Bioinformatics, Volume 27

Volume 27, Number 1, January 2011

Original Papers - Genome Analysis

• 
  Qianchuan He,Dan-Yu Lin:
  A variable selection method for genome-wide association studies.1-8
• 
  Maria Elena Sana,Maria Iascone,Daniela Marchetti,Jeffrey J. T. Palatini,Marco Galasso,Stefano Volinia:
  GAMES identifies and annotates mutations in next-generation sequencing projects.9-13
• 
  Dong Seon Kim,Yoonsoo Hahn:
  Identification of human-specific transcript variants induced by DNA insertions in the human genome.14-21

Sequence Analysis

• 
  Monzoorul Haque Mohammed,Tarini Shankar Ghosh,Nitin Kumar Singh,Sharmila S. Mande:
  SPHINX - an algorithm for taxonomic binning of metagenomic sequences.22-30
• 
  Yuheng Li,Nicholas Chia,Mario Lauria,Ralf Bundschuh:
  A performance enhanced PSI-BLAST based on hybrid alignment.31-37

Phylogenetics

• 
  Jaime Huerta-Cepas,Toni Gabaldón:
  Assigning duplication events to relative temporal scales in genome-wide studies.38-45

Structural Bioinformatics

• 
  R. Dustin Schaeffer,Amanda L. Jonsson,Andrew M. Simms,Valerie Daggett:
  Generation of a consensus protein domain dictionary.46-54
• 
  Chandrajit L. Bajaj,Rezaul Alam Chowdhury,Muhibur Rasheed:
  A dynamic data structure for flexible molecular maintenance and informatics.55-62

Gene Expression

• 
  Haimao Zhan,Xin Chen,Shizhong Xu:
  A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes.63-69
• 
  Johannes M. Freudenberg,Siva Sivaganesan,Mukta Phatak,Kaustubh Shinde,Mario Medvedovic:
  Generalized random set framework for functional enrichment analysis using primary genomics datasets.70-77
• 
  Sunghee Oh,Dongwan D. Kang,Guy N. Brock,George C. Tseng:
  Biological impact of missing-value imputation on downstream analyses of gene expression profiles.78-86
• 
  Vanya Van Belle,Kristiaan Pelckmans,Sabine Van Huffel,Johan A. K. Suykens:
  Improved performance on high-dimensional survival data by application of Survival-SVM.87-94

Genetics and Population Analysis

• 
  Peilin Jia,Siyuan Zheng,Jirong Long,Wei Zheng,Zhongming Zhao:
  dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.95-102

Systems Biology

• 
  Nidhal Bouaynaya,Roman Shterenberg,Dan Schonfeld:
  Inverse perturbation for optimal intervention in gene regulatory networks.103-110
• 
  Guy Geva,Roded Sharan:
  Identification of protein complexes from co-immunoprecipitation data.111-117

Data and Text Mining

• 
  Shi Yu,Xinhai Liu,Léon-Charles Tranchevent,Wolfgang Glänzel,Johan A. K. Suykens,Bart De Moor,Yves Moreau:
  Optimized data fusion for K-means Laplacian clustering.118-126

Applications Note Genome Analysis

• 
  Gail L. Rosen,Erin R. Reichenberger,Aaron M. Rosenfeld:
  NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads.127-129

Sequence Analysis

• 
  Timo Lassmann,Yoshihide Hayashizaki,Carsten O. Daub:
  SAMStat: monitoring biases in next generation sequencing data.130-131

Structural Bioinformatics

• 
  Jean-Christophe Gelly,Alexandre G. de Brevern:
  Protein Peeling 3D: new tools for analyzing protein structures.132-133

Genetics and Population Analysis

• 
  Ryan Abo,Stacey Knight,Alun Thomas,Nicola J. Camp:
  Automated construction and testing of multi-locus gene-gene associations.134-136

Systems Biology

• 
  Fernando García-Alcalde,Federico García-López,Joaquín Dopazo,Ana Conesa:
  Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.137-139
• 
  Laurin A. J. Mueller,Karl G. Kugler,Andreas Dander,Armin Graber,Matthias Dehmer:
  QuACN: an R package for analyzing complex biological networks quantitatively.140-141
• 
  Ronan M. T. Fleming,Ines Thiele:
  von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.142-143

Data and Text Mining

• 
  Paul Martin,Anne Barton,Stephen Eyre:
  ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies.144-146

Volume 27, Number 2, January 2011

Original Papers - Genome Analysis

• 
  Dong Dong,Xiaojian Shao,Zhaolei Zhang:
  Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.147-152
• 
  Giuseppe Narzisi,Bud Mishra:
  Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons.153-160
• 
  Vito M. R. Muggeo,Giada Adelfio:
  Efficient change point detection for genomic sequences of continuous measurements.161-166

Sequence Analysis

• 
  Pramila Nuwantha Ariyaratne,Wing-Kin Sung:
  PE-Assembler:de novo assembler using short paired-end reads.167-174
• 
  Ahrim Youn,Richard Simon:
  Identifying cancer driver genes in tumor genome sequencing studies.175-181
• 
  Panagiotis D. Vouzis,Nikolaos V. Sahinidis:
  GPU-BLAST: using graphics processors to accelerate protein sequence alignment.182-188
• 
  Sanchit Misra,Ankit Agrawal,Wei-keng Liao,Alok N. Choudhary:
  Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.189-195
• 
  Fabio Gori,Gianluigi Folino,Mike S. M. Jetten,Elena Marchiori:
  MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.196-203

Structural Bioinformatics

• 
  Tobias Hamp,Fabian Birzele,Fabian Buchwald,Stefan Kramer:
  Improving structure alignment-based prediction of SCOP families using Vorolign Kernels.204-210
• 
  Stefan E. Seemann,Andreas S. Richter,Tanja Gesell,Rolf Backofen,Jan Gorodkin:
  PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.211-219

Gene Expression

• 
  Gregory Riddick,Hua Song,Susie Ahn,Jennifer Walling,Diego Borges-Rivera,Wei Zhang,Howard A. Fine:
  Predictingin vitro drug sensitivity using Random Forests.220-224
• 
  Hong-Qiang Wang,Lindsey K. Tuominen,Chung-Jui Tsai:
  SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.225-231

Systems Biology

• 
  Darong Lai,Xinyi Yang,Gang Wu,Yuanhua Liu,Christine Nardini:
  Inference of gene networks - application toBifidobacterium.232-237
• 
  Holger Fröhlich,Paurush Praveen,Achim Tresch:
  Fast and efficient dynamic nested effects models.238-244
• 
  Tae-Hwan Kim,Junil Kim,Pat Heslop-Harrison,Kwang-Hyun Cho:
  Evolutionary design principles and functional characteristics based on kingdom-specific network motifs.245-251
• 
  Isabel A. Nepomuceno-Chamorro,Francisco Azuaje,Yvan Devaux,Petr V. Nazarov,Arnaud Muller,Jesús S. Aguilar-Ruiz,Daniel R. Wagner:
  Prognostic transcriptional association networks: a new supervised approach based on regression trees.252-258

Data and Text Mining

• 
  Quoc-Chinh Bui,Sophia Katrenko,Peter M. A. Sloot:
  A hybrid approach to extract protein-protein interactions.259-265

Applications Note - Genome Analysis

• 
  Qing Yu,Elizabeth M. Ryan,Todd M. Allen,Bruce W. Birren,Matthew R. Henn,Niall J. Lennon:
  PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.266-267
• 
  Valentina Boeva,Andrei Yu. Zinovyev,Kevin Bleakley,Jean-Philippe Vert,Isabelle Janoueix-Lerosey,Olivier Delattre,Emmanuel Barillot:
  Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.268-269
• 
  Simon J. van Heeringen,Gert Jan C. Veenstra:
  GimmeMotifs: ade novo motif prediction pipeline for ChIP-sequencing experiments.270-271
• 
  Ryan Koehler,Hadar Issac,Nicole Cloonan,Sean M. Grimmond:
  The uniqueome: a mappability resource for short-tag sequencing.272-274

Sequence Analysis

• 
  Paulo C. Carvalho,Juliana S. G. Fischer,Jonas Perales,John R. Yates III,Valmir Carneiro Barbosa,Elias Bareinboim:
  Analyzing marginal cases in differential shotgun proteomics.275-276
• 
  Emese Meglécz,Sylvain Piry,Erick Desmarais,Maxime Galan,André Gilles,Emmanuel Guivier,Nicolas Pech,Jean-François Martin:
  SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing.277-278
• 
  Stephanie Kehr,Sebastian Bartschat,Peter F. Stadler,Hakim Tafer:
  PLEXY: efficient target prediction for box C/D snoRNAs.279-280

Gene Expression

• 
  Lukas Habegger,Andrea Sboner,Tara A. Gianoulis,Joel S. Rozowsky,Ashish Agarwal,Michael Snyder,Mark Gerstein:
  RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.281-283

Genetics and Population Analysis

• 
  Nicholas A. Davis,Ahwan Pandey,Brett A. McKinney:
  Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.284-285
• 
  Rebecca Rooke,Guojun Yang:
  TE Displayer for post-genomic analysis of transposable elements.286-287

Systems Biology

• 
  Matthias Vigelius,Aidan Lane,Bernd Meyer:
  Accelerating reaction-diffusion simulations with general-purpose graphics processing units.288-290

Volume 27, Number 3, February 2011

Iscb

• 
  Lucian Ilie,Farideh Fazayeli,Silvana Ilie:
  HiTEC: accurate error correction in high-throughput sequencing data.295-302
• 
  Lars Halvor Gidskehaug,Matthew Kent,Ben J. Hayes,Sigbjørn Lien:
  Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array.303-310
• 
  Haitao Jiang,Binhai Zhu,Daming Zhu:
  Algorithms for sorting unsigned linear genomes by the DCJ operations.311-316

Sequence Analysis

• 
  Peter Menzel,Peter F. Stadler,Jan Gorodkin:
  maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.317-325
• 
  Leonard Apeltsin,John H. Morris,Patricia C. Babbitt,Thomas E. Ferrin:
  Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.326-333
• 
  Samuel V. Angiuoli,Steven L. Salzberg:
  Mugsy: fast multiple alignment of closely related whole genomes.334-342

Structural Bioinformatics

• 
  Pascal Benkert,Marco Biasini,Torsten Schwede:
  Toward the estimation of the absolute quality of individual protein structure models.343-350
• 
  Hongbo Zhu,M. Teresa Pisabarro:
  MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets.351-358

Gene Expression

• 
  Vinícius Bonato,Veerabhadran Baladandayuthapani,Bradley M. Broom,Erik P. Sulman,Kenneth D. Aldape,Kim-Anh Do:
  Bayesian ensemble methods for survival prediction in gene expression data.359-367
• 
  António dos Anjos,Anders L. B. Møller,Bjarne Kjær Ersbøll,Christine Finnie,Hamid Reza Shahbazkia:
  New approach for segmentation and quantification of two-dimensional gel electrophoresis images.368-375

Systems Biology

• 
  Todd A. Gibson,Debra Goldberg:
  Improving evolutionary models of protein interaction networks.376-382
• 
  Xiaojian Shao,Chris Soon Heng Tan,Courtney Voss,Shawn S. C. Li,Naiyang Deng,Gary D. Bader:
  A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.383-390
• 
  Yongsoo Kim,Taek-Kyun Kim,Yungu Kim,Jiho Yoo,Sungyong You,Inyoul Y. Lee,George Carlson,Leroy Hood,Seungjin Choi,Daehee Hwang:
  Principal network analysis: identification of subnetworks representing major dynamics using gene expression data.391-398
• 
  Ming Zhou,Xiliang Zheng,Jin Wang,Shaojun Dong:
  'Non-destructive' biocomputing security system based on gas-controlled biofuel cell and potentially used for intelligent medical diagnostics.399-404
• 
  Gábor Iván,Vince Grolmusz:
  When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks.405-407

Data and Text Mining

• 
  Emily Doughty,Attila Kertész-Farkas,Olivier Bodenreider,Gary Thompson,Asa Adadey,Thomas A. Peterson,Maricel G. Kann:
  Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.408-415

Applications Note - Genome Analysis

• 
  Vijay Garla,Yong Kong,Sebastian Szpakowski,Michael Krauthammer:
  MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions.416-418
• 
  Philippe Lamy,Carsten Wiuf,Torben F. Ørntoft,Claus L. Andersen:
  Rseg - an R package to optimize segmentation of SNP array data.419-420

Sequence Analysis

• 
  Shao-Ke Lou,Bing Ni,Leung-Yau Lo,Stephen Kwok-Wing Tsui,Ting-Fung Chan,Kwong-Sak Leung:
  ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.421-422

Structural Bioinformatics

• 
  Daniel Aioanei,Marco Brucale,Bruno Samorì:
  Open source platform for the execution and analysis of mechanical refolding experiments.423-425
• 
  Per Larsson,Marcin J. Skwark,Björn Wallner,Arne Elofsson:
  Improved predictions by Pcons.net using multiple templates.426-427

Gene Expression

• 
  Xun Lan,Russell Bonneville,Jeff Apostolos,Wangcheng Wu,Victor X. Jin:
  W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.428-430

Systems Biology

• 
  Michael E. Smoot,Keiichiro Ono,Johannes Ruscheinski,Peng-Liang Wang,Trey Ideker:
  Cytoscape 2.8: new features for data integration and network visualization.431-432
• 
  Albert Gevorgyan,Michael E. Bushell,Claudio Avignone-Rossa,Andrzej M. Kierzek:
  SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.433-434

Databases and Ontologies

• 
  Miquel Miquel,I. López-Ribera,Miquel Ràmia,Sònia Casillas,Antonio Barbadilla,Carlos M. Vicient:
  MASISH: a database for gene expression in maize seeds.435-436
• 
  Y. Wayne Huang,Adam P. Arkin,John-Marc Chandonia:
  WIST: toolkit for rapid, customized LIMS development.437-438

Corrigendum - Databases and Ontologies

• 
  Daniel F. Schwarz,Inke R. König,Andreas Ziegler:
  On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data.439

Volume 27, Number 4, February 2011

Review Genome Analysis

• 
  Melissa S. Cline,Rachel Karchin:
  Using bioinformatics to predict the functional impact of SNVs.441-448

Original Papers - Genome Analysis

• 
  Bernhard Haubold,Floyd A. Reed,Peter Pfaffelhuber:
  Alignment-free estimation of nucleotide diversity.449-455

Sequence Analysis

• 
  Andrew X. Li,Manja Marz,Jing Qin,Christian M. Reidys:
  RNA-RNA interaction prediction based on multiple sequence alignments.456-463
• 
  Kana Shimizu,Koji Tsuda:
  SlideSort: all pairs similarity search for short reads.464-470
• 
  Tak-Ming Chan,Ka-Chun Wong,Kin-Hong Lee,Man Hon Wong,Chi-Kong Lau,Stephen Kwok-Wing Tsui,Kwong-Sak Leung:
  Discovering approximate-associated sequence patterns for protein-DNA interactions.471-478
• 
  Thomas C. Conway,Andrew J. Bromage:
  Succinct data structures for assembling large genomes.479-486

Structural Bioinformatics

• 
  Teppei Ebina,Hiroyuki Toh,Yutaka Kuroda:
  DROP: an SVM domain linker predictor trained with optimal features selected by random forest.487-494

Gene Expression

• 
  Francesco C. Stingo,Marina Vannucci:
  Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data.495-501
• 
  Zhengpeng Wu,Xi Wang,Xuegong Zhang:
  Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.502-508
• 
  Sangsoon Woo,Jeffrey T. Leek,John D. Storey:
  A computationally efficient modular optimal discovery procedure.509-515

Genetics and Population Analysis

• 
  Jiahan Li,Kiranmoy Das,Guifang Fu,Runze Li,Rongling Wu:
  The Bayesian lasso for genome-wide association studies.516-523

Systems Biology

• 
  Frank-Michael Schleif,T. Riemer,U. Börner,L. Schnapka-Hille,Michael Cross:
  Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications.524-533
• 
  Alberto Rezola,Luis F. de Figueiredo,Matthias Brock,Jon Pey,Adam Podhorski,Christoph Wittmann,Stefan Schuster,Alexander Bockmayr,Francisco J. Planes:
  Exploring metabolic pathways in genome-scale networks via generating flux modes.534-540
• 
  Paul A. Jensen,Jason A. Papin:
  Functional integration of a metabolic network model and expression data without arbitrary thresholding.541-547
• 
  Ritwik Layek,Aniruddha Datta,Michael L. Bittner,Edward R. Dougherty:
  Cancer therapy design based on pathway logic.548-555
• 
  Wessel N. van Wieringen,Aad van der Vaart:
  Statistical analysis of the cancer cell's molecular entropy using high-throughput data.556-563

Data and Text Mining

• 
  Hang Xiao,Ying Li,Jiulin Du,Axel Mosig:
  Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach.564-571
• 
  Jürgen Hartler,Martin Trötzmüller,Chandramohan Chitraju,Friedrich Spener,Harald C. Köfeler,Gerhard G. Thallinger:
  Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data.572-577

Applications Note - Genome Analysis

• 
  Marten Boetzer,Christiaan V. Henkel,Hans J. Jansen,Derek Butler,Walter Pirovano:
  Scaffolding pre-assembled contigs using SSPACE.578-579

Sequence Analysis

• 
  David L. A. Wood,Qinying Xu,John V. Pearson,Nicole Cloonan,Sean M. Grimmond:
  X-MATE: a flexible system for mapping short read data.580-581

Structural Bioinformatics

• 
  Jose Ignacio Agulleiro Baldo,José-Jesús Fernández:
  Fast tomographic reconstruction on multicore computers.582-583

Systems Biology

• 
  Clive G. Bowsher:
  Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.584-586

Data and Text Mining

• 
  Leonardo Bottolo,Marc Chadeau-Hyam,David I. Hastie,Sarah R. Langley,Enrico Petretto,Laurence Tiret,David Tregouet,Sylvia Richardson:
  ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration.587-588

Databases and Ontologies

• 
  Mikhail Gostev,Julio Fernandez-Banet,Johan Rung,Joern Dietrich,Inga Prokopenko,Samuli Ripatti,Mark I. McCarthy,Alvis Brazma,Maria Krestyaninova:
  SAIL - a software system for sample and phenotype availability across biobanks and cohorts.589-591

Phylogenetics

• 
  Klaus Peter Schliep:
  phangorn: phylogenetic analysis in R.592-593

Volume 27, Number 5, March 2011

Original Papers - Genome Analysis

• 
  Alexej Abyzov,Mark Gerstein:
  AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.595-603
• 
  Christopher Oldmeadow,Jonathan M. Keith:
  Model selection in Bayesian segmentation of multiple DNA alignments.604-610

Sequence Analysis

• 
  Xiaolin Hao,Rui Jiang,Ting Chen:
  Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.611-618

Structural Bioinformatics

• 
  Anna Katharina Dehof,Alexander Rurainski,Quang Bao Anh Bui,Sebastian Böcker,Hans-Peter Lenhof,Andreas Hildebrandt:
  Automated bond order assignment as an optimization problem.619-625
• 
  Zhenjiang Xu,David H. Mathews:
  Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.626-632

Gene Expression

• 
  Ryung S. Kim,Juan Lin:
  Multi-level mixed effects models for bead arrays.633-640
• 
  Eric Dugat-Bony,Mohieddine Missaoui,Eric Peyretaillade,Corinne Biderre-Petit,Ourdia Bouzid,Christophe Gouinaud,David R. C. Hill,Pierre Peyret:
  HiSpOD: probe design for functional DNA microarrays.641-648
• 
  Xiujie Chen,Jiankai Xu,Bangqing Huang,Jin Li,Xin Wu,Ling Ma,Xiaodong Jia,Xiusen Bian,Fujian Tan,Lei Liu,Sheng Chen,Xia Li:
  A sub-pathway-based approach for identifying drug response principal network.649-654
• 
  Yosef Prat,Menachem Fromer,Nathan Linial,Michal Linial:
  Recovering key biological constituents through sparse representation of gene expression.655-661
• 
  Liyan Gao,Zhide Fang,Kui Zhang,Degui Zhi,Xiangqin Cui:
  Length bias correction for RNA-seq data in gene set analyses.662-669

Genetics and Population Analysis

• 
  Xuexia Wang,Xiaofeng Zhu,Huaizhen Qin,Richard S. Cooper,Warren J. Ewens,Chun Li,Mingyao Li:
  Adjustment for local ancestry in genetic association analysis of admixed populations.670-677
• 
  Vonn Walter,Andrew B. Nobel,Fred A. Wright:
  DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors.678-685
• 
  Lily Wang,Peilin Jia,Russell D. Wolfinger,Xi Chen,Britney L. Grayson,Thomas M. Aune,Zhongming Zhao:
  An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.686-692

Systems Biology

• 
  Marco Grzegorczyk,Dirk Husmeier:
  Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.693-699
• 
  Hung Xuan Ta,Patrik Koskinen,Liisa Holm:
  A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.700-706

Data and Text Mining

• 
  Feng Feng,Ana Paula Sales,Thomas B. Kepler:
  A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays.707-712

Applications Note - Genome Analysis

• 
  Jonathan M. Cairns,Christiana Spyrou,Rory Stark,Mike L. Smith,Andy G. Lynch,Simon Tavaré:
  BayesPeak - an R package for analysing ChIP-seq data.713-714
• 
  Lakshmi Kuttippurathu,Michael Hsing,Yongchao Liu,Bertil Schmidt,Douglas L. Maskell,Kyungjoon Lee,Aibin He,William T. Pu,Sek Won Kong:
  CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.715-717

Sequence Analysis

• 
  Heng Li:
  Tabix: fast retrieval of sequence features from generic TAB-delimited files.718-719
• 
  Troy B. Hawkins,Jessica Dantzer,Brandon Peters,Mary Dinauer,Keithanne Mockaitis,Sean D. Mooney,Kenneth Cornetta:
  Identifying viral integration sites using SeqMap 2.0.720-722

Structural Bioinformatics

• 
  Kliment Olechnovic,Mindaugas Margelevicius,Ceslovas Venclovas:
  Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.723-724

Gene Expression

• 
  Daniel Baron,Audrey Bihouée,Raluca Teusan,Emeric Dubois,Frédérique Savagner,Marja Steenman,Rémi Houlgatte,Gérard Ramstein:
  MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets.725-726

Genetics and Population Analysis

• 
  Bevan Emma Huang,Andrew W. George:
  R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines.727-729

Systems Biology

• 
  Monica Chagoyen,Florencio Pazos:
  MBRole: enrichment analysis of metabolomic data.730-731
• 
  Francois Ribalet,David M. Schruth,E. Virginia Armbrust:
  flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data.732-733
• 
  Chuan Hock Koh,Masao Nagasaki,Ayumu Saito,Chen Li,Limsoon Wong,Satoru Miyano:
  MIRACH: efficient model checker for quantitative biological pathway models.734-735

Data and Text Mining

• 
  Guoqiang Yu,Huai Li,Sook Shin Ha,Ie-Ming Shih,Robert Clarke,Eric P. Hoffman,Subha Madhavan,Jianhua Xuan,Yue Joseph Wang:
  PUGSVM: a caBIG^TM analytical tool for multiclass gene selection and predictive classification.736-738
• 
  Ming Li,Shuo Chen,Joan Zhang,Heidi Chen,Yu Shyr:
  Wave-spec: a preprocessing package for mass spectrometry data.739-740

Databases and Ontologies

• 
  Mark R. Southern,Patrick R. Griffin:
  A Java API for working with PubChem datasets.741-742
• 
  Tommy Yu,Catherine M. Lloyd,David P. Nickerson,Mike T. Cooling,Andrew K. Miller,Alan Garny,Jonna R. Terkildsen,James R. Lawson,Randall Britten,Peter J. Hunter,Poul M. F. Nielsen:
  The Physiome Model Repository 2.743-744

Volume 27, Number 6, March 2011

Discovery Note - Data and Text Mining

• 
  Wai-Ki Yip,Christoph Lange:
  Quantitative trait prediction based on genetic marker-array data, a simulation study.745-748

Original Papers Genome Analysis

• 
  Jan Fostier,Sebastian Proost,Bart Dhoedt,Yvan Saeys,Piet Demeester,Yves Van de Peer,Klaas Vandepoele:
  A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.749-756
• 
  Oliver Keller,Martin Kollmar,Mario Stanke,Stephan Waack:
  A novel hybrid gene prediction method employing protein multiple sequence alignments.757-763

Sequence Analysis

• 
  Guillaume Marçais,Carl Kingsford:
  A fast, lock-free approach for efficient parallel counting of occurrences ofk-mers.764-770
• 
  Yi Zhang,Xianhui Wang,Le Kang:
  Ak-mer scheme to predict piRNAs and characterize locust piRNAs.771-776
• 
  Yejun Wang,Qing Zhang,Ming-an Sun,Dianjing Guo:
  High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles.777-784

Structural Bioinformatics

• 
  Yang Cao,Lin Song,Zhichao Miao,Yun Hu,Liqing Tian,Taijiao Jiang:
  Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.785-790
• 
  Guy Tsafnat,Jaron Schaeffer,Andrew Clayphan,Jonathan R. Iredell,Sally R. Partridge,Enrico W. Coiera:
  Computational inference of grammars for larger-than-gene structures from annotated gene sequences.791-796

Gene Expression

• 
  Clement Chung,Jian Liu,Andrew Emili,Brendan J. Frey:
  Computational refinement of post-translational modifications predicted from tandem mass spectrometry.797-806
• 
  Alexandra Posekany,K. Felsenstein,Peter Sykacek:
  Biological assessment of robust noise models in microarray data analysis.807-814

Genetics and Population Analysis

• 
  Vanda M. Lourenço,Ana M. Pires,M. Kirst:
  Robust linear regression methods in association studies.815-821
• 
  Rick Twee-Hee Ong,Xuanyao Liu,Wan-Ting Poh,Xueling Sim,Kee Seng Chia,Yik-Ying Teo:
  A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.822-828
• 
  Christian Rödelsperger,Peter M. Krawitz,Sebastian Bauer,Jochen Hecht,Abigail W. Bigham,Michael Bamshad,Birgit Jonske de Condor,Michal R. Schweiger,Peter N. Robinson:
  Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders.829-836
• 
  Tianqi Zhu,Yucheng Hu,Zhiming Ma,De-Xing Zhang,Tiejun Li,Ziheng Yang:
  Efficient simulation under a population genetics model of carcinogenesis.837-843

Systems Biology

• 
  Stuart R. Jefferys,Morgan C. Giddings:
  Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data.844-852
• 
  Lin Hou,Lin Wang,Minping Qian,Dong Li,Chao Tang,Yunping Zhu,Minghua Deng,Fangting Li:
  Modular analysis of the probabilistic genetic interaction network.853-859

Applications Note - Sequence Analysis

• 
  Sebastian Deorowicz,Szymon Grabowski:
  Compression of DNA sequence reads in FASTQ format.860-862
• 
  Robert Schmieder,Robert A. Edwards:
  Quality control and preprocessing of metagenomic datasets.863-864
• 
  Michael N. Edmonson,Jinghui Zhang,Chunhua Yan,Richard P. Finney,Daoud M. Meerzaman,Kenneth H. Buetow:
  Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.865-866

Gene Expression

• 
  Ângela Gonçalves,Andrew Tikhonov,Alvis Brazma,Misha Kapushesky:
  A pipeline for RNA-seq data processing and quality assessment.867-869
• 
  Qiang Song,Andrew D. Smith:
  Identifying dispersed epigenomic domains from ChIP-Seq data.870-871
• 
  Andrew T. Magis,John C. Earls,Youn-Hee Ko,James A. Eddy,Nathan D. Price:
  Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup.872-873

Systems Biology

• 
  Yanxiang Zhou,Juliane Liepe,Xia Sheng,Michael P. H. Stumpf,Chris P. Barnes:
  GPU accelerated biochemical network simulation.874-876
• 
  Xuejian Xiong,Hongyan Song,Tuan On,Lucas Lochovsky,Nicholas J. Provart,John Parkinson:
  PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.877-878
• 
  Xin Wang,Camille Terfve,John C. Rose,Florian Markowetz:
  HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.879-880
• 
  Matthieu Vignes,Juliette Blanchet,Damien Leroux,Florence Forbes:
  SpaCEM³: a software for biological module detection when data is incomplete, high dimensional and dependent.881-882
• 
  Yanqi Hao,Anna Merkoulovitch,James Vlasblom,Shuye Pu,Andrei L. Turinsky,Denitza Roudeva,Brian Turner,Jack Greenblatt,Shoshana J. Wodak:
  OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.883-884

Data and Text Mining

• 
  Francesca Chignola,Silvia Mari,Tim J. Stevens,Rasmus H. Fogh,Valeria Mannella,Wayne Boucher,Giovanna Musco:
  The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR.885-886
• 
  Riku Louhimo,Sampsa Hautaniemi:
  CNAmet: an R package for integrating copy number, methylation and expression data.887-888

Databases and Ontologies

• 
  Thomas A. Down,Matias Piipari,Tim J. P. Hubbard:
  Dalliance: interactive genome viewing on the web.889-890
• 
  Mark Y. Tong,Christopher A. Cassa,Isaac S. Kohane:
  Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations.891-893

Volume 27, Number 7, April 2011

Discovery Note - Genome Analysis

• 
  K. J. Siddle,Judith A. Goodship,Bernard D. Keavney,Mauro F. Santibanez-Koref:
  Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome.895-898

Sequence Analysis

• 
  Katja Luck,Gilles Travé:
  Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions.899-902

Original Papers - Genome Analysis

• 
  Burkhard Linke,Robert Giegerich,Alexander Goesmann:
  Conveyor: a workflow engine for bioinformatic analyses.903-911
• 
  Grace S. Shieh,Shurong Zheng,Richard A. Johnson,Yi-Feng Chang,Kunio Shimizu,Chia-Chang Wang,Sen-Lin Tang:
  Modeling and comparing the organization of circular genomes.912-918
• 
  Stefan Götz,Roland Arnold,Patricia Sebastián-León,Samuel Martín-Rodríguez,Patrick Tischler,Marc-André Jehl,Joaquín Dopazo,Thomas Rattei,Ana Conesa:
  B2G-FAR, a species-centered GO annotation repository.919-924

Structural Bioinformatics

• 
  Ilona Kifer,Ruth Nussinov,Haim J. Wolfson:
  GOSSIP: a method for fast and accurate global alignment of protein structures.925-932
• 
  James W. Shirley,Sereyvathana Ty,Shin-ichiro Takebayashi,Xiuwen Liu,David M. Gilbert:
  FISH Finder: a high-throughput tool for analyzing FISH images.933-938
• 
  Francois Berenger,Yong Zhou,Rojan Shrestha,Kam Y. J. Zhang:
  Entropy-accelerated exact clustering of protein decoys.939-945

Gene Expression

• 
  Christoph Hafemeister,Ivan G. Costa,Alexander Schönhuth,Alexander Schliep:
  Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.946-952
• 
  Florian Klinglmueller,Thomas Tuechler,Martin Posch:
  Cross-platform comparison of microarray data using order restricted inference.953-960
• 
  Tomasz Konopka:
  Automated analysis of biological oscillator models using mode decomposition.961-967

Genetics and Population Analysis

• 
  Alexander T. Dilthey,Loukas Moutsianas,Stephen Leslie,Gil McVean:
  HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes.968-972

Systems Biology

• 
  Goksel Misirli,Jennifer Hallinan,Tommy Yu,James R. Lawson,Sarala M. Wimalaratne,Mike T. Cooling,Anil Wipat:
  Model annotation for synthetic biology: automating model to nucleotide sequence conversion.973-979

Data and Text Mining

• 
  Maximilian Haeussler,Martin Gerner,Casey M. Bergman:
  Annotating genes and genomes with DNA sequences extracted from biomedical articles.980-986
• 
  Björn Voss,Michael Hanselmann,Bernhard Y. Renard,Martin S. Lindner,Ullrich Köthe,Marc Kirchner,Fred A. Hamprecht:
  SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists.987-993
• 
  Sach Mukherjee,Steven M. Hill:
  Network clustering: probing biological heterogeneity by sparse graphical models.994-1000

Databases and Ontologies

• 
  Robert Hoehndorf,Michel Dumontier,Anika Oellrich,Sarala M. Wimalaratne,Dietrich Rebholz-Schuhmann,Paul N. Schofield,Georgios V. Gkoutos:
  A common layer of interoperability for biomedical ontologies based on OWL EL.1001-1008

Applications Note - Genome Analysis

• 
  Mitchell J. Sullivan,Nicola K. Petty,Scott A. Beatson:
  Easyfig: a genome comparison visualizer.1009-1010
• 
  Matei David,Misko Dzamba,Dan Lister,Lucian Ilie,Michael Brudno:
  SHRiMP2: Sensitive yet Practical Short Read Mapping.1011-1012
• 
  Francesco Strozzi,Jan Aerts:
  A Ruby API to query the Ensembl database for genomic features.1013-1014
• 
  Brent S. Pedersen,Haibao Tang,Michael Freeling:
  Gobe: an interactive, web-based tool for comparative genomic visualization.1015-1016

Sequence Analysis

• 
  Charles E. Grant,Timothy L. Bailey,William Stafford Noble:
  FIMO: scanning for occurrences of a given motif.1017-1018
• 
  Zachary Dwight,Robert Palais,Carl T. Wittwer:
  uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application.1019-1020

Structural Bioinformatics

• 
  Gerd Neudert,Gerhard Klebe:
  fconv: format conversion, manipulation and feature computation of molecular data.1021-1022

Gene Expression

• 
  Rendong Yang,Chen Zhang,Zhen Su:
  LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.1023-1025
• 
  Antti Honkela,Pei Gao,Jonatan Ropponen,Magnus Rattray,Neil D. Lawrence:
  tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.1026-1027

Systems Biology

• 
  Zhike Zi:
  SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.1028-1029
• 
  Michael E. Smoot,Keiichiro Ono,Trey Ideker,Steven Maere:
  PiNGO: a Cytoscape plugin to find candidate genes in biological networks.1030-1031

Data and Text Mining

• 
  Minlie Huang,Jingchen Liu,Xiaoyan Zhu:
  GeneTUKit: a software for document-level gene normalization.1032-1033
• 
  Annekathrin Bartsch,Boyke Bunk,Isam Haddad,Johannes Klein,Richard Münch,Thorsten Johl,Uwe Kärst,Lothar Jänsch,Dieter Jahn,Ida Retter:
  GeneReporter - sequence-based document retrieval and annotation.1034-1035
• 
  Bai Zhang,Ye Tian,Lu Jin,Huai Li,Ie-Ming Shih,Subha Madhavan,Robert Clarke,Eric P. Hoffman,Jianhua Xuan,Leena Hilakivi-Clarke,Yue Joseph Wang:
  DDN: a caBIG^® analytical tool for differential network analysis.1036-1038
• 
  Kamil Tamiola,Frans A. A. Mulder:
  ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.1039-1040
• 
  Ketil Malde:
  Flower: extracting information from pyrosequencing data.1041-1042

Databases and Ontologies

• 
  Andrew G. Winter,Jan Wildenhain,Mike Tyers:
  BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID.1043-1044

Volume 27, Number 8, April 2011

Original Papers - Genome Analysis

• 
  Zhengkui Wang,Yue Wang,Kian-Lee Tan,Limsoon Wong,Divyakant Agrawal:
  eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study.1045-1051
• 
  Eitan Halper-Stromberg,Laurence Frelin,Ingo Ruczinski,Robert B. Scharpf,Chunfa Jie,Benilton S. Carvalho,Haiping Hao,Kurt N. Hetrick,Anne Jedlicka,Amanda Dziedzic,Kim Doheny,Alan F. Scott,Steve Baylin,Jonathan Pevsner,Forrest Spencer,Rafael A. Irizarry:
  Performance assessment of copy number microarray platforms using a spike-in experiment.1052-1060

Sequence Analysis

• 
  David Koslicki:
  Topological entropy of DNA sequences.1061-1067
• 
  Marcus Kinsella,Olivier Harismendy,Masakazu Nakano,Kelly A. Frazer,Vineet Bafna:
  Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.1068-1075

Structural Bioinformatics

• 
  Christian M. Reidys,Fenix W. D. Huang,Jørgen E. Andersen,Robert C. Penner,Peter F. Stadler,Markus E. Nebel:
  Topology and prediction of RNA pseudoknots.1076-1085
• 
  Emidio Capriotti,Tomás Norambuena,Marc A. Martí-Renom,Francisco Melo:
  All-atom knowledge-based potential for RNA structure prediction and assessment.1086-1093

Gene Expression

• 
  Jessica Cara Mar,Christine A. Wells,John Quackenbush:
  Defining an informativeness metric for clustering gene expression data.1094-1100
• 
  Liangxiu Han,Jano I. van Hemert,Richard A. Baldock:
  Automatically identifying and annotating mouse embryo gene expression patterns.1101-1107

Systems Biology

• 
  Marie Brown,David C. Wedge,Royston Goodacre,Douglas B. Kell,Philip N. Baker,Louise C. Kenny,Mamas A. Mamas,Ludwig Neyses,Warwick B. Dunn:
  Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets.1108-1112
• 
  Duc-Hau Le,Yung-Keun Kwon:
  The effects of feedback loops on disease comorbidity in human signaling networks.1113-1120
• 
  Thanet Praneenararat,Toshihisa Takagi,Wataru Iwasaki:
  Interactive, multiscale navigation of large and complicated biological networks.1121-1127
• 
  Victor Spirin,Alexander Shpunt,Jan Seebacher,Marc Gentzel,Andrej Shevchenko,Steven Gygi,Shamil R. Sunyaev:
  Assigning spectrum-specificP-values to protein identifications by mass spectrometry.1128-1134
• 
  Andrew D. Fox,Benjamin J. Hescott,Anselm Blumer,Donna K. Slonim:
  Connectedness of PPI network neighborhoods identifies regulatory hub proteins.1135-1142

Data and Text Mining

• 
  Jung-Hsien Chiang,Heng-Hui Liu,Yi-Ting Huang:
  Condensing biomedical journal texts through paragraph ranking.1143-1149

Applications Note - Genome Analysis

• 
  Marcela Dávila López,Tore Samuelsson:
  eGOB: eukaryotic Gene Order Browser.1150-1151
• 
  Justin Jee,Joel S. Rozowsky,Kevin Y. Yip,Lucas Lochovsky,Robert D. Bjornson,Guoneng Zhong,Zhengdong D. Zhang,Yutao Fu,Jie Wang,Zhiping Weng,Mark Gerstein:
  ACT: aggregation and correlation toolbox for analyses of genome tracks.1152-1154
• 
  Anthony P. Fejes,Alireza Hadj Khodabakhshi,Inanç Birol,Steven J. M. Jones:
  Human variation database: an open-source database template for genomic discovery.1155-1156

Sequence Analysis

• 
  Heng Li:
  Improving SNP discovery by base alignment quality.1157-1158
• 
  William A. Walters,J. Gregory Caporaso,Christian L. Lauber,Donna Berg-Lyons,Noah Fierer,Rob Knight:
  PrimerProspector:de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.1159-1161
• 
  Hans-Ulrich Klein,Christoph Bartenhagen,Alexander Kohlmann,Vera Grossmann,Christian Ruckert,Torsten Haferlach,Martin Dugas:
  R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.1162-1163

Phylogenetics

• 
  Diego Darriba,Guillermo L. Taboada,Ramon Doallo,David Posada:
  ProtTest 3: fast selection of best-fit models of protein evolution.1164-1165

Gene Expression

• 
  Marc Kirchner,Buote Xu,Hanno Steen,Judith A. J. Steen:
  libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data.1166-1167
• 
  Haleh Yasrebi:
  SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data.1168-1169

Systems Biology

• 
  Guido Klingbeil,Radek Erban,Mike B. Giles,Philip K. Maini:
  STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.1170-1171
• 
  Yoshinori Tamada,Rui Yamaguchi,Seiya Imoto,Osamu Hirose,Ryo Yoshida,Masao Nagasaki,Satoru Miyano:
  SiGN-SSM: open source parallel software for estimating gene networks with state space models.1172-1173
• 
  George C. Linderman,Vishal N. Patel,Mark R. Chance,Gürkan Bebek:
  BiC: a web server for calculating bimodality of coexpression between gene and protein networks.1174-1175
• 
  Isthiaq Ahmad,Frank Suits,Berend Hoekman,Morris A. Swertz,Heorhiy Byelas,Martijn Dijkstra,Rob W. W. Hooft,Dmitry Katsubo,Bas van Breukelen,Rainer Bischoff,Peter Horvatovich:
  A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.1176-1178
• 
  Lee Kamentsky,Thouis R. Jones,Adam Fraser,Mark-Anthony Bray,David J. Logan,Katherine L. Madden,Vebjorn Ljosa,Curtis Rueden,Kevin W. Eliceiri,Anne E. Carpenter:
  Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.1179-1180
• 
  Ruth Dannenfelser,Alexander Lachmann,Mariola Szenk,Avi Ma'ayan:
  FNV: light-weight flash-based network and pathway viewer.1181-1182

Data and Text Mining

• 
  Michael Specht,Sebastian Kuhlgert,Christian Fufezan,Michael Hippler:
  Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.1183-1184
• 
  Simon Kocbek,Rune Sætre,Gregor Stiglic,Jin-Dong Kim,Igor Pernek,Yoshimasa Tsuruoka,Peter Kokol,Sophia Ananiadou,Jun'ichi Tsujii:
  AGRA: analysis of gene ranking algorithms.1185-1186

Databases and Ontologies

• 
  Bryan Brancotte,Anne Biton,Isabelle Bernard-Pierrot,François Radvanyi,Fabien Reyal,Sarah Cohen Boulakia:
  Gene List significance at-a-glance with GeneValorization.1187-1189
• 
  Hongzhan Huang,Peter B. McGarvey,Baris E. Suzek,Raja Mazumder,Jian Zhang,Yongxing Chen,Cathy H. Wu:
  A comprehensive protein-centric ID mapping service for molecular data integration.1190-1191
• 
  Javed Mohammed Khan,Harish Reddy Cheruku,Joo Chuan Tong,Shoba Ranganathan:
  MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.1192-1193

Letter to the Editor - Gene Expression

• 
  Meïli C. Baragatti,Denys Pommeret:
  Comments on 'Bayesian variable selection for disease classification using gene expression data'.1194

Volume 27, Number 9, May 2011

Original Papers - Genome Analysis

• 
  Tomas W. Fitzgerald,Lee D. Larcombe,Solena Le Scouarnec,Stephen Clayton,Diana Rajan,Nigel P. Carter,Richard Redon:
  aCGH.Spline - an R package for aCGH dye bias normalization.1195-1200
• 
  Jie Huang,Andrew D. Johnson,Christopher J. O'Donnell:
  PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies.1201-1206
• 
  António C. M. Costa,José António Tenreiro Machado,Maria Dulce Quelhas:
  Histogram-based DNA analysis for the visualization of chromosome, genome and species information.1207-1214
• 
  Christoph J. Thieme,Lydia Gramzow,Dajana Lobbes,Günter Theißen:
  SplamiR - prediction of spliced miRNAs in plants.1215-1223

Sequence Analysis

• 
  Andrea Pierleoni,Pier Luigi Martelli,Rita Casadio:
  MemLoci: predicting subcellular localization of membrane proteins in eukaryotes.1224-1230
• 
  Celine Vens,Marie-Noëlle Rosso,Etienne G. J. Danchin:
  Identifying discriminative classification-based motifs in biological sequences.1231-1238
• 
  Ahmed M. Mehdi,Muhammad Shoaib B. Sehgal,Bostjan Kobe,Timothy L. Bailey,Mikael Bodén:
  A probabilistic model of nuclear import of proteins.1239-1246
• 
  Liisa Heikkinen,Mikko Kolehmainen,Garry Wong:
  Prediction of microRNA targets inCaenorhabditis elegans using a self-organizing map.1247-1254

Phylogenetics

• 
  Jianfu Zhou,Xiaoguang Liu,Douglas S. Stones,Qiang Xie,Gang Wang:
  MrBayes on a Graphics Processing Unit.1255-1261

Structural Bioinformatics

• 
  Wei Zhao,Meng Xu,Zhi Liang,Bo Ding,Liwen Niu,Haiyan Liu,Maikun Teng:
  Structure-basedde novo prediction of zinc-binding sites in proteins of unknown function.1262-1268

Gene Expression

• 
  Jangsun Baek,Geoffrey J. McLachlan:
  Mixtures of commont-factor analyzers for clustering high-dimensional microarray data.1269-1276
• 
  Hafiz Muhammad Shahzad Asif,Guido Sanguinetti:
  Large-scale learning of combinatorial transcriptional dynamics from gene expression.1277-1283
• 
  Qianqian Zhu,Jeffrey C. Miecznikowski,Marc S. Halfon:
  A wholly defined Agilent microarray spike-in dataset.1284-1289
• 
  Haisu Ma,Eric E. Schadt,Lee M. Kaplan,Hongyu Zhao:
  COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.1290-1298

Systems Biology

• 
  Jochen Weile,Matthew R. Pocock,Simon J. Cockell,Phillip W. Lord,James M. Dewar,Eva-Maria Holstein,Darren J. Wilkinson,David A. Lydall,Jennifer Hallinan,Anil Wipat:
  Customizable views on semantically integrated networks for systems biology.1299-1306

Applications Note - Genome Analysis

• 
  Micha Bayer,Iain Milne,Gordon Stephen,Paul D. Shaw,Linda Cardle,Frank Wright,David F. Marshall:
  Comparative visualization of genetic and physical maps with Strudel.1307-1308
• 
  Ling Sing Yung,Can Yang,Xiang Wan,Weichuan Yu:
  GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies.1309-1310
• 
  Ernesto Picardi,Mattia D'Antonio,Danilo Carrabino,Tiziana Castrignanò,Graziano Pesole:
  ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.1311-1312
• 
  Matteo Cereda,Manuela Sironi,Matteo Cavalleri,Uberto Pozzoli:
  GeCo++: a C++ library for genomic features computation and annotation in the presence of variants.1313-1315

Sequence Analysis

• 
  Manuela Hummel,Sarah Bonnin,Ernesto Lowy-Gallego,Guglielmo Roma:
  TEQC: an R package for quality control in target capture experiments.1316-1317
• 
  Andrzej Zielezinski,Wojciech M. Karlowski:
  Agos - a universal web tool for GW Argonaute-binding domain prediction.1318-1319

Structural Bioinformatics

• 
  Teong Han Chew,Kwee Hong Joyce-Tan,Farizuwana Akma,Mohd Shahir Shamsir:
  birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.1320-1321
• 
  Aron Hennerdal,Arne Elofsson:
  Rapid membrane protein topology prediction.1322-1323
• 
  Jamel Meslamani,Didier Rognan,Esther Kellenberger:
  sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.1324-1326
• 
  David Shirvanyants,Anastassia N. Alexandrova,Nikolay V. Dokholyan:
  Rigid substructure search.1327-1329

Gene Expression

• 
  Amy L. Olex,Jacquelyn S. Fetrow:
  SC²ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data.1330-1331

Genetics and Population Analysis

• 
  Laurent Excoffier,Matthieu Foll:
  fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.1332-1334
• 
  Tiago Antao,Ian M. Hastings:
  ogaraK: a population genetics simulator for malaria.1335-1336

Systems Biology

• 
  Asad Naeem,Andrew P. French,Darren M. Wells,Tony P. Pridmore:
  High-throughput feature counting and measurement of roots.1337-1338
• 
  Arnald Alonso,Antonio Julià,Antoni Beltran,Maria Vinaixa,Marta Díaz,Lourdes Ibañez,Xavier Correig,Sara Marsal:
  AStream: an R package for annotating LC/MS metabolomic data.1339-1340

Data and Text Mining

• 
  Björn A. Grüning,Christian Senger,Anika Erxleben,Stephan Flemming,Stefan Günther:
  Compounds In Literature (CIL): screening for compounds and relatives in PubMed.1341-1342

Databases and Ontologies

• 
  Catherine A. Hayes,Niclas G. Karlsson,Weston B. Struwe,Frédérique Lisacek,Pauline M. Rudd,Nicolle H. Packer,Matthew P. Campbell:
  UniCarb-DB: a database resource for glycomic discovery.1343-1344

Volume 27, Number 10, May 2011

Editorial

• 
  Olli-P. Kallioniemi,Lodewyk F. A. Wessels,Alfonso Valencia:
  On the organization of bioinformatics core services in biology-based research institutes.1345

Discovery Note - Sequence Analysis

• 
  Daniel C. Ellwanger,Florian A. Büttner,Hans-Werner Mewes,Volker Stümpflen:
  The sufficient minimal set of miRNA seed types.1346-1350

Original Papers - Sequence Analysis

• 
  Jochen Blom,Tobias Jakobi,Daniel Doppmeier,Sebastian Jaenicke,Jörn Kalinowski,Jens Stoye,Alexander Goesmann:
  Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.1351-1358

Phylogenetics

• 
  W. Timothy J. White,Barbara R. Holland:
  Faster exact maximum parsimony search with XMP.1359-1367

Structural Bioinformatics

• 
  Ping Xuan,Maozu Guo,Xiaoyan Liu,Yangchao Huang,Wenbin Li,Yufei Huang:
  PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs.1368-1376

Gene Expression

• 
  Klaus Jung,Benjamin Becker,Edgar Brunner,Tim Beißbarth:
  Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes.1377-1383

Genetics and Population Analysis

• 
  Erdal Cosgun,Nita A. Limdi,Christine W. Duarte:
  High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans.1384-1389

Systems Biology

• 
  Oleksii Kuchaiev,Natasa Przulj:
  Integrative network alignment reveals large regions of global network similarity in yeast and human.1390-1396
• 
  Georg Basler,Oliver Ebenhöh,Joachim Selbig,Zoran Nikoloski:
  Mass-balanced randomization of metabolic networks.1397-1403
• 
  Martial Sankar,Karen S. Osmont,Jakub Rolcik,Bojan Gujas,Danuse Tarkowska,Miroslav Strnad,Ioannis Xenarios,Christian S. Hardtke:
  A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk.1404-1412

Data and Text Mining

• 
  Christophe Bécavin,Nicolas Tchitchek,Colette Mintsa-Eya,Annick Lesne,Arndt Benecke:
  Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition.1413-1421
• 
  Hei-Chia Wang,Yi-Hsiu Chen,Hung-Yu Kao,Shaw-Jenq Tsai:
  Inference of transcriptional regulatory network by bootstrapping patterns.1422-1428

Databases and Ontologies

• 
  Lauren Becnel Boyd,Scott P. Hunicke-Smith,Grace A. Stafford,Elaine T. Freund,Michele Ehlman,Uma Chandran,Robert Dennis,Anna T. Fernandez,Stephen Goldstein,David Steffen,Benjamin Tycko,Juli D. Klemm:
  The caBIG® Life Science Business Architecture Model.1429-1435

Applications Note - Sequence Analysis

• 
  Yuanwei Zhang,Yifan Yang,Huan Zhang,Xiaohua Jiang,Bo Xu,Yu Xue,Yunxia Cao,Qian Zhai,Yong Zhai,Mingqing Xu,Howard J. Cooke,Qinghua Shi:
  Prediction of novel pre-microRNAs with high accuracy through boosting and SVM.1436-1437

Structural Bioinformatics

• 
  Timothy Nugent,Sean Ward,David T. Jones:
  The MEMPACK alpha-helical transmembrane protein structure prediction server.1438-1439

Gene Expression

• 
  Ola Larsson,Nahum Sonenberg,Robert Nadon:
  anota: analysis of differential translation in genome-wide studies.1440-1441
• 
  Marc Johannes,Holger Fröhlich,Holger Sültmann,Tim Beißbarth:
  pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.1442-1443

Databases and Ontologies

• 
  Xinan Yang,Jianrong Li,Younghee Lee,Yves A. Lussier:
  GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.1444-1446
• 
  Li Chen,George Wu,Hongkai Ji:
  hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.1447-1448

Volume 27, Number 11, June 2011

Review - Structural Bioinformatics

• 
  Ferenc Orosz,Judit Ovádi:
  Proteins without 3D structure: definition, detection and beyond.1449-1454

Original Papers - Genome Analysis

• 
  Leena Salmela,Jan Schröder:
  Correcting errors in short reads by multiple alignments.1455-1461
• 
  Gibran Hemani,Athanasios Theocharidis,Wenhua Wei,Chris S. Haley:
  EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards.1462-1465
• 
  Mirjana Domazet-Loso,Bernhard Haubold:
  Alignment-free detection of local similarity among viral and bacterial genomes.1466-1472
• 
  Guoqiang Yu,Bai Zhang,G. Steven Bova,Jianfeng Xu,Ie-Ming Shih,Yue Joseph Wang:
  BACOM:in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.1473-1480

Sequence Analysis

• 
  Andrew W. McPherson,Chunxiao Wu,Iman Hajirasouliha,Fereydoun Hormozdiari,Faraz Hach,Anna Lapuk,Stanislav Volik,Sohrab P. Shah,Colin C. Collins,Süleyman Cenk Sahinalp:
  Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.1481-1488
• 
  Henry C. M. Leung,Siu-Ming Yiu,Bin Yang,Yu Peng,Yi Wang,Zhihua Liu,Jing-Chi Chen,Junjie Qin,Ruiqiang Li,Francis Y. L. Chin:
  A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio.1489-1495

Gene Expression

• 
  Andrew E. Teschendorff,Joanna Zhuang,Martin Widschwendter:
  Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.1496-1505
• 
  Bin Wang,Xiao-Feng Wang,Yaguang Xi:
  Normalizing bead-based microRNA expression data: a measurement error model-based approach.1506-1512

Genetics and Population Analysis

• 
  Dan He,Farhad Hormozdiari,Nicholas A. Furlotte,Eleazar Eskin:
  Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.1513-1520

Systems Biology

• 
  Qianghu Wang,Jie Sun,Meng Zhou,Haixiu Yang,Yan Li,Xiang Li,Sali Lv,Xia Li,Yixue Li:
  A novel network-based method for measuring the functional relationship between gene sets.1521-1528
• 
  Markus Maucher,Barbara Kracher,Michael Kühl,Hans A. Kestler:
  Inferring Boolean network structure via correlation.1529-1536
• 
  Fangping Mu,Clifford J. Unkefer,Pat J. Unkefer,William S. Hlavacek:
  Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.1537-1545

Data and Text Mining

• 
  Kai Christian Bader,Christian Grothoff,Harald Meier:
  Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets.1546-1554
• 
  Teo Shu Mei,Yudi Pawitan,Vikrant Kumar,Anbupalam Thalamuthu,Mark Seielstad,Kee Seng Chia,Agus Salim:
  Multi-platform segmentation for joint detection of copy number variants.1555-1561

Databases and Ontologies

• 
  Ward Blondé,Vladimir Mironov,Aravind Venkatesan,Erick Antezana,Bernard De Baets,Martin Kuiper:
  Reasoning with bio-ontologies: using relational closure rules to enable practical querying.1562-1568

Applications Note - Sequence Analysis

• 
  Cenny Taslim,Tim Hui-Ming Huang,Shili Lin:
  DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models.1569-1570
• 
  Felix Krueger,Simon R. Andrews:
  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.1571-1572

Structural Bioinformatics

• 
  Corinna Vehlow,Henning Stehr,Matthias Winkelmann,Jose M. Duarte,Lars Petzold,Juliane Dinse,Michael Lappe:
  CMView: Interactive contact map visualization and analysis.1573-1574
• 
  Ahmet Bakan,Lidio M. C. Meireles,Ivet Bahar:
  ProDy: Protein Dynamics Inferred from Theory and Experiments.1575-1577

Systems Biology

• 
  Tian Xia,John L. Van Hemert,Julie A. Dickerson:
  CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling.1578-1580
• 
  Deguo Xia,Haoran Zheng,Zhiqiang Liu,Guisheng Li,Jinlong Li,Jiong Hong,Kai Zhao:
  MRSD: a web server for Metabolic Route Search and Design.1581-1582
• 
  Ahmet Emre Aladag,Cesim Erten,Melih Sözdinler:
  Reliability-Oriented bioinformatic networks visualization.1583-1584
• 
  Ambarish Biswas,Raghuraj Rao,Shivshankar Umashankar,Kalyan C. Mynampati,Sheela Reuben,Gauri Parab,Sanjay Swarup:
  datPAV - an online processing, analysis and visualization tool for exploratory investigation of experimental data.1585-1586
• 
  Pieter Audenaert,Thomas Van Parys,Florian Brondel,Mario Pickavet,Piet Demeester,Yves Van de Peer,Tom Michoel:
  CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.1587-1588

Data and Text Mining

• 
  Soumya Raychaudhuri:
  VIZ-GRAIL: visualizing functional connections across disease loci.1589-1590

Databases and Ontologies

• 
  Masao Nagasaki,Ayumu Saito,André Fujita,Georg Tremmel,Kazuko Ueno,Emi Ikeda,Euna Jeong,Satoru Miyano:
  Systems biology model repository for macrophage pathway simulation.1591-1593

Volume 27, Number 12, June 2011

Original Papers - Genome Analysis

• 
  Michael C. Wendl,John W. Wallis,Ling Lin,Cyriac Kandoth,Elaine R. Mardis,Richard K. Wilson,Li Ding:
  PathScan: a tool for discerning mutational significance in groups of putative cancer genes.1595-1602
• 
  Emi Tanaka,Timothy L. Bailey,Charles E. Grant,William Stafford Noble,Uri Keich:
  Improved similarity scores for comparing motifs.1603-1609
• 
  Justin Bedo,Adam Kowalczyk:
  Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data.1610-1617

Sequence Analysis

• 
  Peter Meinicke,Kathrin Petra Aßhauer,Thomas Lingner:
  Mixture models for analysis of the taxonomic composition of metagenomes.1618-1624

Structural Bioinformatics

• 
  Matteo Floris,Domenico Raimondo,Guido Leoni,Massimiliano Orsini,Paolo Marcatili,Anna Tramontano:
  MAISTAS: a tool for automatic structural evaluation of alternative splicing products.1625-1629
• 
  Ali Abdul-Gader,Andrew John Miles,B. A. Wallace:
  A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy.1630-1636

Gene Expression

• 
  Cheng Zheng,Shucha Zhang,Susanne Ragg,Daniel Raftery,Olga Vitek:
  Identification and quantification of metabolites in¹H NMR spectra by Bayesian model selection.1637-1644
• 
  Michael Seifert,Marc Strickert,Alexander Schliep,Ivo Grosse:
  Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models.1645-1652
• 
  Timothy L. Bailey:
  DREME: motif discovery in transcription factor ChIP-seq data.1653-1659

Systems Biology

• 
  Seongho Kim,Aiqin Fang,Bing Wang,Jaesik Jeong,Xiang Zhang:
  An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure.1660-1666
• 
  Senol Isci,Cengizhan Ozturk,Jon Jones,Hasan H. Otu:
  Pathway analysis of high-throughput biological data within a Bayesian network framework.1667-1674

Data and Text Mining

• 
  Mohammadmahdi R. Yousefi,Jianping Hua,Edward R. Dougherty:
  Multiple-rule bias in the comparison of classification rules.1675-1683

Databases and Ontologies

• 
  Olga Ivchenko,Erfan Younesi,Mohammad Shahid,Antje Wolf,Bernd Müller,Martin Hofmann-Apitius:
  PLIO: an ontology for formal description of protein-ligand interactions.1684-1690

Applications Note - Genome Analysis

• 
  Derek W. Barnett,Erik K. Garrison,Aaron R. Quinlan,Michael Strömberg,Gabor T. Marth:
  BamTools: a C++ API and toolkit for analyzing and managing BAM files.1691-1692
• 
  Camille Sabbah,Gildas Mazo,Caroline Paccard,Fabien Reyal,Philippe Hupé:
  SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip.1693-1695
• 
  Philip Machanick,Timothy L. Bailey:
  MEME-ChIP: motif analysis of large DNA datasets.1696-1697
• 
  Irina Ostrovnaya,Venkatraman E. Seshan,Adam B. Olshen,Colin B. Begg:
  Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.1698-1699

Sequence Analysis

• 
  Daniel Beck,Matt Settles,James A. Foster:
  OTUbase: an R infrastructure package for operational taxonomic unit data.1700-1701
• 
  Nanjiang Shu,Arne Elofsson:
  KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2.1702-1703
• 
  Beifang Niu,Zhengwei Zhu,Limin Fu,Sitao Wu,Weizhong Li:
  FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.1704-1705
• 
  Jesse Stombaugh,Jeremy Widmann,Daniel McDonald,Rob Knight:
  Boulder ALignment Editor (ALE): a web-based RNA alignment tool.1706-1707
• 
  Yang Li,Jeremy Chien,David I. Smith,Jian Ma:
  FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.1708-1710

Structural Bioinformatics

• 
  Joost J. J. van Durme,Javier Delgado Blanco,Francois Stricher,Luis Serrano,Joost Schymkowitz,Frederic Rousseau:
  A graphical interface for the FoldX forcefield.1711-1712
• 
  Fabien Mareuil,Christophe Blanchet,Therese E. Malliavin,Michael Nilges:
  Grid computing for improving conformational sampling in NMR structure calculation.1713-1714
• 
  Zheng Wang,Jesse Eickholt,Jianlin Cheng:
  APOLLO: a quality assessment service for single and multiple protein models.1715-1716

Genetics and Population Analysis

• 
  Tiago Antao,Mark A. Beaumont:
  Mcheza: a workbench to detect selection using dominant markers.1717-1718

Systems Biology

• 
  Ola Spjuth,Martin Eklund,Maris Lapins,Muhammad Junaid,Jarl E. S. Wikberg:
  Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre.1719-1720
• 
  Wen Xu,Adam M. Smith,James R. Faeder,G. Elisabeta Marai:
  RuleBender: a visual interface for rule-based modeling.1721-1722

Data and Text Mining

• 
  Shashank Agarwal,Hong Yu:
  Figure summarizer browser extensions for PubMed Central.1723-1724
• 
  Joachim von Eichborn,Philip E. Bourne,Robert Preissner:
  Cobweb: a Java applet for network exploration and visualisation.1725-1726
• 
  Woonghee Lee,Jin Hae Kim,William M. Westler,John L. Markley:
  PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.1727-1728
• 
  Vlad Popovici,Eva Budinska,Mauro Delorenzi:
  Rgtsp: a generalized top scoring pairs package for class prediction.1729-1730
• 
  Kangseok Kim,Wonil Kim,Sunshin Kim:
  ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms.1731-1733

Databases and Ontologies

• 
  Dominic Sebastian Lütjohann,Asmi H. Shah,Michael P. Christen,Florian Richter,Karsten Knese,Urban Liebel:
  'Sciencenet' - towards a global search and share engine for all scientific knowledge.1734-1735
• 
  Ashok Reddy Dinasarapu,Brian Saunders,Iley Ozerlat,Kenan Azam,Shankar Subramaniam:
  Signaling gateway molecule pages - a data model perspective.1736-1738
• 
  Arthur Liberzon,Aravind Subramanian,Reid Pinchback,Helga Thorvaldsdóttir,Pablo Tamayo,Jill P. Mesirov:
  Molecular signatures database (MSigDB) 3.0.1739-1740

Volume 27, Number 13, July 2011

ISMB/ECCB 2011 Proceedings

• 
  Denis C. Bauer,Kai Willadsen,Fabian A. Buske,Kim-Anh Lê Cao,Timothy L. Bailey,Graham Dellaire,Mikael Bodén:
  Sorting the nuclear proteome.7-14
• 
  Jamie R. Hill,Sebastian Kelm,Jiye Shi,Charlotte M. Deane:
  Environment specific substitution tables improve membrane protein alignment.15-23
• 
  Marcin J. Mizianty,Lukasz A. Kurgan:
  Sequence-based prediction of protein crystallization, purification and production propensity.24-33
• 
  Charles W. O'Donnell,Jérôme Waldispühl,Mieszko Lis,Randal Halfmann,Srinivas Devadas,Susan Lindquist,Bonnie Berger:
  A method for probing the mutational landscape of amyloid structure.34-42
• 
  Arun Siddharth Konagurthu,Lloyd Allison,Peter J. Stuckey,Arthur M. Lesk:
  Piecewise linear approximation of protein structures using the principle of minimum message length.43-51
• 
  Andrej J. Savol,Virginia M. Burger,Pratul K. Agarwal,Arvind Ramanathan,Chakra S. Chennubhotla:
  QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin.52-60
• 
  S. Shivashankar,S. Srivathsan,Balaraman Ravindran,Ashish V. Tendulkar:
  Multi-view methods for protein structure comparison using latent dirichlet allocation.61-68
• 
  Min Xu,Martin Beck,Frank Alber:
  Template-free detection of macromolecular complexes in cryo electron tomograms.69-76
• 
  André Altmann,Peter Weber,Carina Quast,Monika Rex-Haffner,Elisabeth B. Binder,Bertram Müller-Myhsok:
  vipR: variant identification in pooled DNA using R.77-84
• 
  Kengo Sato,Yuki Kato,Michiaki Hamada,Tatsuya Akutsu,Kiyoshi Asai:
  IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.85-93
• 
  Yu Peng,Henry C. M. Leung,Siu-Ming Yiu,Francis Y. L. Chin:
  Meta-IDBA: ade Novo assembler for metagenomic data.94-101
• 
  Zhiyong Wang,Jinbo Xu:
  A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling.102-110
• 
  Yoshimasa Tsuruoka,Makoto Miwa,Kaisei Hamamoto,Jun'ichi Tsujii,Sophia Ananiadou:
  Discovering and visualizing indirect associations between biomedical concepts.111-119
• 
  Sanmitra Bhattacharya,Viet Ha-Thuc,Padmini Srinivasan:
  MeSH: a window into full text for document summarization.120-128
• 
  Christian Höner zu Siederdissen,Stephan H. Bernhart,Peter F. Stadler,Ivo L. Hofacker:
  A folding algorithm for extended RNA secondary structures.129-136
• 
  Paul Medvedev,Eric Scott,Boyko Kakaradov,Pavel A. Pevzner:
  Error correction of high-throughput sequencing datasets with non-uniform coverage.137-141
• 
  Regev Schweiger,Michal Linial,Nathan Linial:
  Generative probabilistic models for protein-protein interaction networks - the biclique perspective.142-148
• 
  Günhan Gülsoy,Tamer Kahveci:
  RINQ: Reference-based Indexing for Network Queries.149-158
• 
  Zhipeng Xie,Chee Keong Kwoh,Xiaoli Li,Min Wu:
  Construction of co-complex score matrix for protein complex prediction from AP-MS data.159-166
• 
  Yong Chen,Tao Jiang,Rui Jiang:
  Uncover disease genes by maximizing information flow in the phenome-interactome network.167-176
• 
  Noa Novershtern,Aviv Regev,Nir Friedman:
  Physical Module Networks: an integrative approach for reconstructing transcription regulation.177-185
• 
  Sara Berthoumieux,Matteo Brilli,Hidde de Jong,Daniel Kahn,Eugenio Cinquemani:
  Identification of metabolic network models from incomplete high-throughput datasets.186-195
• 
  Ankur P. Parikh,Wei Wu,Ross E. Curtis,Eric P. Xing:
  TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages.196-204
• 
  Phuong Dao,Kendric Wang,Colin C. Collins,Martin Ester,Anna Lapuk,Süleyman Cenk Sahinalp:
  Optimally discriminative subnetwork markers predict response to chemotherapy.205-213
• 
  Tony Kam-Thong,Benno Pütz,Nazanin Karbalai,Bertram Müller-Myhsok,Karsten M. Borgwardt:
  Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs.214-221
• 
  Jing Li,Benjamin Horstman,Yixuan Chen:
  Detecting epistatic effects in association studies at a genomic level based on an ensemble approach.222-229
• 
  Theodore Alexandrov,Jan Hendrik Kobarg:
  Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering.230-238
• 
  Hanchuan Peng,Fuhui Long,Gene Myers:
  Automatic 3D neuron tracing using all-path pruning.239-247
• 
  Céline Scornavacca,Franziska Zickmann,Daniel H. Huson:
  Tanglegrams for rooted phylogenetic trees and networks.248-256
• 
  Haris Gavranovic,Cédric Chauve,Jérôme Salse,Eric Tannier:
  Mapping ancestral genomes with massive gene loss: A matrix sandwich problem.257-265
• 
  Javad Sadri,Abdoulaye Baniré Diallo,Mathieu Blanchette:
  Predicting site-specific human selective pressure using evolutionary signatures.266-274
• 
  Michael F. Lin,Irwin Jungreis,Manolis Kellis:
  PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.275-282
• 
  Nicola Bonzanni,Nianshu Zhang,Stephen G. Oliver,Jasmin Fisher:
  The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity inSaccharomyces cerevisiae.283-287
• 
  Nicholas A. Furlotte,Hyun Min Kang,Chun Ye,Eleazar Eskin:
  Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity.288-294
• 
  Michael B. Mayhew,Joshua W. Robinson,Boyoun Jung,Steven B. Haase,Alexander J. Hartemink:
  A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.295-303
• 
  Susanne Balzer,Ketil Malde,Inge Jonassen:
  Systematic exploration of error sources in pyrosequencing flowgram data.304-309
• 
  Guangxu Jin,Hong Zhao,Xiaobo Zhou,Stephen T. C. Wong:
  An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.310-316
• 
  David Golan,Saharon Rosset:
  Accurate estimation of heritability in genome wide studies using random effects models.317-323
• 
  Suyash Shringarpure,Daegun Won,Eric P. Xing:
  StructHDP: automatic inference of number of clusters and population structure from admixed genotype data.324-332
• 
  Sofia Kyriazopoulou-Panagiotopoulou,Dorna Kashef Haghighi,Sarah J. Aerni,Andreas Sundquist,Sivan Bercovici,Serafim Batzoglou:
  Reconstruction of genealogical relationships with applications to Phase III of HapMap.333-341
• 
  Limin Li,Barbara Rakitsch,Karsten M. Borgwardt:
  ccSVM: correcting Support Vector Machines for confounding factors in biological data classification.342-348
• 
  Filipe Santana,Daniel Schober,Zulma Medeiros,Fred Freitas,Stefan Schulz:
  Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases.349-356
• 
  Henning Redestig,Ivan G. Costa:
  Detection and interpretation of metabolite-transcript coresponses using combined profiling data.357-365
• 
  Ludwig Geistlinger,Gergely Csaba,Robert Küffner,Nicola J. Mulder,Ralf Zimmer:
  From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems.366-373
• 
  Edoardo M. Airoldi,Katherine A. Heller,Ricardo Bezerra de Andrade e Silva:
  Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning.374-382
• 
  Pawel P. Labaj,Germán G. Leparc,Bryan E. Linggi,Lye Meng Markillie,H. Steven Wiley,David P. Kreil:
  Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.383-391
• 
  Julia Sivriver,Naomi Habib,Nir Friedman:
  An integrative clustering and modeling algorithm for dynamical gene expression data.392-400
• 
  Shi-Hua Zhang,Qingjiao Li,Juan Liu,Xianghong Jasmine Zhou:
  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.401-409
• 
  Guy Haskin Fernald,Emidio Capriotti,Roxana Daneshjou,Konrad J. Karczewski,Russ B. Altman:
  Genome Analysis.1741-1748

Discovery Note

• 
  Yong E. Zhang,Maria D. Vibranovski,Benjamin H. Krinsky,Manyuan Long:
  A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.1749-1753
• 
  Roberto Chignola,Vladislav Vyshemirsky,Marcello Farina,Alessio Del Fabbro,Edoardo Milotti:
  Modular model of TNFα cytotoxicity.1754-1757

Original Papers

• 
  Zhiming Dai,Xianhua Dai,Qian Xiang:
  Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast.1758-1764
• 
  Josue Samayoa,Fitnat H. Yildiz,Kevin Karplus:
  Identification of prokaryotic small proteins using a comparative genomic approach.1765-1771
• 
  Qiwei Li,Xiaodan Fan,Tong Liang,Shuo-Yen Robert Li:
  An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences.1772-1779
• 
  Tzong-Yi Lee,Zong-Qing Lin,Sheng-Jen Hsieh,Neil Arvin Bretaña,Cheng-Tsung Lu:
  Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences.1780-1787
• 
  Hisanori Kiryu,Goro Terai,Osamu Imamura,Hiroyuki Yoneyama,Kenji Suzuki,Kiyoshi Asai:
  A detailed investigation of accessibilities around target sites of siRNAs and miRNAs.1788-1797
• 
  Sungroh Yoon,Jinkyu Kim,Justine Hum,Hanjoo Kim,Seunghyun Park,Wipapat Kladwang,Rhiju Das:
  HiTRACE: high-throughput robust analysis for capillary electrophoresis.1798-1805
• 
  Ferenc Zsila,Zsolt Bikádi,David Malik,Péter Hári,Imre Pechan,Attila Bérces,Eszter Hazai:
  Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking.1806-1813
• 
  Tingjun Hou,Youyong Li,Wei Wang:
  Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy.1814-1821
• 
  Lori A. Dalton,Edward R. Dougherty:
  Application of the Bayesian MMSE estimator for classification error to gene expression microarray data.1822-1831
• 
  Sushmita Roy,Margaret Werner-Washburne,Terran Lane:
  A multiple network learning approach to capture system-wide condition-specific responses.1832-1838
• 
  Hendrik Rohn,Christian Klukas,Falk Schreiber:
  Creating views on integrated multidomain data.1839-1845
• 
  Jaegyoon Ahn,Youngmi Yoon,Chihyun Park,Eunji Shin,Sanghyun Park:
  Integrative gene network construction for predicting a set of complementary prostate cancer genes.1846-1853
• 
  Charles Jackson,Estelle Glory-Afshar,Robert F. Murphy,Jelena Kovacevic:
  Model building and intelligent acquisition with application to protein subcellular location classification.1854-1859
• 
  Jesse A. Gillis,Paul Pavlidis:
  The role of indirect connections in gene networks in predicting function.1860-1866

Applications Note

• 
  Clifford A. Meyer,Housheng H. He,Myles Brown,Xiaole Shirley Liu:
  BINOCh: binding inference from nucleosome occupancy changes.1867-1868
• 
  Brian Walenz,Liliana Florea:
  Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.1869-1870
• 
  Fernando Muñiz-Fernandez,Angel Carreño-Torres,Carlos Morcillo-Suarez,Arcadi Navarro:
  Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management.1871-1872
• 
  Hariklia Eleftherohorinou,Johanna C. Andersson-Assarsson,Robin G. Walters,Julia S. El-Sayed Moustafa,Lachlan J. M. Coin,Peter Jacobson,Lena M. S. Carlsson,Alexandra I. F. Blakemore,Philippe Froguel,Andrew J. Walley,Mario Falchi:
  famCNV: copy number variant association for quantitative traits in families.1873-1875
• 
  Gabriele Sales,Chiara Romualdi:
  parmigene - a parallel R package for mutual information estimation and gene network reconstruction.1876-1877
• 
  Matti Kankainen,Peddinti V. Gopalacharyulu,Liisa Holm,Matej Oresic:
  MPEA - metabolite pathway enrichment analysis.1878-1879
• 
  Ross E. Curtis,Amos Yuen,Le Song,Anuj Goyal,Eric P. Xing:
  TVNViewer: An interactive visualization tool for exploring networks that change over time or space.1880-1881
• 
  Sebastian Bauer,Peter N. Robinson,Julien Gagneur:
  Model-based gene set analysis for Bioconductor.1882-1883

Volume 27, Number 14, July 2011

Discovery Note - Sequence Analysis

• 
  Luis Sánchez-Pulido,Chris P. Ponting:
  Cdc45: the missing RecJ ortholog in eukaryotes?1885-1888

Original Paper - Genome Analysis

• 
  Julien Lajugie,Eric E. Bouhassira:
  GenPlay, a multipurpose genome analyzer and browser.1889-1893
• 
  Dominic Rose,Michael Hiller,Katharina Schutt,Jörg Hackermüller,Rolf Backofen,Peter F. Stadler:
  Computational discovery of human coding and non-coding transcripts with conserved splice sites.1894-1900
• 
  Hieu Dinh,Sanguthevar Rajasekaran:
  A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly.1901-1907

Sequence Analysis

• 
  Craig T. Armstrong,Thomas L. Vincent,Peter J. Green,Derek N. Woolfson:
  SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences.1908-1914
• 
  Farhad Hormozdiari,Faraz Hach,Süleyman Cenk Sahinalp,Evan E. Eichler,Can Alkan:
  Sensitive and fast mapping of di-base encoded reads.1915-1921
• 
  Huanying Ge,Kejun Liu,Todd Juan,Fang Fang,Matthew Newman,Wolfgang Hoeck:
  FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.1922-1928
• 
  Bas E. Dutilh,Rasa Jurgelenaite,Radek Szklarczyk,Sacha A. F. T. van Hijum,Harry R. Harhangi,Markus Schmid,Bart de Wild,Kees-Jan Françoijs,Henk Stunnenberg,Marc Strous,Mike S. M. Jetten,Huub J. M. Op den Camp,Martijn A. Huynen:
  FACIL: Fast and Accurate Genetic Code Inference and Logo.1929-1933

Structural Bioinformatics

• 
  Hakim Tafer,Fabian Amman,Florian Eggenhofer,Peter F. Stadler,Ivo L. Hofacker:
  Fast accessibility-based prediction of RNA-RNA interactions.1934-1940
• 
  Haim Ashkenazy,Ron Unger,Yossef Kliger:
  Hidden conformations in protein structures.1941-1947

Gene Expression

• 
  Riet De Smet,Kathleen Marchal:
  An ensemble biclustering approach for querying gene expression compendia with experimental lists.1948-1956

Systems Biology

• 
  Wanding Zhou,Luay Nakhleh:
  The strength of chemical linkage as a criterion for pruning metabolic graphs.1957-1963
• 
  Gengjie Jia,Gregory Stephanopoulos,Rudiyanto Gunawan:
  Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method.1964-1970
• 
  Ales Maver,Borut Peterlin:
  Positional integratomic approach in identification of genomic candidate regions for Parkinson's disease.1971-1978

Data and Text Mining

• 
  Maurice Berk,Timothy M. D. Ebbels,Giovanni Montana:
  A statistical framework for biomarker discovery in metabolomic time course data.1979-1985
• 
  Laura Tolosi,Thomas Lengauer:
  Classification with correlated features: unreliability of feature ranking and solutions.1986-1994

Applications Note - Genome Analysis

• 
  Yufeng Shen,Ruijie Song,Itsik Pe'er:
  Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.1995-1997
• 
  Dongliang Ge,Elizabeth K. Ruzzo,Kevin V. Shianna,Min He,Kimberly Pelak,Erin L. Heinzen,Anna C. Need,Elizabeth T. Cirulli,Jessica M. Maia,Samuel P. Dickson,Mingfu Zhu,Abanish Singh,Andrew S. Allen,David B. Goldstein:
  SVA: software for annotating and visualizing sequenced human genomes.1998-2000

Sequence Analysis

• 
  Peter V. Troshin,James B. Procter,Geoffrey J. Barton:
  Java bioinformatics analysis web services for multiple sequence alignment - JABAWS: MSA.2001-2002

Structural Bioinformatics

• 
  Alberto J. M. Martin,Michele Vidotto,Filippo Boscariol,Tomás Di Domenico,Ian Walsh,Silvio C. E. Tosatto:
  RING: networking interacting residues, evolutionary information and energetics in protein structures.2003-2005

Genetics and Population Analysis

• 
  Chunfa Tong,Zhong Wang,Bo Zhang,Jisen Shi,Rongling Wu:
  3FunMap: full-sib family functional mapping of dynamic traits.2006-2008

Systems Biology

• 
  Stefan Gretar Thorleifsson,Ines Thiele:
  rBioNet: A COBRA toolbox extension forreconstructing high-qualitybiochemicalnetworks.2009-2010
• 
  Alex T. Kalinka,Pavel Tomancak:
  linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.2011-2012
• 
  Nicolas Rapin,Ole Lund,Filippo Castiglione:
  Immune system simulation online.2013-2014

Data and Text Mining

• 
  Supawadee Ingsriswang,Sunai Yokwai,Duangdao Wichadakul:
  LinkinPath: from sequence to interconnected pathway.2015-2017
• 
  David Lagorce,Julien Maupetit,Jonathan B. Baell,Olivier Sperandio,Pierre Tufféry,Maria A. Miteva,Hervé Galons,Bruno O. Villoutreix:
  The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections.2018-2020

Databases and Ontologies

• 
  Katy Wolstencroft,Stuart Owen,Matthew Horridge,Olga Krebs,Wolfgang Müller,Jacky L. Snoep,Franco B. du Preez,Carole A. Goble:
  RightField: embedding ontology annotation in spreadsheets.2021-2022
• 
  Sudhir Kumar,S. Blair Hedges:
  TimeTree2: species divergence times on the iPhone.2023-2024

Letter to the Editor - Data and Text Mining

• 
  Jonathan D. Wren:
  Question answering systems in biology and medicine - the time is now.2025-2026

Volume 27, Number 15, August 2011

Discovery Note - Sequence Analysis

• 
  Ofer Isakov,Shira Modai,Noam Shomron:
  Pathogen detection using short-RNA deep sequencing subtraction and assembly.2027-2030

Original Papers - Genome Analysis

• 
  Yong Lin,Jian Li,Hui Shen,Lei Zhang,Christopher J. Papasian,Hong-Wen Deng:
  Comparative studies ofde novo assembly tools for next-generation sequencing technologies.2031-2037
• 
  Adam B. Olshen,Henrik Bengtsson,Pierre Neuvial,Paul T. Spellman,Richard A. Olshen,Venkatraman E. Seshan:
  Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.2038-2046

Sequence Analysis

• 
  Vikas Bansal,Ondrej Libiger:
  A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.2047-2053
• 
  Rui Yan,Paul C. Boutros,Igor Jurisica:
  A tree-based approach for motif discovery and sequence classification.2054-2061
• 
  Shu-An Chen,Yu-Yen Ou,Tzong-Yi Lee,M. Michael Gromiha:
  Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties.2062-2067

Phylogenetics

• 
  Simon A. Berger,Alexandros Stamatakis:
  Aligning short reads to reference alignments and trees.2068-2075

Structural Bioinformatics

• 
  Yuedong Yang,Eshel Faraggi,Huiying Zhao,Yaoqi Zhou:
  Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.2076-2082
• 
  Zengming Zhang,Yu Li,Biaoyang Lin,Michael Schroeder,Bingding Huang:
  Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction.2083-2088

Gene Expression

• 
  Martin Sill,Sebastian Kaiser,Axel Benner,Annette Kopp-Schneider:
  Robust biclustering by sparse singular value decomposition incorporating stability selection.2089-2097
• 
  Stan Pounds,Cuilan Lani Gao,Robert A. Johnson,Karen D. Wright,Helen Poppleton,David Finkelstein,Sarah E. S. Leary,Richard J. Gilbertson:
  A procedure to statistically evaluate agreement of differential expression for cross-species genomics.2098-2103

Genetics and Population Analysis

• 
  Harm-Jan Westra,Ritsert C. Jansen,Rudolf S. N. Fehrmann,Gerard J. te Meerman,David van Heel,Cisca Wijmenga,Lude Franke:
  MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects.2104-2111
• 
  Todd L. Edwards,Zhuo Song,Chun Li:
  Enriching targeted sequencing experiments for rare disease alleles.2112-2118
• 
  Shujie Ma,Lijian Yang,Roberto Romero,Yuehua Cui:
  Varying coefficient model for gene-environment interaction: a non-linear look.2119-2126

Systems Biology

• 
  Luca Beltrame,Enrica Calura,Razvan R. Popovici,Lisa Rizzetto,Damariz Rivero Guedez,Michele Donato,Chiara Romualdi,Sorin Draghici,Duccio Cavalieri:
  The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.2127-2133
• 
  Oleg Paliy,Brent D. Foy:
  Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays.2134-2140

Applications Note - Genome Analysis

• 
  Rong She,Jeffrey Shih-Chieh Chu,Bora Uyar,Jun Wang,Ke Wang,Nansheng Chen:
  genBlastG: using BLAST searches to build homologous gene models.2141-2143
• 
  Joseph K. Pickrell,Daniel J. Gaffney,Yoav Gilad,Jonathan K. Pritchard:
  False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions.2144-2146
• 
  Wing Chung Wong,Dewey Kim,Hannah Carter,Mark Diekhans,Michael C. Ryan,Rachel Karchin:
  CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.2147-2148
• 
  Oscar Flores,Modesto Orozco:
  nucleR: a package for non-parametric nucleosome positioning.2149-2150

Sequence Analysis

• 
  Thomas K. F. Wong,Kwok-Lung Wan,Bay-Yuan Hsu,Brenda W. Y. Cheung,Wing-Kai Hon,Tak Wah Lam,Siu-Ming Yiu:
  RNASAlign: RNA Structural Alignment System.2151-2152
• 
  Aurelien Ginolhac,Morten Rasmussen,M. Thomas P. Gilbert,Eske Willerslev,Ludovic Orlando:
  mapDamage: testing for damage patterns in ancient DNA sequences.2153-2155
• 
  Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin:
  The variant call format and VCFtools.2156-2158
• 
  Luca Pireddu,Simone Leo,Gianluigi Zanetti:
  SEAL: a distributed short read mapping and duplicate removal tool.2159-2160

Structural Bioinformatics

• 
  Mark Moll,Drew H. Bryant,Lydia E. Kavraki:
  The LabelHash Server and Tools for substructure-based functional annotation.2161-2162
• 
  Abdullah Kahraman,Lars Malmström,Ruedi Aebersold:
  Xwalk: computing and visualizing distances in cross-linking experiments.2163-2164

Systems Biology

• 
  Augustin Luna,Margot Sunshine,Martijn P. van Iersel,Mirit I. Aladjem,Kurt W. Kohn:
  PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).2165-2166
• 
  Andreas Dräger,Nicolas Rodriguez,Marine Dumousseau,Alexander Dörr,Clemens Wrzodek,Nicolas Le Novère,Andreas Zell,Michael Hucka:
  JSBML: a flexible Java library for working with SBML.2167-2168

Letter to the Editor - Gene Expression

• 
  Xin-Yuan Song,Zhaohua Lu:
  Response to "Comments on 'Bayesian variable selection for disease classification using gene expression data'".2169-2170

Corrigendum - Gene Expression

• 
  Susanne Balzer,Ketil Malde,Anders Lanzén,Animesh Sharma,Inge Jonassen:
  Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim.2171

Volume 27, Number 16, August 2011

Original Papers - Genome Analysis

• 
  Danni Yu,John Danku,Ivan Baxter,Sungjin Kim,Olena K. Vatamaniuk,David E. Salt,Olga Vitek:
  Noise reduction in genome-wide perturbation screens using linear mixed-effect models.2173-2180
• 
  Lucy F. Stead,I. C. Wood,David R. Westhead:
  KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels.2181-2186
• 
  Eva-Maria Willing,Margarete Hoffmann,Juliane Damaris Klein,Detlef Weigel,Christine Dreyer:
  Paired-end RAD-seq forde novo assembly and marker design without available reference.2187-2193

Sequence Analysis

• 
  Robert C. Edgar,Brian J. Haas,José Carlos Clemente,Christopher Quince,Rob Knight:
  UCHIME improves sensitivity and speed of chimera detection.2194-2200

Structural Bioinformatics

• 
  Yong-Min Lao,Lan Xiao,Zhi-Wei Ye,Jian-Guo Jiang,Shi-Shui Zhou:
  In silico analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis inDuanliella bardawil.2201-2208
• 
  Pradeep Kota,Feng Ding,Srinivas Ramachandran,Nikolay V. Dokholyan:
  Gaia: automated quality assessment of protein structure models.2209-2215
• 
  Seymour Knowles-Barley,Nancy J. Butcher,Ian A. Meinertzhagen,J. Douglas Armstrong:
  Biologically inspired EM image alignment and neural reconstruction.2216-2223
• 
  Castrense Savojardo,Piero Fariselli,Monther Alhamdoosh,Pier Luigi Martelli,Andrea Pierleoni,Rita Casadio:
  Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.2224-2230

Gene Expression

• 
  Matthias Maneck,Alexandra Schrader,Dieter Kube,Rainer Spang:
  Genomic data integration using guided clustering.2231-2238
• 
  Tobias Bauer,Roland Eils,Rainer König:
  RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors.2239-2247

Systems Biology

• 
  Stephan Symons,Kay Nieselt:
  MGV: a generic graph viewer for comparative omics data.2248-2255
• 
  Siu Hung Joshua Chan,Ping Ji:
  Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks.2256-2262
• 
  Thomas Schaffter,Daniel Marbach,Dario Floreano:
  GeneNetWeaver:in silico benchmark generation and performance profiling of network inference methods.2263-2270

Data and Text Mining

• 
  Sanjay Joshua Swamidass,Bradley T. Calhoun,Joshua A. Bittker,Nicole E. Bodycombe,Paul A. Clemons:
  Enhancing the rate of scaffold discovery with diversity-oriented prioritization.2271-2278
• 
  Timothy Driscoll,Joseph L. Gabbard,Chunhong Mao,Oral Dalay,Maulik Shukla,Clark C. Freifeld,Anne Gatewood Hoen,John S. Brownstein,Bruno W. S. Sobral:
  Integration and visualization of host-pathogen data related to infectious diseases.2279-2287

Databases and Ontologies

• 
  Carissa G. Fonseca,Michael Backhaus,David A. Bluemke,Randall Britten,Jae Do Chung,Brett R. Cowan,Ivo D. Dinov,J. Paul Finn,Peter J. Hunter,Alan H. Kadish,Daniel C. Lee,Joao A. C. Lima,Pau Medrano-Gracia,Kalyanam Shivkumar,Avan Suinesiaputra,Wenchao Tao,Alistair A. Young:
  The Cardiac Atlas Project - an imaging database for computational modeling and statistical atlases of the heart.2288-2295

Applications Note - Genome Analysis

• 
  Yurong Xin,Yongchao Ge,Fatemeh G. Haghighi:
  Methyl-Analyzer - whole genome DNA methylation profiling.2296-2297
• 
  Chien-Hao Su,Ming-Tsung Hsu,Tse-Yi Wang,Sufeng Chiang,Jen-Hao Cheng,Francis C. Weng,Cheng-Yan Kao,Daryi Wang,Huai-Kuang Tsai:
  MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering.2298-2299

Sequence Analysis

• 
  Jason R. Grant,Adriano S. Arantes,Xiaoping Liao,Paul Stothard:
  In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.2300-2301
• 
  Xinyi Liu,Xubo Su,Fei Wang,Zhimin Huang,Qi Wang,Zhen Li,Ruina Zhang,Lifang Wu,Yi Pan,Yingyi Chen,Hanyi Zhuang,Guoqiang Chen,Ting Shi,Jian Zhang:
  ODORactor: a web server for deciphering olfactory coding.2302-2303

Genetics and Population Analysis

• 
  Zhan Su,Jonathan Marchini,Peter Donnelly:
  HAPGEN2: simulation of multiple disease SNPs.2304-2305
• 
  Martin Konopac,Petra Dusatkova,Ondrej Cinek:
  SNPman: a program for genotype calling using run data from TaqMan allelic discrimination.2306-2308

Systems Biology

• 
  Hamid Bolouri,Rajiv Dulepet,Michael Angerman:
  Menu-driven cloud computing and resource sharing for R and Bioconductor.2309-2310
• 
  Eva Balsa-Canto,Julio R. Banga:
  AMIGO, a toolbox for advanced model identification in systems biology using global optimization.2311-2313
• 
  Clemens Wrzodek,Andreas Dräger,Andreas Zell:
  KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.2314-2315
• 
  Raphael B. M. Aggio,Silas Granato Villas-Bôas,Katya Ruggiero:
  Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS.2316-2318
• 
  Jialiang Huang,Yi Liu,Wei Zhang,Hong Yu,Jing-Dong J. Han:
  eResponseNet: a package prioritizing candidate disease genes through cellular pathways.2319-2320

Data and Text Mining

• 
  Kai J. Kohlhoff,Marc H. Sosnick,William T. Hsu,Vijay S. Pande,Russ B. Altman:
  CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.2321-2322

Corrigendum - Data and Text Mining

• 
  Guy Haskin Fernald,Emidio Capriotti,Roxana Daneshjou,Konrad J. Karczewski,Russ B. Altman:
  Bioinformatics challenges for personalized medicine.2323

Volume 27, Number 17, September 2011

Original Papers - Genome Analysis

• 
  Adam Roberts,Harold Pimentel,Cole Trapnell,Lior Pachter:
  Identification of novel transcripts in annotated genomes using RNA-Seq.2325-2329
• 
  Fabian Menges,Giuseppe Narzisi,Bud Mishra:
  TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.2330-2337
• 
  Catherine Stamoulis,Rebecca A. Betensky:
  A novel signal processing approach for the detection of copy number variations in the human genome.2338-2345
• 
  Hisanori Kiryu:
  Sufficient statistics and expectation maximization algorithms in phylogenetic tree models.2346-2353

Sequence Analysis

• 
  Robert C. McLeay,Chris J. Leat,Timothy L. Bailey:
  Tissue-specific prediction of directly regulated genes.2354-2360
• 
  Peter Huggins,Shan Zhong,Idit Shiff,Rachel Beckerman,Oleg Laptenko,Carol Prives,Marcel H. Schulz,Itamar Simon,Ziv Bar-Joseph:
  DECOD: fast and accurate discriminative DNA motif finding.2361-2367

Structural Bioinformatics

• 
  Alexander Goncearenco,Igor N. Berezovsky:
  Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins.2368-2375
• 
  Miguel Rojas-Chertó,Piotr T. Kasper,Egon L. Willighagen,Rob J. Vreeken,Thomas Hankemeier,Theo H. Reijmers:
  Elemental composition determination based on MSⁿ.2376-2383
• 
  Ivano Bertini,David A. Case,Lucio Ferella,Andrea Giachetti,Antonio Rosato:
  A Grid-enabled web portal for NMR structure refinement with AMBER.2384-2390

Gene Expression

• 
  Mikhail Jiline,Stan Matwin,Marcel Turcotte:
  Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments.2391-2398

Systems Biology

• 
  Yuichi Shiraishi,Mariko Okada-Hatakeyama,Satoru Miyano:
  A rank-based statistical test for measuring synergistic effects between two gene sets.2399-2405
• 
  Yiming Lu,Yang Zhou,Wubin Qu,Minghua Deng,Chenggang Zhang:
  A Lasso regression model for the construction of microRNA-target regulatory networks.2406-2413

Databases and Ontologies

• 
  Tiago J. S. Lopes,Martin H. Schaefer,Jason E. Shoemaker,Yukiko Matsuoka,Jean-Fred Fontaine,Gabriele Neumann,Miguel A. Andrade-Navarro,Yoshihiro Kawaoka,Hiroaki Kitano:
  Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.2414-2421
• 
  Alan Tan,Ben W. Tripp,Denise Daley:
  BRISK - research-oriented storage kit for biology-related data.2422-2425

Applications Note - Genome Analysis

• 
  Daniel J. Blankenberg,James Taylor,Anton Nekrutenko:
  Making whole genome multiple alignments usable for biologists.2426-2428
• 
  Mitchell J. Brittnacher,Christine Fong,H. S. Hayden,M. A. Jacobs,Matthew Radey,Laurence Rohmer:
  PGAT: a multistrain analysis resource for microbial genomes.2429-2430
• 
  Matthew Z. DeMaere,Federico M. Lauro,Torsten Thomas,Sheree Yau,Ricardo Cavicchioli:
  Simple high-throughput annotation pipeline (SHAP).2431-2432

Sequence Analysis

• 
  Lucian Ilie,Silvana Ilie,Anahita Mansouri Bigvand:
  SpEED: fast computation of sensitive spaced seeds.2433-2434
• 
  Brent Pedersen,Tzung-Fu Hsieh,Christian Ibarra,Robert L. Fischer:
  MethylCoder: software pipeline for bisulfite-treated sequences.2435-2436

Phylogenetics

• 
  Jonathan M. Eastman,C. E. Timothy Paine,Olivier J. Hardy:
  spacodiR: structuring of phylogenetic diversity in ecological communities.2437-2438
• 
  Martin Ryberg,R. Henrik Nilsson,P. Brandon Matheny:
  DivBayes and SubT: exploring species diversification using Bayesian statistics.2439-2440

Structural Bioinformatics

• 
  Magdalena Rother,Kaja Milanowska,Tomasz Puton,Jaroslaw Jeleniewicz,Kristian Rother,Janusz M. Bujnicki:
  ModeRNA server: an online tool for modeling RNA 3D structures.2441-2442
• 
  J. Y. Semegni,Mark Wamalwa,R. Gaujoux,G. W. Harkins,A. Gray,D. P. Martin:
  NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.2443-2445

Gene Expression

• 
  Francesco Ferrari,Aldo Solari,Cristina Battaglia,Silvio Bicciato:
  PREDA: an R-package to identify regional variations in genomic data.2446-2447

Genetics and Population Analysis

• 
  Asif Javed,Marc Pybus,Marta Melé,Filippo Utro,Jaume Bertranpetit,Francesc Calafell,Laxmi Parida:
  IRiS: Construction of ARG networks at genomic scales.2448-2450

Systems Biology

• 
  Jan Bot,Marcel J. T. Reinders:
  CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.2451-2452
• 
  Mark Longair,Dean A. Baker,J. Douglas Armstrong:
  Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes.2453-2454
• 
  Jianguo Xia,Igor Sinelnikov,David S. Wishart:
  MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets.2455-2456
• 
  Kevin R. Sanft,Sheng Wu,Min K. Roh,Jin Fu,Rone Kwei Lim,Linda R. Petzold:
  StochKit2: software for discrete stochastic simulation of biochemical systems with events.2457-2458
• 
  Andrea Pinna,Nicola Soranzo,Ina Hoeschele,Alberto de la Fuente:
  Simulating systems genetics data with SysGenSIM.2459-2462

Data and Text Mining

• 
  Ulrich Bodenhofer,Andreas Kothmeier,Sepp Hochreiter:
  APCluster: an R package for affinity propagation clustering.2463-2464
• 
  Qian-Nan Hu,Zhe Deng,Huanan Hu,Dong-Sheng Cao,Yi-Zeng Liang:
  RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.2465-2467

Databases and Ontologies

• 
  Natalja Kurbatova,Tomasz Adamusiak,Pavel Kurnosov,Morris A. Swertz,Misha Kapushesky:
  ontoCAT: an R package for ontology traversal and search.2468-2470
• 
  Euna Jeong,Masao Nagasaki,Emi Ikeda,Yayoi Sekiya,Ayumu Saito,Satoru Miyano:
  CSO validator: improving manual curation workflow for biological pathways.2471-2472

Volume 27, Number 18, September 2011

Discovery Note - Genome Analysis

• 
  Adrian Schröder,Johannes Wollnik,Clemens Wrzodek,Andreas Dräger,Michael Bonin,Oliver Burk,Maria Thomas,Wolfgang E. Thasler,Ulrich M. Zanger,Andreas Zell:
  Inferring statin-induced gene regulatory relationships in primary human hepatocytes.2473-2477

Original Papers - Genome Analysis

• 
  Luciana Ferrer,Alexander Glennon Shearer,Peter D. Karp:
  Discovering novel subsystems using comparative genomics.2478-2485

Sequence Analysis

• 
  Donglai Wei,Lauren V. Alpert,Charles E. Lawrence:
  RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences.2486-2493
• 
  Dong Seon Kim,Yoonsoo Hahn:
  Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence.2494-2501
• 
  Ergude Bao,Tao Jiang,Isgouhi Kaloshian,Thomas Girke:
  SEED: efficient clustering of next-generation sequences.2502-2509
• 
  Matej Lexa,Tomás Martínek,Ivana Burgetova,Daniel Kopecek,Marie Brázdová:
  A dynamic programming algorithm for identification of triplex-forming sequences.2510-2517
• 
  Gregory R. Grant,Michael H. Farkas,Angel D. Pizarro,Nicholas F. Lahens,Jonathan Schug,Brian P. Brunk,Christian J. Stoeckert Jr.,John B. Hogenesch,Eric A. Pierce:
  Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).2518-2528

Structural Bioinformatics

• 
  Qian Liu,Steven C. H. Hoi,Chinh T. T. Su,Zhenhua Li,Chee Keong Kwoh,Limsoon Wong,Jinyan Li:
  Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding?2529-2536
• 
  Sheng Wang,Jian Peng,Jinbo Xu:
  Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling.2537-2545

Gene Expression

• 
  Lan Zagar,Francesca Mulas,Silvia Garagna,Maurizio Zuccotti,Riccardo Bellazzi,Blaz Zupan:
  Stage prediction of embryonic stem cell differentiation from genome-wide expression data.2546-2553
• 
  Hui Yuan Xiong,Yoseph Barash,Brendan J. Frey:
  Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.2554-2562
• 
  Inka J. Appel,Wolfram Gronwald,Rainer Spang:
  Estimating classification probabilities in high-dimensional diagnostic studies.2563-2570

Genetics and Population Analysis

• 
  Fan Xia,Ji-Yuan Zhou,Wing Kam Fung:
  A powerful approach for association analysis incorporating imprinting effects.2571-2577
• 
  Can Yang,Xiaowei Zhou,Xiang Wan,Qiang Yang,Hong Xue,Weichuan Yu:
  Identifying disease-associated SNP clusters via contiguous outlier detection.2578-2585

Data and Text Mining

• 
  Hong-Jie Dai,Yen-Ching Chang,Richard Tzong-Han Tsai,Wen-Lian Hsu:
  Integration of gene normalization stages and co-reference resolution using a Markov logic network.2586-2594

Applications Note - Genome Analysis

• 
  Igor Lukashin,Pavel S. Novichkov,Dario Boffelli,Alex R. Paciorkowski,Simon Minovitsky,Song Yang,Inna Dubchak:
  VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies.2595-2597

Sequence Analysis

• 
  Ying Wang,Gaurang Mehta,Rajiv Mayani,Jingxi Lu,Tade Souaiaia,Yangho Chen,Andrew P. Clark,Hee Jae Yoon,Lin Wan,Oleg V. Evgrafov,James A. Knowles,Ewa Deelman,Ting Chen:
  RseqFlow: workflows for RNA-Seq data analysis.2598-2600
• 
  Kristian Cibulskis,Aaron McKenna,Tim Fennell,Eric Banks,Mark A. DePristo,Gad Getz:
  ContEst: estimating cross-contamination of human samples in next-generation sequencing data.2601-2602

Phylogenetics

• 
  Marc J. Lajeunesse:
  phyloMeta: a program for phylogenetic comparative analyses with meta-analysis.2603-2604

Structural Bioinformatics

• 
  David Fournier,Miguel A. Andrade-Navarro:
  PDBpaint, a visualization webservice to tag protein structures with sequence annotations.2605-2606

Systems Biology

• 
  Li Chen,Tsung-Han Chan,Peter L. Choyke,Elizabeth M. C. Hillman,Chong-Yung Chi,Zaver M. Bhujwalla,Ge Wang,Sean S. Wang,Zsolt Szabo,Yue Joseph Wang:
  CAM-CM: a signal deconvolution tool forin vivo dynamic contrast-enhanced imaging of complex tissues.2607-2609
• 
  Oana Chis,Julio R. Banga,Eva Balsa-Canto:
  GenSSI: a software toolbox for structural identifiability analysis of biological models.2610-2611
• 
  Florian Battke,Stephan Symons,Alexander Herbig,Kay Nieselt:
  GaggleBridge: collaborative data analysis.2612-2613

Data and Text Mining

• 
  Xiaozeng Yang,Lei Li:
  miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.2614-2615

Databases and Ontologies

• 
  Jose M. Villaveces,Rafael C. Jiménez,Leyla J. García,Gustavo A. Salazar,Bernat Gel,Nicola J. Mulder,Maria Jesus Martin,Alexander García Castro,Henning Hermjakob:
  Dasty3, a WEB framework for DAS.2616-2617
• 
  Jacek Sroka,Lukasz Krupa,Andrzej M. Kierzek,Jerzy Tyszkiewicz:
  CalcTav - integration of a spreadsheet andTaverna workbench.2618-2619

Volume 27, Number 19, October 2011

Discovery Note - Sequence Analysis

• 
  Ivan V. Kulakovskiy,A. A. Belostotsky,Artem S. Kasianov,Natalia G. Esipova,Yulia A. Medvedeva,I. A. Eliseeva,Vsevolod J. Makeev:
  A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.2621-2624

Original Papers - Sequence Analysis

• 
  Mengyuan Xu,Clarice R. Weinberg,David M. Umbach,Leping Li:
  coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data.2625-2632
• 
  Darshan Singh,Christian F. Orellana,Yin Hu,Corbin D. Jones,Yufeng Liu,Derek Y. Chiang,Jinze Liu,Jan F. Prins:
  FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.2633-2640
• 
  He Quan Sun,Malcolm Yoke Hean Low,Wen-Jing Hsu,Ching-Wai Tan,Jagath C. Rajapakse:
  Tree-structured algorithm for long weak motif discovery.2641-2647
• 
  Jarupon Fah Sathirapongsasuti,Hane Lee,Basil A. J. Horst,Georg Brunner,Alistair J. Cochran,Scott Binder,John Quackenbush,Stanley F. Nelson:
  Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.2648-2654
• 
  Daniel Gaston,Edward Susko,Andrew J. Roger:
  A phylogenetic mixture model for the identification of functionally divergent protein residues.2655-2663

Phylogenetics

• 
  Aïda Ouangraoua,Eric Tannier,Cédric Chauve:
  Reconstructing the architecture of the ancestral amniote genome.2664-2671

Gene Expression

• 
  Yi-Hui Zhou,Kai Xia,Fred A. Wright:
  A powerful and flexible approach to the analysis of RNA sequence count data.2672-2678

Systems Biology

• 
  Yinyin Yuan,Oscar M. Rueda,Christina Curtis,Florian Markowetz:
  Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.2679-2685
• 
  Zheng Li,Ping Li,Arun Krishnan,Jingdong Liu:
  Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis.2686-2691
• 
  TaeHyun Hwang,Wei Zhang,Maoqiang Xie,Jinfeng Liu,Rui Kuang:
  Inferring disease and gene set associations with rank coherence in networks.2692-2699
• 
  Chih-Hung Wu,Hsiao-Ching Lee,Bor-Sen Chen:
  Robust synthetic gene network design via library-based search method.2700-2706
• 
  Orland R. Gonzalez,Ralf Zimmer:
  Contextual analysis of RNAi-based functional screens using interaction networks.2707-2713
• 
  Jarno Mäkelä,Heikki Huttunen,Meenakshisundaram Kandhavelu,Olli Yli-Harja,Andre S. Ribeiro:
  Automatic detection of changes in the dynamics of delayed stochastic gene networks andin vivo production of RNA molecules inEscherichia coli.2714-2720

Data and Text Mining

• 
  Nona Naderi,Thomas Kappler,Christopher J. O. Baker,René Witte:
  OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents.2721-2729
• 
  Xinglong Wang,Iain McKendrick,Ian Barrett,Ian Dix,Tim French,Jun'ichi Tsujii,Sophia Ananiadou:
  Automatic extraction of angiogenesis bioprocess from text.2730-2737
• 
  Domingo S. Rodríguez-Baena,Antonio J. Pérez-Pulido,Jesús S. Aguilar-Ruiz:
  A biclustering algorithm for extracting bit-patterns from binary datasets.2738-2745
• 
  Elizabeth Rossin,Tsung-I Lin,Hsiu J. Ho,Steven J. Mentzer,Saumyadipta Pyne:
  A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues.2746-2753

Applications Note - Genome Analysis

• 
  Ricardo Ramirez-Gonzalez,Mario Cáccamo,Daniel MacLean:
  Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.2754-2755
• 
  Aaron E. Darling,Andrew J. Tritt,Jonathan A. Eisen,Marc T. Facciotti:
  Mauve Assembly Metrics.2756-2757

Phylogenetics

• 
  Cuong Cao Dang,Vincent Lefort,Le Sy Vinh,Si Quang Le,Olivier Gascuel:
  ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.2758-2760

Systems Biology

• 
  Georg Basler,Zoran Nikoloski:
  JMassBalance: mass-balanced randomization and analysis of metabolic networks.2761-2762
• 
  Christoph Gille,Katrin Hübner,Andreas Hoppe,Hermann-Georg Holzhütter:
  Metannogen: annotation of biological reaction networks.2763-2764
• 
  Xuan Vinh Nguyen,Madhu Chetty,Ross L. Coppel,Pramod P. Wangikar:
  GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion.2765-2766
• 
  Duc-Hau Le,Yung-Keun Kwon:
  NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks.2767-2768

Data and Text Mining

• 
  Jörg Hakenberg,Martin Gerner,Maximilian Haeussler,Illés Solt,Conrad Plake,Michael Schroeder,Graciela Gonzalez,Goran Nenadic,Casey M. Bergman:
  The GNAT library for local and remote gene mention normalization.2769-2771

Databases and Ontologies

• 
  Yoona Kim,Steven Bark,Vivian Hook,Nuno Bandeira:
  NeuroPedia: neuropeptide database and spectral library.2772-2773

Volume 27, Number 20, October 2011

Original Papers - Genome Analysis

• 
  Xiaohua Douglas Zhang,Francesca Santini,Raul Lacson,Shane D. Marine,Qian Wu,Luca Benetti,Ruojing Yang,Alex McCampbell,Joel P. Berger,Dawn M. Toolan,Erica M. Stec,Daniel J. Holder,Keith A. Soper,Joseph F. Heyse,Marc Ferrer:
  cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens.2775-2781

Sequence Analysis

• 
  Lucía Spangenberg,Florian Battke,Martí Graña,Kay Nieselt,Hugo Naya:
  Identifying associations between amino acid changes and meta information in alignments.2782-2789
• 
  Matthew Ruffalo,Thomas LaFramboise,Mehmet Koyutürk:
  Comparative analysis of algorithms for next-generation sequencing read alignment.2790-2796
• 
  Tilo Eißler,Christopher P. Hodges,Harald Meier:
  PTPan - overcoming memory limitations in oligonucleotide string matching for primer/probe design.2797-2805
• 
  Eugen Fazius,Vladimir Shelest,Ekaterina Shelest:
  SiTaR: a novel tool for transcription factor binding site prediction.2806-2811
• 
  Catherine Mooney,Yong-Hong Wang,Gianluca Pollastri:
  SCLpred: protein subcellular localization prediction by N-to-1 neural networks.2812-2819

Structural Bioinformatics

• 
  Anisah W. Ghoorah,Marie-Dominique Devignes,Malika Smaïl-Tabbone,David W. Ritchie:
  Spatial clustering of protein binding sites for template based protein docking.2820-2827
• 
  Ying Shen,Hau-San Wong,Shaohong Zhang,Zhiwen Yu:
  Feature-based 3D motif filtering for ribosomal RNA.2828-2835
• 
  Elad Donsky,Haim J. Wolfson:
  PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors.2836-2842
• 
  José Ramón López-Blanco,José Ignacio Garzón,Pablo Chacón:
  iMod: multipurpose normal mode analysis in internal coordinates.2843-2850

Gene Expression

• 
  Zhengyu Ouyang,Mingzhou Song,Robert Güth,Thomas Ha,Matt Larouche,Daniel Goldowitz:
  Conserved and differential gene interactions in dynamical biological systems.2851-2858
• 
  Pushpike Jayantha Thilakarathne,Lieven Clement,Dan Lin,Ziv Shkedy,Adetayo Kasim,Willem Talloen,Matthias Versele,Geert Verbeke:
  The use of semiparametric mixed models to analyze PamChip^® peptide array data: an application to an oncology experiment.2859-2865
• 
  Melissa M. Matzke,Katrina M. Waters,Thomas O. Metz,Jon M. Jacobs,Amy C. Sims,Ralph S. Baric,Joel G. Pounds,Bobbie-Jo M. Webb-Robertson:
  Improved quality control processing of peptide-centric LC-MS proteomics data.2866-2872
• 
  Andrea Ocone,Guido Sanguinetti:
  Reconstructing transcription factor activities in hierarchical transcription network motifs.2873-2879

Genetics and Population Analysis

• 
  Barak Markus,Ohad S. Birk,Dan Geiger:
  Integration of SNP genotyping confidence scores in IBD inference.2880-2887

Systems Biology

• 
  Anthony R. Soltis,Jeffrey J. Saucerman:
  Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty.2888-2894

Data and Text Mining

• 
  Lei Qu,Fuhui Long,Xiao Liu,Stuart K. Kim,Eugene W. Myers,Hanchuan Peng:
  Simultaneous recognition and segmentation of cells: application inC.elegans.2895-2902

Applications Note - Genome Analysis

• 
  Matthew K. Iyer,Arul M. Chinnaiyan,Christopher A. Maher:
  ChimeraScan: a tool for identifying chimeric transcription in sequencing data.2903-2904
• 
  Arnaud Despalins,Souhir Marsit,Jacques Oberto:
  Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters.2905-2906

Sequence Analysis

• 
  Bernd Jagla,Bernd Wiswedel,Jean-Yves Coppée:
  Extending KNIME for next-generation sequencing data analysis.2907-2909

Phylogenetics

• 
  Filip Bielejec,Andrew Rambaut,Marc A. Suchard,Philippe Lemey:
  SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.2910-2912

Structural Bioinformatics

• 
  Shide Liang,Dandan Zheng,Chi Zhang,Daron M. Standley:
  Fast and accurate prediction of protein side-chain conformations.2913-2914
• 
  Anna Vangone,Raffaele Spinelli,Vittorio Scarano,Luigi Cavallo,Romina Oliva:
  COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes.2915-2916

Systems Biology

• 
  Atanas Kamburov,Rachel Cavill,Timothy M. D. Ebbels,Ralf Herwig,Hector C. Keun:
  Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.2917-2918

Data and Text Mining

• 
  Jike Cui,Todd F. DeLuca,Jae-Yoon Jung,Dennis P. Wall:
  Detecting biological network organization and functional gene orthologs.2919-2920
• 
  Rui-Ru Ji,Nathan O. Siemers,Ming Lei,Liang Schweizer,Robert E. Bruccoleri:
  SDRS - an algorithm for analyzing large-scale dose-response data.2921-2923

Databases and Ontologies

• 
  Christina M. Bergey:
  AluHunter: a database of potentially polymorphicAlu insertions for use in primate phylogeny and population genetics.2924-2925

Volume 27, Number 21, November 2011

Reviews- Sequence Analysis

• 
  Brett Trost,Anthony J. Kusalik:
  Computational prediction of eukaryotic phosphorylation sites.2927-2935

Genetics and Population Analysis

• 
  Yue Wang,Guimei Liu,Mengling Feng,Limsoon Wong:
  An empirical comparison of several recent epistatic interaction detection methods.2936-2943

Discovery Note - Systems Biology

• 
  Chaitanya A. Athale,Hemangi Chaudhari:
  Population length variability and nucleoid numbers inEscherichia coli.2944-2948

Original Papers - Genome Analysis

• 
  Sandro Morganella,Stefano Maria Pagnotta,Michele Ceccarelli:
  Finding recurrent copy number alterations preserving within-sample homogeneity.2949-2956
• 
  Tanja Magoc,Steven L. Salzberg:
  FLASH: fast length adjustment of short reads to improve genome assemblies.2957-2963
• 
  Sergey Koren,Todd J. Treangen,Mihai Pop:
  Bambus 2: scaffolding metagenomes.2964-2971

Sequence Analysis

• 
  Shu Yang,Hari Krishna Yalamanchili,Xinran Li,Kwok-Ming Yao,Pak Chung Sham,Michael Q. Zhang,Junwen Wang:
  Correlated evolution of transcription factors and their binding sites.2972-2978
• 
  Sebastian Deorowicz,Szymon Grabowski:
  Robust relative compression of genomes with random access.2979-2986
• 
  Heng Li:
  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.2987-2993

Structural Bioinformatics

• 
  Yuan Li,Shaojie Zhang:
  Finding stable local optimal RNA secondary structures.2994-3001
• 
  Iain H. Moal,Rudi Agius,Paul A. Bates:
  Protein-protein binding affinity prediction on a diverse set of structures.3002-3009

Gene Expression

• 
  Jie Wu,Martin Akerman,Shuying Sun,W. Richard McCombie,Adrian R. Krainer,Michael Q. Zhang:
  SpliceTrap: a method to quantify alternative splicing under single cellular conditions.3010-3016
• 
  Mingguang Shi,Bing Zhang:
  Semi-supervised learning improves gene expression-based prediction of cancer recurrence.3017-3023

Systems Biology

• 
  Yungki Park,Edward M. Marcotte:
  Revisiting the negative example sampling problem for predicting protein-protein interactions.3024-3028
• 
  Genevera I. Allen,Mirjana Maletic-Savatic:
  Sparse non-negative generalized PCA with applications to metabolomics.3029-3035

Data and Text Mining

• 
  Twan van Laarhoven,Sander B. Nabuurs,Elena Marchiori:
  Gaussian interaction profile kernels for predicting drug-target interaction.3036-3043
• 
  Bin Chen,Kevin J. McConnell,Nikil Wale,David J. Wild,Eric M. Gifford:
  Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology.3044-3049
• 
  X. G. Zhao,W. Dai,Y. Li,Lu Tian:
  AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density.3050-3055
• 
  Chao Sima,Ulisses M. Braga-Neto,Edward R. Dougherty:
  High-dimensional bolstered error estimation.3056-3064

Applications Note - Genetics and Population Analysis

• 
  Huat Chye Lim,Marcel E. Curlin,John E. Mittler:
  HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens.3065-3066
• 
  Meg Pirrung,Ryan Kennedy,J. Gregory Caporaso,Jesse Stombaugh,Doug Wendel,Rob Knight:
  TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.3067-3069
• 
  Thibaut Jombart,Ismaïl Ahmed:
  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.3070-3071

Systems Biology

• 
  Ananth Kalyanaraman,William R. Cannon,Benjamin Latt,Douglas J. Baxter:
  MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.3072-3073

Data and Text Mining

• 
  Simon Roux,Michaël Faubladier,Antoine Mahul,Nils Paulhe,Aurélien Bernard,Didier Debroas,François Enault:
  Metavir: a web server dedicated to virome analysis.3074-3075

Databases and Ontologies

• 
  Wenming Zhao,Wanfei Liu,Dongmei Tian,Bixia Tang,Yanqing Wang,Caixia Yu,Rujiao Li,Yunchao Ling,Jiayan Wu,Shuhui Song,Songnian Hu:
  wapRNA: a web-based application for the processing of RNA sequences.3076-3077

Volume 27, Number 22, November 2011

Discovery Note - Genome Analysis

• 
  Kai Wang,Rasmus Wernersson,Søren Brunak:
  The strength of intron donor splice sites in human genes displays a bell-shaped pattern.3079-3084

Original Papers - Genome Analysis

• 
  Michiaki Hamada,Edward Wijaya,Martin C. Frith,Kiyoshi Asai:
  Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.3085-3092
• 
  Naama Elefant,Yael Altuvia,Hanah Margalit:
  A wide repertoire of miRNA binding sites: prediction and functional implications.3093-3101

Sequence Analysis

• 
  Diana L. Kolbe,Sean R. Eddy:
  Fast filtering for RNA homology search.3102-3109

Structural Bioinformatics

• 
  Ivan Kalev,Michael Habeck:
  HHfrag: HMM-based fragment detection using HHpred.3110-3116
• 
  Zhichao Miao,Yang Cao,Taijiao Jiang:
  RASP: rapid modeling of protein side chain conformations.3117-3122
• 
  Castrense Savojardo,Piero Fariselli,Rita Casadio:
  Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.3123-3128

Gene Expression

• 
  Kevin K. Dobbin,Stephanie Cooke:
  Lower confidence bounds for prediction accuracy in high dimensions via AROHIL Monte Carlo.3129-3134
• 
  Christopher Minas,Simon J. Waddell,Giovanni Montana:
  Distance-based differential analysis of gene curves.3135-3141
• 
  Yu-Cheng Liu,Chun-Pei Cheng,Vincent S. Tseng:
  Discovering relational-based association rules with multiple minimum supports on microarray datasets.3142-3148

Systems Biology

• 
  Joana P. Gonçalves,Alexandre P. Francisco,Nuno P. Mira,Miguel C. Teixeira,Isabel Sá-Correia,Arlindo L. Oliveira,Sara C. Madeira:
  TFRank: network-based prioritization of regulatory associations underlying transcriptional responses.3149-3157
• 
  Ruiqi Wang,Kaihui Liu,Luonan Chen,Kazuyuki Aihara:
  Neural fate decisions mediated bytrans-activation andcis-inhibition in Notch signaling.3158-3165
• 
  Anna Goldenberg,Sara Mostafavi,Gerald T. Quon,Paul C. Boutros,Quaid Morris:
  Unsupervised detection of genes of influence in lung cancer using biological networks.3166-3172
• 
  Qiang Huang,Ling-Yun Wu,Xiang-Sun Zhang:
  An efficient network querying method based on conditional random fields.3173-3178

Data and Text Mining

• 
  Yufan Guo,Anna Korhonen,Ilona Silins,Ulla Stenius:
  Weakly supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine?3179-3185
• 
  Solange Delagenière,Patrice Brenchereau,Ludovic Launer,Alun W. Ashton,Ricardo Leal,Stéphanie Veyrier,José Gabadinho,Elspeth J. Gordon,Samuel D. Jones,Karl Erik Levik,Seán M. McSweeney,Stéphanie Monaco,Max Nanao,Darren Spruce,Olof Svensson,Martin A. Walsh,Gordon A. Leonard:
  ISPyB: an information management system for synchrotron macromolecular crystallography.3186-3192

Databases and Ontologies

• 
  Nico Adams,Robert Hoehndorf,Georgios V. Gkoutos,Gesine Hansen,Christian Hennig:
  PIDO: the primary immunodeficiency disease ontology.3193-3199

Applications Note - Genome Analysis

• 
  Pierre Lindenbaum,Solena Le Scouarnec,Vincent Portero,Richard Redon:
  Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.3200-3201

Sequence Analysis

• 
  Lorena Pantano,Xavier Estivill,Eulalia Martí:
  A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.3202-3203

Gene Expression

• 
  Jonatan Taminau,David Steenhoff,Alain Coletta,Stijn Meganck,Cosmin Lazar,Virginie de Schaetzen,Robin Duque,Colin Molter,Hugues Bersini,Ann Nowé,David Y. Weiss Solís:
  inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.3204-3205
• 
  Markus S. Schröder,Aedín C. Culhane,John Quackenbush,Benjamin Haibe-Kains:
  survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.3206-3208
• 
  Eleanor Howe,Raktim Sinha,Daniel Schlauch,John Quackenbush:
  RNA-Seq analysis in MeV.3209-3210

Systems Biology

• 
  Matthew R. Lakin,Simon Youssef,Filippo Polo,Stephen Emmott,Andrew Phillips:
  Visual DSD: a design and analysis tool for DNA strand displacement systems.3211-3213

Data and Text Mining

• 
  Zeqiang Ma,David L. Tabb,Joseph Burden,Matthew Chambers,Matthew B. Cox,Michael J. Cantrell,Amy-Joan L. Ham,Michael D. Litton,Michael R. Oreto,William C. Schultz,Scott M. Sobecki,Tina Y. Tsui,Gregory R. Wernke,Daniel C. Liebler:
  Supporting tool suite for production proteomics.3214-3215

Databases and Ontologies

• 
  Gustavo Glusman,Juan Caballero,Denise E. Mauldin,Leroy E. Hood,Jared C. Roach:
  Kaviar: an accessible system for testing SNV novelty.3216-3217
• 
  Meng-Pin Weng,Ben-Yang Liao:
  DroPhEA:Drosophila phenotype enrichment analysis for insect functional genomics.3218-3219

Volume 27, Number 23, December 2011

Original Papers - Genome Analysis

• 
  Chao Cheng,Renqiang Min,Mark Gerstein:
  TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.3221-3227
• 
  Jin Zhang,Yufeng Wu:
  SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.3228-3234
• 
  Geir Kjetil Sandve,Egil Ferkingstad,Ståle Nygård:
  Sequential Monte Carlo multiple testing.3235-3241

Sequence Analysis

• 
  Zhenqiu Liu,William Hsiao,Brandi L. Cantarel,Elliott Franco Drábek,Claire Fraser-Liggett:
  Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.3242-3249
• 
  Siavash Mirarab,Tandy J. Warnow:
  FASTSP: linear time calculation of alignment accuracy.3250-3258
• 
  Leena Salmela,Veli Mäkinen,Niko Välimäki,Johannes Ylinen,Esko Ukkonen:
  Fast scaffolding with small independent mixed integer programs.3259-3265
• 
  Minmei Hou,Ping Yao,Angela Antonou,Mitrick A. Johns:
  Pico-inplace-inversions between human and chimpanzee.3266-3275

Structural Bioinformatics

• 
  Peter Schmidtke,Axel Bidon-Chanal,F. Javier Luque,Xavier Barril:
  MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.3276-3285
• 
  Gilad Wainreb,Lior Wolf,Haim Ashkenazy,Yves Dehouck,Nir Ben-Tal:
  Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site.3286-3292

Gene Expression

• 
  Shuiwang Ji:
  Computational network analysis of the anatomical and genetic organizations in the mouse brain.3293-3299
• 
  A. Sofia Silva,Shona H. Wood,Sipko van Dam,Sven Berres,Anne McArdle,João Pedro de Magalhães:
  Gathering insights on disease etiology from gene expression profiles of healthy tissues.3300-3305

Data and Text Mining

• 
  Aurélie Névéol,W. John Wilbur,Zhiyong Lu:
  Extraction of data deposition statements from the literature: a method for automatically tracking research results.3306-3312

Applications Note - Genome Analysis

• 
  Michal Wozniak,Limsoon Wong,Jerzy Tiuryn:
  CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains.3313-3314

Structural Bioinformatics

• 
  Alex D. Stivala,Michael Wybrow,Anthony Wirth,James C. Whisstock,Peter J. Stuckey:
  Automatic generation of protein structure cartoons with Pro-origami.3315-3316

Gene Expression

• 
  Jesse M. Engreitz,Rong Chen,Alexander A. Morgan,Joel Dudley,Rohan Mallelwar,Atul J. Butte:
  ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.3317-3318
• 
  Sudhir Kumar,Charlotte Konikoff,Bernard Van Emden,Christopher Busick,Kailah T. Davis,Shuiwang Ji,Lin-Wei Wu,Hector Ramos,Thomas Brody,Sethuraman Panchanathan,Jieping Ye,Timothy L. Karr,Kristyn Gerold,Michael McCutchan,Stuart J. Newfeld:
  FlyExpress: visual mining of spatiotemporal patterns for genes and publications inDrosophila embryogenesis.3319-3320

Systems Biology

• 
  Donglin Huang,Yiling Huang,Youhuang Bai,Dijun Chen,Ralf Hofestädt,Christian Klukas,Ming Chen:
  MyBioNet: interactively visualize, edit and merge biological networks on the Web.3321-3322
• 
  Jonathan Blakes,Jamie Twycross,Francisco José Romero-Campero,Natalio Krasnogor:
  The Infobiotics Workbench: an integratedin silico modelling platform for Systems and Synthetic Biology.3323-3324
• 
  Assaf Gottlieb,Oded Magger,Igor Berman,Eytan Ruppin,Roded Sharan:
  PRINCIPLE: a tool for associating genes with diseases via network propagation.3325-3326

Data and Text Mining

• 
  Nikolas Papanikolaou,Evangelos Pafilis,Stavros Nikolaou,Christos A. Ouzounis,Ioannis Iliopoulos,Vasilis J. Promponas:
  BioTextQuest: a web-based biomedical text mining suite for concept discovery.3327-3328

Databases and Ontologies

• 
  Qingqing Yang,Chengxiang Qiu,Jie Yang,Qing Wu,Qinghua Cui:
  miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes.3329-3330

Volume 27, Number 24, December 2011

Editorial

• 
  Lars Juhl Jensen,Alex Bateman:
  The rise and fall of supervised machine learning techniques.3331-3332

Original Papers - Genome Analysis

• 
  Sonja Althammer,Juan González-Vallinas,Cecilia Ballaré,Miguel Beato,Eduardo Eyras:
  Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.3333-3340
• 
  Tse-Yi Wang,Chien-Hao Su,Huai-Kuang Tsai:
  MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions.3341-3347

Sequence Analysis

• 
  Scott Hazelhurst,Zsuzsanna Lipták:
  KABOOM! A new suffix array based algorithm for clustering expression data.3348-3355
• 
  Xugang Ye,Guoli Wang,Stephen F. Altschul:
  An assessment of substitution scores for protein profile-profile comparison.3356-3363

Structural Bioinformatics

• 
  Mahmoud ElHefnawi,Nafisa Hassan,Mona Kamar,Rania Siam,Anna Lisa Remoli,Iman El-Azab,Osama Alaidi,Giulia Marsili,Marco Sgarbanti:
  The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus.3364-3370
• 
  Qian Cong,Lisa N. Kinch,Jimin Pei,Shuoyong Shi,Vyacheslav N. Grishin,Wenlin Li,Nick V. Grishin:
  An automatic method for CASP9 free modeling structure prediction assessment.3371-3378
• 
  Yunqi Li,Yaping Fang,Jianwen Fang:
  Predicting residue-residue contacts using random forest models.3379-3384
• 
  Carsten Kemena,Jean-François Taly,Jens Kleinjung,Cédric Notredame:
  STRIKE: evaluation of protein MSAs using a single 3D structure.3385-3391
• 
  Robbie P. Joosten,Krista Joosten,Serge X. Cohen,Gert Vriend,Anastassis Perrakis:
  Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.3392-3398

Gene Expression

• 
  Levi Waldron,Melania Pintilie,Ming-Sound Tsao,Frances A. Shepherd,Curtis Huttenhower,Igor Jurisica:
  Optimized application of penalized regression methods to diverse genomic data.3399-3406

Systems Biology

• 
  Mattia Zampieri,Giuseppe Legname,Daniel Segrè,Claudio Altafini:
  A system-level approach for deciphering the transcriptional response to prion infection.3407-3414

Data and Text Mining

• 
  Nicholas E. Newell:
  Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop.3415-3422

Applications Note - Genome Analysis

• 
  Ryan K. Dale,Brent S. Pedersen,Aaron R. Quinlan:
  Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.3423-3424
• 
  Oksana Riba-Grognuz,Laurent Keller,Laurent Falquet,Ioannis Xenarios,Yannick Wurm:
  Visualization and quality assessment ofde novo genome assemblies.3425-3426
• 
  Marcelo Rivas-Astroza,Dan Xie,Xiaoyi Cao,Sheng Zhong:
  Mapping personal functional data to personal genomes.3427-3429

Sequence Analysis

• 
  Douglas M. Fowler,Carlos L. Araya,Wayne Gerard,Stanley Fields:
  Enrich: software for analysis of protein function by enrichment and depletion of variants.3430-3431

Gene Expression

• 
  Yang Zhou,Wubin Qu,Yiming Lu,Yanchun Zhang,Xiaolei Wang,Dongsheng Zhao,Yi Yang,Chenggang Zhang:
  VizPrimer: a web server for visualized PCR primer design based on known gene structure.3432-3434

Genetics and Population Analysis

• 
  Robert Kofler,Ram Vinay Pandey,Christian Schlötterer:
  PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).3435-3436

Systems Biology

• 
  Huaiyu Mi,Anushya Muruganujan,Emek Demir,Yukiko Matsuoka,Akira Funahashi,Hiroaki Kitano,Paul D. Thomas:
  BioPAX support in CellDesigner.3437-3438

Data and Text Mining

• 
  Kamil Fijorek,Damian Fijorek,Barbara Wisniowska,Sebastian Polak:
  BDTcomparator: a program for comparing binary classifiers.3439-3440