:
  Fixed point characterization of biological networks with complex graph topology.2874-2880

Data and Text Mining

• 
  Tiejun Cheng,Yanli Wang,Stephen H. Bryant:
  Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules.2881-2888
• 
  Eneko Agirre,Aitor Soroa,Mark Stevenson:
  Graph-based Word Sense Disambiguation of biomedical documents.2889-2896

Applications Note - Genome Analysis

• 
  Mulin Jun Li,Pak Chung Sham,Junwen Wang:
  FastPval: a fast and memory efficient program to calculate very lowP-values from empirical distribution.2897-2899
• 
  Nenad Bartonicek,Anton J. Enright:
  SylArray: a web server for automated detection of miRNA effects from expression data.2900-2901

Sequence Analysis

• 
  Joern Toedling,Constance Ciaudo,Olivier Voinnet,Edith Heard,Emmanuel Barillot:
  girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.2902-2903
• 
  Loredana Le Pera,Paolo Marcatili,Anna Tramontano:
  PICMI: mapping point mutations on genomes.2904-2905
• 
  Arthur Wuster,A. J. Venkatakrishnan,Gebhard F. X. Schertler,M. Madan Babu:
  Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.2906-2907
• 
  Robert P. Davey,Stephen A. James,Jo L. Dicks,Ian N. Roberts:
  TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.2908-2909

Phylogenetics

• 
  Bret R. Larget,Satish K. Kotha,Colin N. Dewey,Cécile Ané:
  BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis.2910-2911
• 
  Zhi-Zhong Chen,Lusheng Wang:
  HybridNET: a tool for constructing hybridization networks.2912-2913
• 
  Ofir Cohen,Haim Ashkenazy,Frida Belinky,Dorothée Huchon,Tal Pupko:
  GLOOME: gain loss mapping engine.2914-2915

Structural Bioinformatics

• 
  Alberto J. M. Martin,Ian Walsh,Silvio C. E. Tosatto:
  MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.2916-2917
• 
  Francois Berenger,Camille Coti,Kam Y. J. Zhang:
  PAR: a PARallel and distributed job crusher.2918-2919
• 
  Daniel B. Roche,Stuart J. Tetchner,Liam J. McGuffin:
  The binding site distance test score: a robust method for the assessment of predicted protein binding sites.2920-2921

Gene Expression

• 
  Michel A. Westenberg,Jos B. T. M. Roerdink,Oscar P. Kuipers,Sacha A. F. T. van Hijum:
  SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.2922-2923

Systems Biology

• 
  Anna Bauer-Mehren,Michael Rautschka,Ferran Sanz,Laura Inés Furlong:
  DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.2924-2926
• 
  Jason Montojo,Khalid Zuberi,Harold Rodriguez,Farzana Kazi,George Wright,Sylva L. Donaldson,Quaid Morris,Gary D. Bader:
  GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.2927-2928

Volume 26, Number 23, December 2010

Discovery Note - Sequence Analysis

• 
  Elizabeth C. Reuman,Severine Margeridon-Thermet,Harrison B. Caudill,Tommy F. Liu,Katyna Borroto-Esoda,Evguenia S. Svarovskaia,Susan P. Holmes,Robert W. Shafer:
  A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.2929-2932
• 
  Krystian Eitner,Uwe Koch,Tomasz Gaweda,Jedrzej Marciniak:
  Statistical distribution of amino acid sequences: a proof of Darwinian evolution.2933-2935

Original Papers - Sequence Analysis

• 
  Christophe N. Magnan,Michael Zeller,Matthew A. Kayala,Adam Vigil,Arlo Z. Randall,Philip L. Felgner,Pierre Baldi:
  High-throughput prediction of protein antigenicity using protein microarray data.2936-2943

Gene Expression

• 
  Wei Huang,Xiaoyi Cao,Sheng Zhong:
  Network-based comparison of temporal gene expression patterns.2944-2951

Genetics and Population Analysis

• 
  Mark H. Wright,Chih-Wei Tung,Keyan Zhao,Andy Reynolds,Susan McCouch,Carlos D. Bustamante:
  ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.2952-2960
• 
  Huaizhen Qin,Nathan Morris,Sun J. Kang,Mingyao Li,Bamidele Tayo,Helen Lyon,Joel Hirschhorn,Richard S. Cooper,Xiaofeng Zhu:
  Interrogating local population structure for fine mapping in genome-wide association studies.2961-2968

Systems Biology

• 
  Raphael B. M. Aggio,Katya Ruggiero,Silas Granato Villas-Bôas:
  Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity.2969-2976

Applications Note - Genome Analysis

• 
  Manimozhiyan Arumugam,Eoghan D. Harrington,Konrad U. Foerstner,Jeroen Raes,Peer Bork:
  SmashCommunity: a metagenomic annotation and analysis tool.2977-2978
• 
  Eoghan D. Harrington,Manimozhiyan Arumugam,Jeroen Raes,Peer Bork,David A. Relman:
  SmashCell: a software framework for the analysis of single-cell amplified genome sequences.2979-2980

Structural Bioinformatics

• 
  Rhonald C. Lua,Olivier Lichtarge:
  PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes.2981-2982
• 
  Andreas Prlic,Spencer Bliven,Peter W. Rose,Wolfgang Bluhm,Chris Bizon,Adam Godzik,Philip E. Bourne:
  Pre-calculated protein structure alignments at the RCSB PDB website.2983-2985
• 
  Michal J. Gajda,Irina Tuszynska,Marta Kaczor,Anastasia Yu. Bakulina,Janusz M. Bujnicki:
  FILTREST3D: discrimination of structural models using restraints from experimental data.2986-2987
• 
  Patrik Rydberg,David E. Gloriam,Lars Olsen:
  The SMARTCyp cytochrome P450 metabolism prediction server.2988-2989

Genetics and Population Analysis

• 
  Danny Arends,Pjotr Prins,Ritsert C. Jansen,Karl W. Broman:
  R/qtl: high-throughput multiple QTL mapping.2990-2992
• 
  Nicolas Ray,Mathias Currat,Matthieu Foll,Laurent Excoffier:
  SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination.2993-2994

Systems Biology

• 
  Tian Xia,John L. Van Hemert,Julie A. Dickerson:
  OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data.2995-2996
• 
  Lope A. Flórez,Christoph R. Lammers,Raphael H. Michna,Jörg Stülke:
  CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways.2997-2999

Data and Text Mining

• 
  Theo Walker,Christopher M. Grulke,Diane Pozefsky,Alexander Tropsha:
  Chembench: a cheminformatics workbench.3000-3001
• 
  Fuliang Xie,Baohong Zhang:
  Target-align: a tool for plant microRNA target identification.3002-3003

Databases and Ontologies

• 
  Jian Zhang,Yang Zhang:
  GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation.3004-3005

Volume 26, Number 24, December 2010

Discovery Note - Data and Text Mining

• 
  Brenton Louie,Roger Higdon,Eugene Kolker:
  The necessity of adjusting tests of protein category enrichment in discovery proteomics.3007-3011

Original Papers Genome Analysis

• 
  István Miklós,Eric Tannier:
  Bayesian sampling of genomic rearrangement scenarios via double cut and join.3012-3019
• 
  Sandro Morganella,Luigi Cerulo,Giuseppe Viglietto,Michele Ceccarelli:
  VEGA: variational segmentation for copy number detection.3020-3027
• 
  Yuchun Guo,Georgios Papachristoudis,Robert C. Altshuler,Georg K. Gerber,Tommi S. Jaakkola,David K. Gifford,Shaun Mahony:
  Discovering homotypic binding events at high spatial resolution.3028-3034
• 
  Bertrand Servin,Simon de Givry,Thomas Faraut:
  Statistical confidence measures for genome maps: application to the validation of genome assemblies.3035-3042

Sequence Analysis

• 
  Vetriselvi Rangannan,Manju Bansal:
  High-quality annotation of promoter regions for 913 bacterial genomes.3043-3050
• 
  Sergii Ivakhno,Tom Royce,Anthony J. Cox,Dirk J. Evers,R. Keira Cheetham,Simon Tavaré:
  CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data.3051-3058

Structural Bioinformatics

• 
  Ryan Day,Kristin P. Lennox,David B. Dahl,Marina Vannucci,Jerry W. Tsai:
  Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure.3059-3066
• 
  Arjun Ray,Erik Lindahl,Björn Wallner:
  Model quality assessment for membrane proteins.3067-3074
• 
  Raquel Cardoso de Melo Minardi,Karine Bastard,François Artiguenave:
  Identification of subfamily-specific sites based on active sites modeling and clustering.3075-3082

Gene Expression

• 
  Edi Prifti,Jean-Daniel Zucker,Karine Clément,Corneliu Henegar:
  Interactional and functional centrality in transcriptional co-expression networks.3083-3089
• 
  Atsushi Niida,Seiya Imoto,Rui Yamaguchi,Masao Nagasaki,André Fujita,Teppei Shimamura,Satoru Miyano:
  Model-free unsupervised gene set screening based on information enrichment in expression profiles.3090-3097

Systems Biology

• 
  Xiaoning Qian,Noushin Ghaffari,Ivan Ivanov,Edward R. Dougherty:
  State reduction for network intervention in probabilistic Boolean networks.3098-3104

Data and Text Mining

• 
  Bing Liu,Lin Liu,Anna Tsykin,Gregory J. Goodall,Jeffrey E. Green,Min Zhu,Chang-Hee Kim,Jiuyong Li:
  Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation.3105-3111

Databases and Ontologies

• 
  Robert Hoehndorf,Anika Oellrich,Dietrich Rebholz-Schuhmann:
  Interoperability between phenotype and anatomy ontologies.3112-3118
• 
  Alexie Papanicolaou,David G. Heckel:
  The GMOD Drupal Bioinformatic Server Framework.3119-3124

Applications Note - Genome Analysis

• 
  Aaron J. Petkau,Matthew Stuart-Edwards,Paul Stothard,Gary H. Van Domselaar:
  Interactive microbial genome visualization with GView.3125-3126

Sequence Analysis

• 
  Li-Yeh Chuang,Jui-Hung Tsai,Cheng-Hong Yang:
  PPO: Predictor for Prokaryotic Operons.3127-3128
• 
  Katherine J. L. Jackson,Scott Boyd,Bruno A. Gaëta,Andrew M. Collins:
  Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset.3129-3130

Gene Expression

• 
  Kevin Le Brigand,Karine Robbe-Sermesant,Bernard Mari,Pascal Barbry:
  MiRonTop: mining microRNAs targets across large scale gene expression studies.3131-3132

Genetics and Population Analysis

• 
  Iain Milne,Paul D. Shaw,Gordon Stephen,Micha Bayer,Linda Cardle,William T. B. Thomas,Andrew J. Flavell,David F. Marshall:
  Flapjack - graphical genotype visualization.3133-3134

Systems Biology

• 
  Gang Su,Allan Kuchinsky,John H. Morris,David J. States,Fan Meng:
  GLay: community structure analysis of biological networks.3135-3137
• 
  Gang Su,Brian D. Athey,Fan Meng:
  GSearcher: Agile Attribute Querying for Biological Networks.3138-3139
• 
  Hadas Zur,Eytan Ruppin,Tomer Shlomi:
  iMAT: an integrative metabolic analysis tool.3140-3142