Bioinformatics, Volume 31

Volume 31, Number 1, January 2015

Review
Genome Analysis

• 
  Vinita Periwal, Vinod Scaria:
  Insights into structural variations and genome rearrangements in prokaryotic genomes. 1-9

Original Papers
Genome Analysis

• 
  Pablo Cingolani, Rob Sladek, Mathieu Blanchette:
  BigDataScript: a scripting language for data pipelines. 10-16
• 
  Ka-Chun Wong, Yue Li, Chengbin Peng, Zhaolei Zhang:
  SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles. 17-24
• 
  Liping Li, Enguo Chen, Chun Yang, Jun Zhu, Pushkala Jayaraman, Jeff de Pons, Catherine C. Kaczorowski, Howard J. Jacob, Andrew S. Greene, Matthew R. Hodges, Allen W. Cowley Jr., Mingyu Liang, Haiming Xu, Pengyuan Liu, Yan Lu:
  Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. 25-32
• 
  P. R. Shidhi, Prashanth Suravajhala, Aysha Nayeema, Achuthsankar S. Nair, Shailja Singh, Pawan K. Dhar:
  Making novel proteins from pseudogenes. 33-39

Sequence Analysis

• 
  Mufleh Al-Shatnawi, M. Omair Ahmad, M. N. Shanmukha Swamy:
  Prediction of Indel flanking regions in protein sequences using a variable-order Markov model. 40-47
• 
  Mahmoud M. Ibrahim, Scott A. Lacadie, Uwe Ohler:
  JAMM: a peak finder for joint analysis of NGS replicates. 48-55
• 
  Darren T. Houniet, Thahira J. Rahman, Saeed Al Turki, Matthew E. Hurles, Yaobo Xu, Judith A. Goodship, Bernard D. Keavney, Mauro F. Santibanez-Koref:
  Using population data for assessing next-generation sequencing performance. 56-61

Gene Expression

• 
  Hongwei Wang, Qiang Sun, Wenyuan Zhao, Lishuang Qi, Yunyan Gu, Pengfei Li, Mengmeng Zhang, Yang Li, Shu-Lin Liu, Zheng Guo:
  Individual-level analysis of differential expression of genes and pathways for personalized medicine. 62-68
• 
  Antti Häkkinen, Andre S. Ribeiro:
  Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. 69-75
• 
  Sheng Qin, Fei Ma, Liming Chen:
  Gene regulatory networks by transcription factors and microRNAs in breast cancer. 76-83
• 
  Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao:
  Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. 84-93

Genetics and Population Analysis

• 
  Bie M. P. Verbist, Kim Thys, Joke Reumers, Yves Wetzels, Koen Van der Borght, Willem Talloen, Jeroen Aerssens, Lieven Clement, Olivier Thas:
  VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering. 94-101

Data and Text Mining

• 
  Yotsawat Pomyen, Marcelo Segura, Timothy M. D. Ebbels, Hector C. Keun:
  Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets. 102-108

Applications Notes
Genome Analysis

• 
  Julien Lajugie, Nicolas Fourel, Eric E. Bouhassira:
  GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface. 109-111

Sequence Analysis

• 
  Pierre Lindenbaum, Richard Redon:
  mod_bio: Apache modules for Next-Generation sequencing data. 112-113
• 
  Mick Watson, Marian Thomson, Judith E. Risse, Richard Talbot, Javier Santoyo-Lopez, Karim Gharbi, Mark L. Blaxter:
  poRe: an R package for the visualization and analysis of nanopore sequencing data. 114-115
• 
  Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano:
  Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. 116-118
• 
  Wei Chen, Xitong Zhang, Jordan Brooker, Hao Lin, Liqing Zhang, Kuo-Chen Chou:
  PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. 119-120

Structural Bioinformatics

• 
  Anna Katharina Hildebrandt, Daniel Stöckel, Nina M. Fischer, Luis de la Garza, Jens Krüger, Stefan Nickels, Marc Röttig, Charlotta Schärfe, Marcel Schumann, Philipp Thiel, Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt:
  ballaxy: web services for structural bioinformatics. 121-122
• 
  Iain H. Moal, Brian Jiménez-García, Juan Fernández-Recio:
  CCharPPI web server: computational characterization of protein-protein interactions from structure. 123-125
• 
  Gregory B. Quinn, Chunxiao Bi, Cole H. Christie, Kyle Pang, Andreas Prlic, Takanori Nakane, Christine Zardecki, Maria Voigt, Helen M. Berman, Philip E. Bourne, Peter W. Rose:
  RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. 126-127

Gene Expression

• 
  Steffen Sass, Florian Buettner, Nikola S. Müller, Fabian J. Theis:
  RAMONA: a Web application for gene set analysis on multilevel omics data. 128-130

Systems Biology

• 
  Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor, Ivet Bahar:
  BalestraWeb: efficient online evaluation of drug-target interactions. 131-133
• 
  John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin:
  cddApp: a Cytoscape app for accessing the NCBI conserved domain database. 134-136

Data and Text Mining

• 
  Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan, Yue Joseph Wang:
  UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. 137-139

Databases and Ontologies

• 
  Manuel Corpas, Rafael C. Jiménez, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas, Pedro L. Fernandes, Bruno A. Gaëta, Celia W. G. van Gelder, Eija Korpelainen, Fran Lewitter, Annette McGrath, Daniel MacLean, Patricia M. Palagi, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson, Maria Victoria Schneider, Teresa K. Attwood:
  The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers. 140-142
• 
  Andrew D. Yates, Kathryn Beal, Stephen Keenan, William M. McLaren, Miguel Pignatelli, Graham R. S. Ritchie, Magali Ruffier, Kieron R. Taylor, Alessandro Vullo, Paul Flicek:
  The Ensembl REST API: Ensembl Data for Any Language. 143-145

Message from ISCB
Databases and Ontologies

• 
  Ilan Samish, Philip E. Bourne, Rafael J. Najmanovich:
  Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. 146-150

Volume 31, Number 2, January 2015

Original Papers
Genome Analysis

• 
  Tatsiana Vaitsiakhovich, Dmitriy Drichel, Christine Herold, André Lacour, Tim Becker:
  METAINTER: meta-analysis of multiple regression models in genome-wide association studies. 151-157
• 
  Naruekamol Pookhao, Michael B. Sohn, Qike Li, Isaac Jenkins, Ruofei Du, Hongmei Jiang, Lingling An:
  A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes. 158-165
• 
  Simon Anders, Paul Theodor Pyl, Wolfgang Huber:
  HTSeq - a Python framework to work with high-throughput sequencing data. 166-169
• 
  Tae-Hyuk Ahn, Juanjuan Chai, Chongle Pan:
  Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance. 170-177
• 
  Sha He, Hai Zhang, Haihua Liu, Hao Zhu:
  LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. 178-186

Sequence Analysis

• 
  Vassily Trubetskoy, Alex A. Rodriguez, Uptal J. Dave, Nicholas Campbell, Emily L. Crawford, Edwin H. Cook Jr., James S. Sutcliffe, Ian T. Foster, Ravi K. Madduri, Nancy J. Cox, Lea K. Davis:
  Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes. 187-193
• 
  Xiang Chen, Shao-Ping Shi, Sheng-Bao Suo, Hao-Dong Xu, Jian-Ding Qiu:
  Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity. 194-200

Structural Bioinformatics

• 
  Ian Walsh, Manuel Giollo, Tomás Di Domenico, Carlo Ferrari, Olav Zimmermann, Silvio C. E. Tosatto:
  Comprehensive large-scale assessment of intrinsic protein disorder. 201-208

Gene Expression

• 
  Marcus A. Badgeley, Stuart C. Sealfon, Maria D. Chikina:
  Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. 209-215
• 
  Timo Itzel, Peter Scholz, Thorsten Maass, Markus Krupp, Jens U. Marquardt, Susanne Strand, Diana Becker, Frank Staib, Harald Binder, Stephanie Roessler, Xin Wei Wang, Snorri Thorgeirsson, Martina Müller, Peter R. Galle, Andreas Teufel:
  Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis. 216-224
• 
  Hachem Saddiki, Jon McAuliffe, Patrick Flaherty:
  GLAD: a mixed-membership model for heterogeneous tumor subtype classification. 225-232
• 
  Hao Wu, Chi Wang, Zhijin Wu:
  PROPER: comprehensive power evaluation for differential expression using RNA-seq. 233-241

Databases and Ontologies

• 
  Khalifeh AlJadda, Melody P. Porterfield, Robert Bridger, Christian Heiss, Michael Tiemeyer, Lance Wells, John A. Miller, William S. York, René Ranzinger:
  EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data. 242-245
• 
  Matteo Giulietti, Sara Armida Milantoni, Tatiana Armeni, Giovanni Principato, Francesco Piva:
  ExportAid: database of RNA elements regulating nuclear RNA export in mammals. 246-251
• 
  Chunhong Mao, David Abraham, Alice R. Wattam, Meredith J. C. Wilson, Maulik Shukla, Hyun Seung Yoo, Bruno W. S. Sobral:
  Curation, integration and visualization of bacterial virulence factors in PATRIC. 252-258

Applications Notes
Genome Analysis

• 
  Thomas W. Winkler, Zoltán Kutalik, Mathias Gorski, Claudio Lottaz, Florian Kronenberg, Iris M. Heid:
  EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. 259-261
• 
  Lili Wang, Takuya Matsushita, Lohith Madireddy, Parvin Mousavi, Sergio Baranzini:
  PINBPA: Cytoscape app for network analysis of GWAS data. 262-264

Sequence Analysis

• 
  Heejoon Chae, SungMin Rhee, Kenneth P. Nephew, Sun Kim:
  BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. 265-267
• 
  Reece K. Hart, Rudolph Rico, Emily Hare, John Garcia, Jody Westbrook, Vincent A. Fusaro:
  A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature. 268-270
• 
  Ishita K. Khan, Qing Wei, Meghana Chitale, Daisuke Kihara:
  PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool. 271-272

Gene Expression

• 
  Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni:
  switchBox: an R package for k-Top Scoring Pairs classifier development. 273-274

Genetics and Population Analysis

• 
  Yunfei Guo, David V. Conti, Kai Wang:
  Enlight: web-based integration of GWAS results with biological annotations. 275-276

Systems Biology

• 
  Daniel G. Hurley, Joseph Cursons, Yi Kan Wang, David M. Budden, Cristin G. Print, Edmund J. Crampin:
  NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. 277-278
• 
  Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, Alex F. Chen:
  Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. 279-281

Data and Text Mining

• 
  Paul J. McMurdie, Susan P. Holmes:
  Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. 282-283
• 
  Qingli Guo, Xiongfei Qu, Weibo Jin:
  PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades. 284-286
• 
  Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
  KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. 287-289
• 
  Zhao Zhang, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen:
  MTide: an integrated tool for the identification of miRNA-target interaction in plants. 290-291

Databases and Ontologies

• 
  Noa Maatuk, Yitav Glantz-Gashai, Maya Rotman, Meirav Baydany, Gennadiy Fonar, Amir Shechvitz, Karin Shemer, Aviva Peleg, Eli Reuveni, Abraham O. Samson:
  PHI-DAC: protein homology database through dihedral angle conservation. 292-294
• 
  Egle Bunkute, Christopher Cummins, Fraser J. Crofts, Gareth Bunce, Ian T. Nabney, Darren R. Flower:
  PIP-DB: the Protein Isoelectric Point database. 295-296

Message from the ISCB
Databases and Ontologies

• 
  Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia:
  Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. 297-298
• 
  Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp:
  The Bioinformatics Open Source Conference (BOSC) 2013. 299-300

Volume 31, Number 3, February 2015

Discovery Notes
Genome Analysis

• 
  Sankar Subramanian:
  Using the plurality of codon positions to identify deleterious variants in human exomes. 301-305

Systems Biology

• 
  James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary D. Bader, Mohan Babu:
  Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. 306-310

Original Papers
Genome Analysis

• 
  Jonathan D. Magasin, Dietlind L. Gerloff:
  Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism. 311-317
• 
  Jing Wang, Leon Raskin, David C. Samuels, Yu Shyr, Yan Guo:
  Genome measures used for quality control are dependent on gene function and ancestry. 318-323

Sequence Analysis

• 
  Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul:
  Log-odds sequence logos. 324-331
• 
  Andrzej Zielezinski, Wojciech M. Karlowski:
  Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs. 332-339

Genetics and Population Analysis

• 
  René Luijk, Jelle J. Goeman, P. Eline Slagboom, Bastiaan T. Heijmans, Erik W. van Zwet:
  An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs. 340-345

Systems Biology

• 
  Katharina Nöh, Peter Droste, Wolfgang Wiechert:
  Visual workflows for ¹³C-metabolic flux analysis. 346-354
• 
  Maria Anna Rapsomaniki, Eugenio Cinquemani, Nickolaos-Nikiforos Giakoumakis, Panagiotis Kotsantis, John Lygeros, Zoi Lygerou:
  Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments. 355-362
• 
  Jialu Hu, Knut Reinert:
  LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. 363-372
• 
  Ralf Schmidt, Silvio Waschina, Daniela Boettger-Schmidt, Christian Kost, Christoph Kaleta:
  Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. 373-381
• 
  Ralph Patrick, Kim-Anh Lê Cao, Bostjan Kobe, Mikael Bodén:
  PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. 382-389
• 
  Hamidreza Khataee, Alan Wee-Chung Liew:
  A stochastic automaton model for simulating kinesin processivity. 390-396

Data and Text Mining

• 
  Philippe Bastien, Frédéric Bertrand, Nicolas Meyer, Myriam Maumy-Bertrand:
  Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data. 397-404

Databases and Ontologies

• 
  Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao, Wei Nie, Yuchen Liu, Renxiao Wang:
  PDB-wide collection of binding data: current status of the PDBbind database. 405-412

Applications Notes
Genome Analysis

• 
  Ulrich Wittelsbürger, Bastian Pfeifer, Martin J. Lercher:
  WhopGenome: high-speed access to whole-genome variation and sequence data in R. 413-415
• 
  Ryan M. Ames, Simon C. Lovell:
  DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML. 416-417
• 
  Tune H. Pers, Pascal N. Timshel, Joel Hirschhorn:
  SNPsnap: a Web-based tool for identification and annotation of matched SNPs. 418-420
• 
  Dina Zhabinskaya, Sally Madden, Craig J. Benham:
  SIST: stress-induced structural transitions in superhelical DNA. 421-422

Sequence Analysis

• 
  Stefan Janssen, Robert Giegerich:
  The RNA shapes studio. 423-425
• 
  Zexuan Zhu, Linsen Li, Yongpeng Zhang, Yanli Yang, Xiao Yang:
  CompMap: a reference-based compression program to speed up read mapping to related reference sequences. 426-428
• 
  Javad Nadaf, Jacek Majewski, Somayyeh Fahiminiya:
  ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data. 429-431

Phylogenetics

• 
  Ruchi Chaudhary, David Fernández-Baca, John Gordon Burleigh:
  MulRF: a software package for phylogenetic analysis using multi-copy gene trees. 432-433

Structural Bioinformatics

• 
  Pier Paolo Olimpieri, Paolo Marcatili, Anna Tramontano:
  Tabhu: tools for antibody humanization. 434-435

Gene Expression

• 
  Marc W. Schmid, Ueli Grossniklaus:
  Rcount: simple and flexible RNA-Seq read counting. 436-437

Genetics and Population Analysis

• 
  Giovanni Marco Dall'Olio, Ali R. Vahdati, Jaume Bertranpetit, Andreas Wagner, Hafid Laayouni:
  VCF2Networks: applying genotype networks to single-nucleotide variants data. 438-439

Systems Biology

• 
  Heiko Giese, Jörg Ackermann, Heinrich Heide, Lea Bleier, Stefan Dröse, Ilka Wittig, Ulrich Brandt, Ina Koch:
  NOVA: a software to analyze complexome profiling data. 440-441
• 
  Avigail Taylor, Julia Steinberg, Tallulah S. Andrews, Caleb Webber:
  GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks. 442-444

Databases and Ontologies

• 
  Steffen Priebe, Christian Kreisel, Fabian Horn, Reinhard Guthke, Jörg Linde:
  FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. 445-446
• 
  Benjamin Linard, Alexis Allot, Raphael Schneider, Can Morel, Raymond Ripp, Marc Bigler, Julie Dawn Thompson, Olivier Poch, Odile Lecompte:
  OrthoInspector 2.0: Software and database updates. 447-448

Message from the ISCB
Databases and Ontologies

• 
  Yana Bromberg, Emidio Capriotti:
  Editor's Choice: SNP-SIG 2013: the state of the art of genomic variant interpretation. 449-450

Volume 31, Number 4, February 2015

Improver Challenge Special Issue; species Translation Challenge
Editorial

• 
  Julia Hoeng, Manuel C. Peitsch, Pablo Meyer, Igor Jurisica:
  Where are we at regarding species translation? A review of the sbv IMPROVER challenge. 451-452

Systems Biology

• 
  Michael Biehl, Peter J. Sadowski, Gyan Bhanot, Erhan Bilal, Adel Dayarian, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Michael D. Zeller, Sahand Hormoz:
  Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. 453-461
• 
  Adel Dayarian, Roberto Romero, Zhiming Wang, Michael Biehl, Erhan Bilal, Sahand Hormoz, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Gyan Bhanot, Feng Luo, Adi L. Tarca:
  Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. 462-470
• 
  Kahn Rhrissorrakrai, Vincenzo Belcastro, Erhan Bilal, Raquel Norel, Carine Poussin, Carole Mathis, Rémi H. J. Dulize, Nikolai V. Ivanov, Leonidas G. Alexopoulos, John Jeremy Rice, Manuel C. Peitsch, Gustavo Stolovitzky, Pablo Meyer, Julia Hoeng:
  Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. 471-483
• 
  Erhan Bilal, Theodore Sakellaropoulos, Challenge Participants, Ioannis N. Melas, Dimitris E. Messinis, Vincenzo Belcastro, Kahn Rhrissorrakrai, Pablo Meyer, Raquel Norel, Anita Iskandar, Elise Blaese, John Jeremy Rice, Manuel C. Peitsch, Julia Hoeng, Gustavo Stolovitzky, Leonidas G. Alexopoulos, Carine Poussin:
  A crowd-sourcing approach for the construction of species-specific cell signaling networks. 484-491

Gene Expression

• 
  Sahand Hormoz, Gyan Bhanot, Michael Biehl, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Adel Dayarian:
  Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. 492-500
• 
  Christoph Hafemeister, Roberto Romero, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Richard Bonneau, Adi L. Tarca:
  Inter-species pathway perturbation prediction via data-driven detection of functional homology. 501-508

Original Papers
Genome Analysis

• 
  Nilesh Khiste, Lucian Ilie:
  E-MEM: efficient computation of maximal exact matches for very large genomes. 509-514

Sequence Analysis

• 
  Chang-Chang Cao, Xiao Sun:
  Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing. 515-522
• 
  Yi-Fei Huang, Geoffrey Brian Golding:
  FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures. 523-531
• 
  Fei Deng, Lusheng Wang, Xiaowen Liu:
  An efficient algorithm for the blocked pattern matching problem. 532-538

Structural Bioinformatics

• 
  Ambrish Roy, Jeffrey Skolnick:
  LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. 539-544

Gene Expression

• 
  Neo Christopher Chung, John D. Storey:
  Statistical significance of variables driving systematic variation in high-dimensional data. 545-554
• 
  Johan Teleman, Hannes L. Röst, George Rosenberger, Uwe Schmitt, Lars Malmström, Johan Malmström, Fredrik Levander:
  DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. 555-562

Systems Biology

• 
  Shining Ma, Tao Jiang, Rui Jiang:
  Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data. 563-571
• 
  Hong-Qiang Wang, Chun-Hou Zheng, Xing-Ming Zhao:
  jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data. 572-580

Databases and Ontologies

• 
  Vassiliki A. Gkantouna, Manousos E. Kambouris, Emmanouil Viennas, Zafeiria-Marina Ioannou, Michael Paraskevas, George Lagoumintzis, Zoi Zagoriti, George P. Patrinos, Giannis E. Tzimas, Konstantinos Poulas:
  Introducing dAUTObase: a first step towards the global scale geoepidemiology of autoimmune syndromes and diseases. 581-586

Applications Notes
Genome Analysis

• 
  David Coil, Guillaume Jospin, Aaron E. Darling:
  A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. 587-589
• 
  Pavel Petrenko, Andrew C. Doxey:
  mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. 590-592

Sequence Analysis

• 
  Bo W. Han, Wei Wang, Phillip D. Zamore, Zhiping Weng:
  piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. 593-595
• 
  Insu Jang, Hyeshik Chang, Yukyung Jun, Seong-Jin Park, Jin Ok Yang, Byungwook Lee, Wan Kyu Kim, V. Narry Kim, Sanghyuk Lee:
  miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data. 596-598
• 
  Cali E. Willet, Bianca Haase, Michael A. Charleston, Claire M. Wade:
  Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker. 599-601

Genetics and Population Analysis

• 
  Daniel Beck, Christopher Dennis, James A. Foster:
  Seed: a user-friendly tool for exploring and visualizing microbial community data. 602-603

Systems Biology

• 
  Rob Johnson, Paul D. W. Kirk, Michael P. H. Stumpf:
  SYSBIONS: nested sampling for systems biology. 604-605
• 
  Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman:
  flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. 606-607
• 
  Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He:
  DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. 608-609
• 
  James J. Kelley, Anatoliy Lane, Xiaowei Li, Brahmaji Mutthoju, Shay Maor, Dennis Egen, Desmond S. Lun:
  MOST: a software environment for constraint-based metabolic modeling and strain design. 610-611
• 
  Teresa Juan-Blanco, Miquel Duran-Frigola, Patrick Aloy:
  IntSide: a web server for the chemical and biological examination of drug side effects. 612-613

Letter to the Editor
Structural Bioinformatics

• 
  Iain H. Moal, Juan Fernández-Recio:
  Comment on 'protein-protein binding affinity prediction from amino acid sequence'. 614-615

Message from the ISCB
Structural Bioinformatics

• 
  Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost:
  Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. 616-617

Corrigendum
Structural Bioinformatics

• 
  Yi Li, Xiaohui Xie:
  Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. 618

Erratum
Structural Bioinformatics

• 
  Gerard Wong, Jeffrey Chan, Bronwyn A. Kingwell, Christopher Leckie, Peter J. Meikle:
  LICRE: unsupervised feature correlation reduction for lipidomics. 619

Volume 31, Number 5, March 2015

Discovery note
Databases and Ontologies

• 
  Ryan M. Taylor, Ryan H. Miller, Ryan D. Miller, Michael Porter, James Dalgleish, John T. Prince:
  Automated structural classification of lipids by machine learning. 621-625

Original Papers
Genome Analysis

• 
  Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
  iDoComp: a compression scheme for assembled genomes. 626-633
• 
  Peng-Jie Jing, Hong-Bin Shen:
  MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies. 634-641
• 
  Reda Younsi, Dan MacLean:
  Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs. 642-646
• 
  Nicolas Terrapon, Vincent Lombard, Harry J. Gilbert, Bernard Henrissat:
  Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. 647-655
• 
  Mingon Kang, Chunling Zhang, Hyung-Wook Chun, Chris H. Q. Ding, Chunyu Liu, Jean Gao:
  eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways. 656-664

Sequence Analysis

• 
  Youri Hoogstrate, Guido Jenster, Elena S. Martens-Uzunova:
  FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. 665-673
• 
  Armin Meier, Johannes Söding:
  Context similarity scoring improves protein sequence alignments in the midnight zone. 674-681
• 
  Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov:
  Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. 682-690

Phylogenetics

• 
  Yufeng Wu:
  A coalescent-based method for population tree inference with haplotypes. 691-698

Structural Bioinformatics

• 
  Gelio Alves, Yi-Kuo Yu:
  Mass spectrometry-based protein identification with accurate statistical significance assignment. 699-706
• 
  Xiaolei Zhu, Yi Xiong, Daisuke Kihara:
  Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. 707-713

Gene Expression

• 
  Igor A. Gula, Alexander M. Samsonov:
  A model for the expression of gap genes based on the Jeffreys-type equation. 714-719

Genetics and Population Analysis

• 
  Eunjung Han, Janet S. Sinsheimer, John Novembre:
  Fast and accurate site frequency spectrum estimation from low coverage sequence data. 720-727

Systems Biology

• 
  Markus Heinonen, Olivier Guipaud, Fabien Milliat, Valérie Buard, Béatrice Micheau, Georges Tarlet, Marc Benderitter, Farida Zehraoui, Florence d'Alché-Buc:
  Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction. 728-735

Data and Text Mining

• 
  Soledad Delgado, Federico Morán, Antonio Mora García, Juan Julián Merelo Guervós, Carlos Briones:
  A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps. 736-744
• 
  Wim Verleyen, Sara Ballouz, Jesse A. Gillis:
  Measuring the wisdom of the crowds in network-based gene function inference. 745-752

Bioimage Informatics

• 
  Parham Aram, Lingli Shen, John A. Pugh, Seetharaman Vaidyanathan, Visakan Kadirkamanathan:
  An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares. 753-760

Applications Notes
Genome Analysis

• 
  Daniel Quang, Yifei Chen, Xiaohui Xie:
  DANN: a deep learning approach for annotating the pathogenicity of genetic variants. 761-763
• 
  Maximilian Haeussler, Brian J. Raney, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Donna Karolchik, Jonathan Casper, Matthew L. Speir, David Haussler, W. James Kent:
  Navigating protected genomics data with UCSC Genome Browser in a Box. 764-766

Sequence Analysis

• 
  Dominic Simm, Klas Hatje, Martin Kollmar:
  Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains). 767-769
• 
  Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, Janet Kelso:
  deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. 770-772

Structural Bioinformatics

• 
  Carlos Fenollosa, Marcel Otón, Pau Andrio, Jorge Cortés, Modesto Orozco, Josep Ramón Goñi:
  SEABED: Small molEcule activity scanner weB servicE baseD. 773-775
• 
  Felix A. Krüger, Anna Gaulton, Michal Nowotka, John P. Overington:
  PPDMs - a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains. 776-778
• 
  Michele Seeber, Angelo Felline, Francesco Raimondi, Simona Mariani, Francesca Fanelli:
  WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules. 779-781

Genetics and Population Analysis

• 
  Christian Fuchsberger, Gonçalo R. Abecasis, David A. Hinds:
  minimac2: faster genotype imputation. 782-784

Systems Biology

• 
  Alberto Castellini, Daniele Paltrinieri, Vincenzo Manca:
  MP-GeneticSynth: inferring biological network regulations from time series. 785-787
• 
  William M. B. Edmands, Dinesh K. Barupal, Augustin Scalbert:
  MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets. 788-790

Data and Text Mining

• 
  Robert Smith, John T. Prince:
  JAMSS: proteomics mass spectrometry simulation in Java. 791-793

Databases and Ontologies

• 
  Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz:
  Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization. 794-796

Bioimage Informatics

• 
  Thomas Pengo, Seamus J. Holden, Suliana Manley:
  PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy. 797-798

Corrigendum
Bioimage Informatics

• 
  Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno:
  Identification of deleterious synonymous variants in human genomes. 799

Volume 31, Number 6, March 2015

Original Papers
Genome Analysis

• 
  Alexandre Gillet-Markowska, Hugues Richard, Gilles Fischer, Ingrid Lafontaine:
  Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries. 801-808
• 
  Tom R. Mayo, Gabriele Beate Schweikert, Guido Sanguinetti:
  M³D: a kernel-based test for spatially correlated changes in methylation profiles. 809-816

Sequence Analysis

• 
  Johannes Dröge, I. Gregor, Alice Carolyn McHardy:
  Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. 817-824
• 
  Junwei Luo, Jianxin Wang, Zhen Zhang, Fang-Xiang Wu, Min Li, Yi Pan:
  EPGA: de novo assembly using the distributions of reads and insert size. 825-833
• 
  Tameera Rahman, Mana Mahapatra, Emma Laing, Yaochu Jin:
  Evolutionary non-linear modelling for selecting vaccines against antigenically variable viruses. 834-840

Phylogenetics

• 
  Céline Scornavacca, Edwin Jacox, Gergely J. Szöllosi:
  Joint amalgamation of most parsimonious reconciled gene trees. 841-848

Structural Bioinformatics

• 
  Abdullah M. Khamis, Magbubah Essack, Xin Gao, Vladimir B. Bajic:
  Distinct profiling of antimicrobial peptide families. 849-856
• 
  David T. Jones, Domenico Cozzetto:
  DISOPRED3: precise disordered region predictions with annotated protein-binding activity. 857-863
• 
  Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, Gisele L. Pappa:
  GASS: identifying enzyme active sites with genetic algorithms. 864-870
• 
  Gerald Weber:
  Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures. 871-877

Gene Expression

• 
  Jing Zhang, C.-C. Jay Kuo, Liang Chen:
  WemIQ: an accurate and robust isoform quantification method for RNA-seq data. 878-885

Genetics and Population Analysis

• 
  Duleepa Jayasundara, Isaam Saeed, Suhinthan Maheswararajah, Bill C. Chang, Sen-Lin Tang, Saman K. Halgamuge:
  ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing. 886-896

Systems Biology

• 
  Jon Pey, Juan A. Villar, Luis Tobalina, Alberto Rezola, José Manuel García Carrasco, John E. Beasley, Francisco J. Planes:
  TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm. 897-904
• 
  Michihiro Araki, Robert Sidney Cox III, Hiroki Makiguchi, Teppei Ogawa, Takeshi Taniguchi, Kohei Miyaoku, Masahiko Nakatsui, Kiyotaka Y. Hara, Akihiko Kondo:
  M-path: a compass for navigating potential metabolic pathways. 905-911

Data and Text Mining

• 
  Zhenlin Ju, Wenbin Liu, Paul L. Roebuck, Doris R. Siwak, Nianxiang Zhang, Yiling Lu, Michael A. Davies, Rehan Akbani, John N. Weinstein, Gordon B. Mills, Kevin R. Coombes:
  Development of a robust classifier for quality control of reverse-phase protein arrays. 912-918

Databases and Ontologies

• 
  René Ranzinger, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, Shin Kawano, Thomas Lütteke, Shujiro Okuda, Daisuke Shinmachi, Toshihide Shikanai, Hiromichi Sawaki, Philip V. Toukach, Masaaki Matsubara, Issaku Yamada, Hisashi Narimatsu:
  GlycoRDF: an ontology to standardize glycomics data in RDF. 919-925
• 
  Baris E. Suzek, Yuqi Wang, Hongzhan Huang, Peter B. McGarvey, Cathy H. Wu:
  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. 926-932
• 
  Dae-Kyum Kim, Jaewook Lee, Sae Rom Kim, Dong-Sic Choi, Yae Jin Yoon, Ji Hyun Kim, Gyeongyun Go, Dinh Nhung, Kahye Hong, Su Chul Jang, Si-Hyun Kim, Kyong-Su Park, Oh Youn Kim, Hyun Taek Park, Ji Hye Seo, Elena Aikawa, Monika Baj-Krzyworzeka, Bas W. M. van Balkom, Mattias Belting, Lionel Blanc, Vincent Bond, Antonella Bongiovanni, Francesc E. Borràs, Luc Buée, Edit I. Buzás, Lesley Cheng, Aled Clayton, Emanuele Cocucci, Charles S. Dela Cruz, Dominic M. Desiderio, Dolores Di Vizio, Karin Ekström, Juan M. Falcon-Perez, Chris Gardiner, Bernd Giebel, David W. Greening, Julia Christina Gross, Dwijendra Gupta, An Hendrix, Andrew F. Hill, Michelle M. Hill, Esther Nolte-'t Hoen, Do Won Hwang, Jameel Inal, Medicharla V. Jagannadham, Muthuvel Jayachandran, Young-Koo Jee, Malene Jørgensen, Kwang Pyo Kim, Yoon-Keun Kim, Thomas Kislinger, Cecilia Lässer, Dong Soo Lee, Hakmo Lee, Johannes van Leeuwen, Thomas Lener, Ming-Lin Liu, Jan Lötvall, Antonio Marcilla, Suresh Mathivanan, Andreas Möller, Jess Morhayim, François Mullier, Irina Nazarenko, Rienk Nieuwland, Diana N. Nunes, Ken C. Pang, Jaesung Park, Tushar Patel, Gabriella Pocsfalvi, Hernando del Portillo, Ulrich Putz, Marcel I. Ramirez, Marcio L. Rodrigues, Tae-Young Roh, Felix Royo, Susmita Sahoo, Raymond Schiffelers, Shivani Sharma, Pia Siljander, Richard J. Simpson, Carolina Soekmadji, Philip Stahl, Allan Stensballe, Ewa L. Stepien, Hidetoshi Tahara, Arne Trummer, Hadi Valadi, Laura J. Vella, Sun Nyunt Wai, Kenneth W. Witwer, María Yáñez-Mó, Hyewon Youn, Reinhard Zeidler, Yong Song Gho:
  EVpedia: a community web portal for extracellular vesicles research. 933-939

Bioimage Informatics

• 
  Louis-François Handfield, Bob Strome, Yolanda T. Chong, Alan M. Moses:
  Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images. 940-947
• 
  Martin Schiegg, Philipp Hanslovsky, Carsten Haubold, Ullrich Köthe, Lars Hufnagel, Fred A. Hamprecht:
  Graphical model for joint segmentation and tracking of multiple dividing cells. 948-956

Applications Notes
Genome Analysis

• 
  Peter Yin, Benjamin Voight:
  MeRP: a high-throughput pipeline for Mendelian randomization analysis. 957-959
• 
  Wenyuan Li, Ke Gong, Qingjiao Li, Frank Alber, Xianghong Jasmine Zhou:
  Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. 960-962

Structural Bioinformatics

• 
  Leonid B. Pereyaslavets, Anna V. Glyakina, Nikita V. Dovidchenko, Igor V. Sokolovskiy, Oxana V. Galzitskaya:
  What handedness and angles between helices has the studied three-helical protein domain? 963-965
• 
  Minh N. Nguyen, Chandra S. Verma:
  Rclick: a web server for comparison of RNA 3D structures. 966-968

Genetics and Population Analysis

• 
  Mohammad Ali Moni, Haoming Xu, Pietro Liò:
  CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks. 969-971

Systems Biology

• 
  Alexander Bläßle, Patrick Müller:
  PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments. 972-974
• 
  James Bradbury, Grégory Genta-Jouve, James William Allwood, Warwick B. Dunn, Royston Goodacre, Joshua D. Knowles, Shan He, Mark R. Viant:
  MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis. 975-977

Letter to the Editor
Structural Bioinformatics

• 
  K. Yugandhar, M. Michael Gromiha:
  Response to the comment on 'protein-protein binding affinity prediction from amino acid sequence'. 978

Errata
Structural Bioinformatics

• 
  Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos:
  BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. 979
• 
  Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa:
  Detecting differential peaks in ChIP-seq signals with ODIN. 980

Volume 31, Number 7, April 2015

Discovery Notes
Genome Analysis

• 
  Takahiro Tsukui, Nozomi Nagano, Myco Umemura, Toshitaka Kumagai, Goro Terai, Masayuki Machida, Kiyoshi Asai:
  Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens. 981-985

Gene Expression

• 
  Peter Keane, Rhodri Ceredig, Cathal Seoighe:
  Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells. 986-990

Original Papers
Phylogenetics

• 
  Graham Jones, Zeynep Aydin, Bengt Oxelman:
  DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. 991-998

Structural Bioinformatics

• 
  David T. Jones, Tanya Singh, Tomasz Kosciólek, Stuart J. Tetchner:
  MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. 999-1006

Genetics and Population Analysis

• 
  Sophie Van der Sluis, Conor V. Dolan, Jiang Li, You-Qiang Song, Pak Chung Sham, Danielle Posthuma, Miao-Xin Li:
  MGAS: a powerful tool for multivariate gene-based genome-wide association analysis. 1007-1015

Systems Biology

• 
  Dante A. Pertusi, Andrew E. Stine, Linda J. Broadbelt, Keith E. J. Tyo:
  Efficient searching and annotation of metabolic networks using chemical similarity. 1016-1024
• 
  Rachita Ramachandra Halehalli, Hampapathalu Adimurthy Nagarajaram:
  Molecular principles of human virus protein-protein interactions. 1025-1033
• 
  Minji Kim, Farzad Farnoud, Olgica Milenkovic:
  HyDRA: gene prioritization via hybrid distance-score rank aggregation. 1034-1043
• 
  Koji Kyoda, Yukako Tohsato, Kenneth H. L. Ho, Shuichi Onami:
  Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. 1044-1052
• 
  Jennifer E. Dent, Valentina Devescovi, Han Li, Pietro Di Lena, Youtao Lu, Yuanhua Liu, Christine Nardini:
  Mechanotransduction map: simulation model, molecular pathway, gene set. 1053-1059
• 
  Haifen Chen, Jing Guo, Shital K. Mishra, Paul Robson, Mahesan Niranjan, Jie Zheng:
  Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development. 1060-1066
• 
  Zhenqiu Liu, Fengzhu Sun, Jonathan Braun, Dermot P. B. McGovern, Steven T. Piantadosi:
  Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. 1067-1074
• 
  Oyebode J. Oyeyemi, Oluwafemi Davies, David L. Robertson, Jean-Marc Schwartz:
  A logical model of HIV-1 interactions with the T-cell activation signalling pathway. 1075-1083

Data and Text Mining

• 
  Douwe Kiela, Yufan Guo, Ulla Stenius, Anna Korhonen:
  Unsupervised discovery of information structure in biomedical documents. 1084-1092
• 
  Christopher Y. Park, Arjun Krishnan, Qian Zhu, Aaron K. Wong, Young-Suk Lee, Olga G. Troyanskaya:
  Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. 1093-1101

Databases and Ontologies

• 
  Meng-Hsiun Tsai, Mu-Yen Chen, Steve G. Huang, Yao-Ching Hung, Hsin-Chieh Wang:
  A bio-inspired computing model for ovarian carcinoma classification and oncogene detection. 1102-1110

Bioimage Informatics

• 
  Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen:
  Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. 1111-1119

Applications Notes
Genome Analysis

• 
  Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei:
  CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. 1120-1123
• 
  Sara J. C. Gosline, Coyin Oh, Ernest Fraenkel:
  SAMNetWeb: identifying condition-specific networks linking signaling and transcription. 1124-1126
• 
  Altuna Akalin, Vedran Franke, Kristian Vlahovicek, Christopher E. Mason, Dirk Schübeler:
  genomation: a toolkit to summarize, annotate and visualize genomic intervals. 1127-1129

Sequence Analysis

• 
  Dimos Gaidatzis, Anita Lerch, Florian Hahne, Michael B. Stadler:
  QuasR: quantification and annotation of short reads in R. 1130-1132

Phylogenetics

• 
  Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu:
  SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. 1133-1135

Structural Bioinformatics

• 
  Matthew K. Matlock, Tyler B. Hughes, Sanjay Joshua Swamidass:
  XenoSite server: a web-available site of metabolism prediction tool. 1136-1137
• 
  Layla Hirsh, Damiano Piovesan, Manuel Giollo, Carlo Ferrari, Silvio C. E. Tosatto:
  The Victor C++ library for protein representation and advanced manipulation. 1138-1140

Systems Biology

• 
  Damian Fermin, Dmitry Avtonomov, Hyungwon Choi, Alexey I. Nesvizhskii:
  LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data. 1141-1143

Bioimage Informatics

• 
  Axel Poulet, Ignacio Arganda-Carreras, David Legland, Aline V. Probst, Philippe Andrey, Christophe Tatout:
  NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. 1144-1146

Data and Text Mining

• 
  Jonathan C. Fuller, Michael Martinez, Stefan Henrich, Antonia Stank, Stefan Richter, Rebecca C. Wade:
  LigDig: a web server for querying ligand-protein interactions. 1147-1149
• 
  Zeeshan Ahmed, Michel Mayr, Saman Zeeshan, Thomas Dandekar, Martin J. Mueller, Agnes Fekete:
  Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. 1150-1153

Letter to the Editor
Systems Biology

• 
  Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya:
  Cooperative development of logical modelling standards and tools with CoLoMoTo. 1154-1159

Corrigendum
Systems Biology

• 
  A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu:
  MIRA: mutual information-based reporter algorithm for metabolic networks. 1160

Volume 31, Number 8, April 2015

Original Papers
Genome Analysis

• 
  Hadas Zur, Tamir Tuller:
  Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge. 1161-1168
• 
  Bernhard Haubold, Fabian Klötzl, Peter Pfaffelhuber:
  andi: Fast and accurate estimation of evolutionary distances between closely related genomes. 1169-1175
• 
  Donghyung Lee, Vernell S. Williamson, T. Bernard Bigdeli, Brien P. Riley, Ayman H. Fanous, Vladimir I. Vladimirov, Silviu-Alin Bacanu:
  JEPEG: a summary statistics based tool for gene-level joint testing of functional variants. 1176-1182

Sequence Analysis

• 
  Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama:
  Faster sequence homology searches by clustering subsequences. 1183-1190
• 
  Prakriti Mudvari, Mercedeh Movassagh, Kamran Kowsari, Ali Seyfi, Maria Kokkinaki, Nathan J. Edwards, Nady Golestaneh, Anelia Horvath:
  SNPlice: variants that modulate Intron retention from RNA-sequencing data. 1191-1198
• 
  Jan Budczies, Michael Bockmayr, Denise Treue, Frederick Klauschen, Carsten Denkert:
  Semiconductor sequencing: how many flows do you need? 1199-1203
• 
  Thorsteinn S. Rögnvaldsson, Liwen You, Daniel Garwicz:
  State of the art prediction of HIV-1 protease cleavage sites. 1204-1210

Phylogenetics

• 
  Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis:
  Improved gene tree error correction in the presence of horizontal gene transfer. 1211-1218

Structural Bioinformatics

• 
  Daniele Raimondi, Gabriele Orlando, Wim F. Vranken:
  Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. 1219-1225

Gene Expression

• 
  Xing-Ming Zhao, Keqin Liu, Guanghui Zhu, Feng He, Béatrice Duval, Jean-Michel Richer, De-Shuang Huang, Changjun Jiang, Jin-Kao Hao, Luonan Chen:
  Identifying cancer-related microRNAs based on gene expression data. 1226-1234

Genetics and Population Analysis

• 
  Chris T. Harvey, Gregory A. Moyerbrailean, Gordon O. Davis, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi:
  QuASAR: quantitative allele-specific analysis of reads. 1235-1242

Systems Biology

• 
  Lam C. Tsoi, James T. Elder, Gonçalo R. Abecasis:
  Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model. 1243-1249
• 
  Aaron Wise, Ziv Bar-Joseph:
  SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. 1250-1257

Data and Text Mining

• 
  Philippe Thomas, Pawel Durek, Illés Solt, Bertram Klinger, Franziska Witzel, Pascal Schulthess, Yvonne Mayer, Domonkos Tikk, Nils Blüthgen, Ulf Leser:
  Computer-assisted curation of a human regulatory core network from the biological literature. 1258-1266
• 
  Rita Silvério-Machado, Bráulio Roberto Gonçalves Marinho Couto, Marcos Augusto dos Santos:
  Retrieval of Enterobacteriaceae drug targets using singular value decomposition. 1267-1273

Databases and Ontologies

• 
  John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young:
  The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. 1274-1278

Bioimage Informatics

• 
  Javier Mazzaferri, Joannie Roy, Stephane Lefrancois, Santiago Costantino:
  Adaptive settings for the nearest-neighbor particle tracking algorithm. 1279-1285

Applications Notes
Genome Analysis

• 
  Michael R. Lindberg, Ira M. Hall, Aaron R. Quinlan:
  Population-based structural variation discovery with Hydra-Multi. 1286-1289
• 
  Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang:
  HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. 1290-1292
• 
  Tetsuya Sato, Mikita Suyama:
  GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences. 1293-1295
• 
  Bo Hu, Jinpu Jin, Anyuan Guo, He Zhang, Jingchu Luo, Ge Gao:
  GSDS 2.0: an upgraded gene feature visualization server. 1296-1297
• 
  Gunnar Völkel, Ludwig Lausser, Florian Schmid, Johann M. Kraus, Hans A. Kestler:
  Sputnik: ad hoc distributed computation. 1298-1301

Sequence Analysis

• 
  Stefanie Mühlhausen, Marcel Hellkamp, Martin Kollmar:
  GenePainter v. 2.0 resolves the taxonomic distribution of intron positions. 1302-1304
• 
  Jeff A. Wintersinger, James D. Wasmuth:
  Kablammo: an interactive, web-based BLAST results visualizer. 1305-1306
• 
  Bin Liu, Fule Liu, Longyun Fang, Xiaolong Wang, Kuo-Chen Chou:
  repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects. 1307-1309
• 
  Daniel Navarro-Gomez, Jeremy Leipzig, Lishuang Shen, Marie T. Lott, Alphons P. M. Stassen, Douglas C. Wallace, Janey L. Wiggs, Marni J. Falk, Mannis van Oven, Xiaowu Gai:
  Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier. 1310-1312

Structural Bioinformatics

• 
  Inbal Sela-Culang, Shaul Ashkenazi, Bjoern Peters, Yanay Ofran:
  PEASE: predicting B-cell epitopes utilizing antibody sequence. 1313-1315
• 
  Spencer E. Bliven, Philip E. Bourne, Andreas Prlic:
  Detection of circular permutations within protein structures using CE-CP. 1316-1318
• 
  Nasrollah Rezaei-Ghaleh, Frederik Klama, Francesca Munari, Markus Zweckstetter:
  HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins. 1319-1321
• 
  Nicholas Rego, David Koes:
  3Dmol.js: molecular visualization with WebGL. 1322-1324
• 
  Woonghee Lee, Marco Tonelli, John L. Markley:
  NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. 1325-1327

Systems Biology

• 
  Luca Marchetti, Vincenzo Manca:
  MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory. 1328-1330

Data and Text Mining

• 
  Jagir R. Hussan, Peter J. Hunter, Patrick A. Gladding, Neil L. Greenberg, G. Richard Christie, Alan Wu, Hugh Sorby, James D. Thomas:
  ICMA: an integrated cardiac modeling and analysis platform. 1331-1333

Databases and Ontologies

• 
  Matthias Arnold, Johannes Raffler, Arne Pfeufer, Karsten Suhre, Gabi Kastenmüller:
  SNiPA: an interactive, genetic variant-centered annotation browser. 1334-1336
• 
  Mélanie Courtot, Justin Meskas, Alexander D. Diehl, Radina Droumeva, Raphael Gottardo, Adrin Jalali, Mohammad Jafar Taghiyar, Holden T. Maecker, J. Philip McCoy, Alan Ruttenberg, Richard H. Scheuermann, Ryan Remy Brinkman:
  flowCL: ontology-based cell population labelling in flow cytometry. 1337-1339

Erratum
Databases and Ontologies

• 
  Yaron Orenstein, Ron Shamir:
  Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. 1340

Volume 31, Number 9, May 2015

Original Papers
Genome Analysis

• 
  Feifei Xiao, Xiaoyi Min, Heping Zhang:
  Modified screening and ranking algorithm for copy number variation detection. 1341-1348
• 
  Salem Malikic, Andrew W. McPherson, Nilgun Donmez, S. Cenk Sahinalp:
  Clonality inference in multiple tumor samples using phylogeny. 1349-1356

Sequence Analysis

• 
  Darui Xu, Kara Marquis, Jimin Pei, Szu-Chin Fu, Tolga Cagatay, Nick V. Grishin, Yuh Min Chook:
  LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. 1357-1365
• 
  Jun Ding, Xiaoman Li, Haiyan Hu:
  MicroRNA modules prefer to bind weak and unconventional target sites. 1366-1374
• 
  Qiang Wei, Xiaowei Zhan, Xue Zhong, Yongzhuang Liu, Yujun Han, Wei Chen, Bingshan Li:
  A Bayesian framework for de novo mutation calling in parents-offspring trios. 1375-1381
• 
  Peter Meinicke:
  UProC: tools for ultra-fast protein domain classification. 1382-1388
• 
  Szymon Grabowski, Sebastian Deorowicz, Lukasz Roguski:
  Disk-based compression of data from genome sequencing. 1389-1395
• 
  Ivan Borozan, Stuart N. Watt, Vincent Ferretti:
  Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification. 1396-1404

Structural Bioinformatics

• 
  Baldo Oliva, Narcis Fernandez-Fuentes:
  Knowledge-based modeling of peptides at protein interfaces: PiPreD. 1405-1410
• 
  Fuyi Li, Chen Li, Mingjun Wang, Geoffrey I. Webb, Yang Zhang, James C. Whisstock, Jiangning Song:
  GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. 1411-1419

Gene Expression

• 
  Andrea Rau, Cathy Maugis-Rabusseau, Marie-Laure Martin-Magniette, Gilles Celeux:
  Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. 1420-1427
• 
  Bernie J. Daigle Jr., Mohammad Soltani, Linda R. Petzold, Abhyudai Singh:
  Inferring single-cell gene expression mechanisms using stochastic simulation. 1428-1435

Databases and Ontologies

• 
  Jing Zhu, Zhiao Shi, Jing Wang, Bing Zhang:
  Empowering biologists with multi-omics data: colorectal cancer as a paradigm. 1436-1443
• 
  Jobie Kirkwood, David Hargreaves, Simon O'Keefe, Julie Wilson:
  Using isoelectric point to determine the pH for initial protein crystallization trials. 1444-1451

Genetic and Population Analysis

• 
  Rui Chen, Qiang Wei, Xiaowei Zhan, Xue Zhong, James S. Sutcliffe, Nancy J. Cox, Edwin H. Cook Jr., Chun Li, Wei Chen, Bingshan Li:
  A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. 1452-1459

Applications Notes
Genome Analysis

• 
  Guangyuan Yang, Wei Jiang, Qiang Yang, Weichuan Yu:
  PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies. 1460-1462
• 
  Jiyuan An, John Lai, Atul Sajjanhar, Jyotsna Batra, Chenwei Wang, Colleen C. Nelson:
  J-Circos: an interactive Circos plotter. 1463-1465
• 
  Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly:
  PRSice: Polygenic Risk Score software. 1466-1468

Sequence Analysis

• 
  John C. Mu, Marghoob Mohiyuddin, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam:
  VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. 1469-1471
• 
  Hyejin Yoon, Thomas Leitner:
  PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes. 1472-1474
• 
  Ogun Adebali, Davi R. Ortega, Igor B. Zhulin:
  CDvist: a webserver for identification and visualization of conserved domains in protein sequences. 1475-1477

Structural Bioinformatics

• 
  Benoist Laurent, Matthieu Chavent, Tristan Cragnolini, Anna Caroline E. Dahl, Samuela Pasquali, Philippe Derreumaux, Mark S. P. Sansom, Marc Baaden:
  Epock: rapid analysis of protein pocket dynamics. 1478-1480
• 
  Edrisse Chermak, Andrea Petta, Luigi Serra, Anna Vangone, Vittorio Scarano, Luigi Cavallo, Romina Oliva:
  CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts. 1481-1483
• 
  Jonathan E. Chen, Conrad C. Huang, Thomas E. Ferrin:
  RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. 1484-1486
• 
  Eran Eyal, Gengkon Lum, Ivet Bahar:
  The anisotropic network model web server at 2015 (ANM 2.0). 1487-1489
• 
  Guillaume Bouvier, Nathan Desdouits, Mathias Ferber, Arnaud Blondel, Michael Nilges:
  An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps. 1490-1492

Gene Expression

• 
  Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot, Christophe Caron:
  Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics. 1493-1495
• 
  Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral:
  RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. 1496-1498

Systems Biology

• 
  Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski:
  The Cyni framework for network inference in Cytoscape. 1499-1501

Databases and Ontologies

• 
  Thanasis Vergoulis, Ilias Kanellos, Nikos Kostoulas, Georgios K. Georgakilas, Timos K. Sellis, Artemis G. Hatzigeorgiou, Theodore Dalamagas:
  mirPub: a database for searching microRNA publications. 1502-1504
• 
  Diana M. Hendrickx, Hugo J. W. L. Aerts, Florian Caiment, Dominic Clark, Timothy M. D. Ebbels, Chris T. A. Evelo, Hans Gmuender, Dennie G. A. J. Hebels, Ralf Herwig, Jürgen Hescheler, Danyel G. J. Jennen, Marlon J. A. Jetten, Stathis Kanterakis, Hector C. Keun, Vera Matser, John P. Overington, Ekaterina Pilicheva, Ugis Sarkans, Marcelo P. Segura-Lepe, Isaia Sotiriadou, Timo Wittenberger, Clemens Wittwehr, Antonella Zanzi, Jos C. S. Kleinjans:
  diXa: a data infrastructure for chemical safety assessment. 1505-1507
• 
  Euna Jeong, Ningning He, Hyerin Park, Mee Song, Nayoung Kim, Seong Joon Lee, Sukjoon Yoon:
  MACE: mutation-oriented profiling of chemical response and gene expression in cancers. 1508-1514

Bioimage Informatics

• 
  Daniel Asarnow, Liliana Rojo-Arreola, Brian M. Suzuki, Conor R. Caffrey, Rahul Singh:
  The QDREC web server: determining dose-response characteristics of complex macroparasites in phenotypic drug screens. 1515-1518

Letter to the Editor
Sequence Analysis

• 
  Agnieszka Prochenka, Piotr Pokarowski, Piotr Gasperowicz, Joanna Kosinska, Piotr Stawinski, Renata Zbiec-Piekarska, Magdalena Spólnicka, Wojciech Branicki, Rafal Ploski:
  A cautionary note on using binary calls for analysis of DNA methylation. 1519-1520

Volume 31, Number 10, May 2015

Discovery note
Sequence Analysis

• 
  Tobias Hamp, Burkhard Rost:
  More challenges for machine-learning protein interactions. 1521-1525

Original Papers
Genome Analysis

• 
  Keegan D. Korthauer, Christina Kendziorski:
  MADGiC: a model-based approach for identifying driver genes in cancer. 1526-1535
• 
  Hashem A. Shihab, Mark F. Rogers, Julian Gough, Matthew E. Mort, David N. Cooper, Ian N. M. Day, Tom R. Gaunt, Colin Campbell:
  An integrative approach to predicting the functional effects of non-coding and coding sequence variation. 1536-1543

Sequence Analysis

• 
  Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm:
  PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. 1544-1552
• 
  Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu:
  Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. 1553-1560
• 
  Hisaki Ikebata, Ryo Yoshida:
  Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets. 1561-1568
• 
  Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz:
  KMC 2: fast and resource-frugal k-mer counting. 1569-1576
• 
  Kouichi Kimura, Asako Koike:
  Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data. 1577-1583

Gene Expression

• 
  Maria D. Chikina, Elena Zaslavsky, Stuart C. Sealfon:
  CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. 1584-1591
• 
  Thomas Bleazard, Janine A. Lamb, Sam Griffiths-Jones:
  Bias in microRNA functional enrichment analysis. 1592-1598

Genetics and Population Analysis

• 
  Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou:
  DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. 1599-1606

Systems Biology

• 
  Qunyuan Zhang, Haley Abel, Alan Wells, Petra Lenzini, Felicia Gomez, Michael A. Province, Alan A. Templeton, George M. Weinstock, Nita H. Salzman, Ingrid B. Borecki:
  Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data. 1607-1613
• 
  Vân Anh Huynh-Thu, Guido Sanguinetti:
  Combining tree-based and dynamical systems for the inference of gene regulatory networks. 1614-1622
• 
  Kieran O'Neill, Nima Aghaeepour, Jeremy Parker, Donna Hogge, Aly Karsan, Bakul Dalal, Ryan Remy Brinkman:
  Deep profiling of multitube flow cytometry data. 1623-1631
• 
  Darren Davis, Ömer Nebil Yaveroglu, Noël Malod-Dognin, Aleksandar Stojmirovic, Natasa Przulj:
  Topology-function conservation in protein-protein interaction networks. 1632-1639

Data and Text Mining

• 
  Renaud Richardet, Jean-Cédric Chappelier, Martin Telefont, Sean L. Hill:
  Large-scale extraction of brain connectivity from the neuroscientific literature. 1640-1647
• 
  Deepak Nag Ayyala, Shili Lin:
  GrammR: graphical representation and modeling of count data with application in metagenomics. 1648-1654

Databases and Ontologies

• 
  Heidi Dowst, Benjamin Pew, Chris Watkins, Apollo McOwiti, Jonathan Barney, Shijing Qu, Lauren B. Becnel:
  Acquire: an open-source comprehensive cancer biobanking system. 1655-1662

Applications Notes
Genome Analysis

• 
  Wolfgang Kaisers, Heiner Schaal, Holger Schwender:
  rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples. 1663-1664
• 
  Burkhard Steuernagel, Florian Jupe, Kamil Witek, Jonathan D. G. Jones, Brande B. H. Wulff:
  NLR-parser: rapid annotation of plant NLR complements. 1665-1667

Sequence Analysis

• 
  Liguo Wang, Jinfu J. Nie, Jean-Pierre A. Kocher:
  PVAAS: identify variants associated with aberrant splicing from RNA-seq. 1668-1670
• 
  Guoli Ji, Lei Li, Qingshun Quinn Li, Xiangdong Wu, Jingyi Fu, Gong Chen, Xiaohui Wu:
  PASPA: a web server for mRNA poly(A) site predictions in plants and algae. 1671-1673
• 
  Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak Wah Lam:
  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 1674-1676

Genetics and Population Analysis

• 
  Tom Druet, Michel Georges:
  LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors. 1677-1679
• 
  Paul R. Staab, Sha Zhu, Dirk Metzler, Gerton Lunter:
  scrm: efficiently simulating long sequences using the approximated coalescent with recombination. 1680-1682

Systems Biology

• 
  Israel Steinfeld, Roy Navon, Michael L. Creech, Zohar Yakhini, Anya Tsalenko:
  ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types. 1683-1685
• 
  Sara Aibar, Celia Fontanillo, Conrad Droste, Javier De Las Rivas:
  Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering. 1686-1688

Data and Text Mining

• 
  Jing Peng, Xinyi Shi, Yiming Sun, Dongye Li, Baohui Liu, Fanjiang Kong, Xiaohui Yuan:
  QTLMiner: QTL database curation by mining tables in literature. 1689-1691
• 
  Pan Tong, Kevin R. Coombes, Faye M. Johnson, Lauren A. Byers, Lixia Diao, Diane D. Liu, J. Jack Lee, John V. Heymach, Jing Wang:
  drexplorer: A tool to explore dose-response relationships and drug-drug interactions. 1692-1694

Databases and Ontologies

• 
  Mark Davies, Nathan Dedman, Anne Hersey, George Papadatos, Matthew D. Hall, Lourdes Cucurull-Sanchez, Phil Jeffrey, Samiul Hasan, Peter J. Eddershaw, John P. Overington:
  ADME SARfari: comparative genomics of drug metabolizing systems. 1695-1697
• 
  Jacinte Beerten, Joost J. J. van Durme, Rodrigo Gallardo, Emidio Capriotti, Louise C. Serpell, Frederic Rousseau, Joost Schymkowitz:
  WALTZ-DB: a benchmark database of amyloidogenic hexapeptides. 1698-1700

Volume 31, Number 11, June 2015

Original Papers
Genome Analysis

• 
  Ruichu Cai, Zhifeng Hao, Marianne Winslett, Xiaokui Xiao, Yin Yang, Zhenjie Zhang, Shuigeng Zhou:
  Deterministic identification of specific individuals from GWAS results. 1701-1707
• 
  Ola Brynildsrud, Lars-Gustav Snipen, Jon Bohlin:
  CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data. 1708-1715

Sequence Analysis

• 
  Valentin Joly, Daniel P. Matton:
  KAPPA, a simple algorithm for discovery and clustering of proteins defined by a key amino acid pattern: a case study of the cysteine-rich proteins. 1716-1723
• 
  Kathleen M. Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M. Carland, Salvatore Loguercio, Andrew I. Su:
  Omics Pipe: a community-based framework for reproducible multi-omics data analysis. 1724-1728

Structural Bioinformatics

• 
  Jessica Andreani, Johannes Söding:
  bbcontacts: prediction of β-strand pairing from direct coupling patterns. 1729-1737
• 
  Nawar Malhis, Jörg Gsponer:
  Computational identification of MoRFs in protein sequences. 1738-1744

Gene Expression

• 
  Ying Shen, Mumtahena Rahman, Stephen R. Piccolo, Daniel Gusenleitner, Nader N. El-Chaar, Luis Cheng, Stefano Monti, Andrea H. Bild, W. Evan Johnson:
  ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. 1745-1753
• 
  Charles K. Fisher, Pankaj Mehta:
  Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics. 1754-1761

Genetics and Population Analysis

• 
  Hande Topa, Ágnes Jónás, Robert Kofler, Carolin Kosiol, Antti Honkela:
  Gaussian process test for high-throughput sequencing time series: application to experimental evolution. 1762-1770

Systems Biology

• 
  Luis Tobalina, Rafael Bargiela, Jon Pey, Florian-Alexander Herbst, Iván Lores, David Rojo, Coral Barbas, Ana I. Peláez, Jesús Sánchez, Martin von Bergen, Jana Seifert, Manuel Ferrer, Francisco J. Planes:
  Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. 1771-1779
• 
  Tianjiao Chu, Jean-Francois Mouillet, Brian L. Hood, Thomas P. Conrads, Yoel Sadovsky:
  The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data. 1780-1787
• 
  Zhongyang Liu, Feifei Guo, Jiangyong Gu, Yong Wang, Yang Li, Dan Wang, Liang Lu, Dong Li, Fuchu He:
  Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources. 1788-1795

Data and Text Mining

• 
  Lei Xu, Jeffrey A. Cruz, Linda J. Savage, David M. Kramer, Jin Chen:
  Plant photosynthesis phenomics data quality control. 1796-1804
• 
  Ping Xuan, Ke Han, Yahong Guo, Jin Li, Xia Li, Yingli Zhong, Zhaogong Zhang, Jian Ding:
  Prediction of potential disease-associated microRNAs based on random walk. 1805-1815

Bioimage Informatics

• 
  Theresa Niederberger, Henrik Failmezger, Diana Uskat, Don Poron, Ingmar Glauche, Nico Scherf, Ingo Roeder, Timm Schroeder, Achim Tresch:
  Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions. 1816-1823

Applications Notes
Genome Analysis

• 
  Daniel Mapleson, Nizar Drou, David Swarbreck:
  RAMPART: a workflow management system for de novo genome assembly. 1824-1826
• 
  S. Evan Staton, John M. Burke:
  Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. 1827-1829

Sequence Analysis

• 
  Ilya Y. Zhbannikov, James A. Foster:
  MetAmp: combining amplicon data from multiple markers for OTU analysis. 1830-1832
• 
  Youngik Yang, Cuncong Zhong, Shibu Yooseph:
  SFA-SPA: a suffix array based short peptide assembler for metagenomic data. 1833-1835
• 
  Carlos N. Fischer, Claudia M. A. Carareto, Renato Augusto Corrêa dos Santos, Ricardo Cerri, Eduardo P. Costa, Leander Schietgat, Celine Vens:
  Learning HMMs for nucleotide sequences from amino acid alignments. 1836-1838

Gene Expression

• 
  Olivier Gevaert:
  MethylMix: an R package for identifying DNA methylation-driven genes. 1839-1841
• 
  Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu:
  dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis. 1842-1844
• 
  Loredana Le Pera, Mariagiovanna Mazzapioda, Anna Tramontano:
  3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments. 1845-1847
• 
  Ohad Manor, Eran Segal:
  GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms. 1848-1850
• 
  Dario Strbenac, Graham J. Mann, John T. Ormerod, Jean Yee Hwa Yang:
  ClassifyR: an R package for performance assessment of classification with applications to transcriptomics. 1851-1853
• 
  Kerstin Haase, Silke Raffegerst, Dolores J. Schendel, Dmitrij Frishman:
  Expitope: a web server for epitope expression. 1854-1856

Systems Biology

• 
  Nan Xiao, Dong-Sheng Cao, Min-Feng Zhu, Qing-Song Xu:
  protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. 1857-1859
• 
  Dmitri A. Papatsenko, Ihor R. Lemischka:
  NetExplore: a web server for modeling small network motifs. 1860-1862
• 
  Stuart Aitken, Alastair M. Kilpatrick, Ozgur E. Akman:
  Dizzy-Beats: a Bayesian evidence analysis tool for systems biology. 1863-1865
• 
  Liye He, Krister Wennerberg, Tero Aittokallio, Jing Tang:
  TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. 1866-1868

Data and Text Mining

• 
  Chi-Yu Shao, Bo-Han Su, Yi-shu Tu, Chieh Lin, Olivia A. Lin, Yufeng J. Tseng:
  CypRules: a rule-based P450 inhibition prediction server. 1869-1871
• 
  Evangelos Pafilis, Sune Pletscher-Frankild, Julia Schnetzer, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Katerina Vasileiadou, Patrick Leary, Jennifer Hammock, Katja Schulz, Cynthia Sims Parr, Christos Arvanitidis, Lars Juhl Jensen:
  ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. 1872-1874

Databases and Ontologies

• 
  Sarala M. Wimalaratne, Jerven T. Bolleman, Nick S. Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
  SPARQL-enabled identifier conversion with Identifiers.org. 1875-1877

Message from the ISCB
Databases and Ontologies

• 
  Christiana N. Fogg, Diane E. Kovats:
  Message from the ISCB: ISMB/ECCB Rebooted: 2015 Brings Major Update to the Conference Program. 1878-1879

Volume 31, Number 12, June 2015

ISMB/ECCB 2015 Proceedings, July 10-14, 2015, Dublin, Ireland
Editorial

• 
  Yves Moreau, Niko Beerenwinkel:
  ISMB/ECCB 2015. 1-2

Genes

• 
  Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi:
  De novo meta-assembly of ultra-deep sequencing data. 9-16
• 
  David Amar, Daniel Yekutieli, Adi Maron-Katz, Talma Hendler, Ron Shamir:
  A hierarchical Bayesian model for flexible module discovery in three-way time-series data. 17-26
• 
  Ibrahim Numanagic, Salem Malikic, Victoria M. Pratt, Todd C. Skaar, David A. Flockhart, Süleyman Cenk Sahinalp:
  Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. 27-34
• 
  Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun:
  Reconstructing 16S rRNA genes in metagenomic data. 35-43
• 
  Siavash Mirarab, Tandy J. Warnow:
  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. 44-52
• 
  Yana Safonova, Stefano Bonissone, Eugene Kurpilyansky, Ekaterina Starostina, Alla L. Lapidus, Jeremy Stinson, Laura DePalatis, Wendy Sandoval, Jennie Lill, Pavel A. Pevzner:
  IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. 53-61
• 
  Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael:
  Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. 62-70
• 
  Valentin Zulkower, Michel Page, Delphine Ropers, Johannes Geiselmann, Hidde de Jong:
  Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. 71-79
• 
  Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher:
  Misassembly detection using paired-end sequence reads and optical mapping data. 80-88
• 
  Andrea Ocone, Laleh Haghverdi, Nikola S. Müller, Fabian J. Theis:
  Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. 89-96
• 
  Christopher A. Penfold, Jonathan B. A. Millar, David L. Wild:
  Inferring orthologous gene regulatory networks using interspecies data fusion. 97-105

Proteins

• 
  Franziska Zickmann, Bernhard Y. Renard:
  MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. 106-115
• 
  Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng:
  Large-scale model quality assessment for improving protein tertiary structure prediction. 116-123
• 
  Laleh Soltan Ghoraie, Forbes J. Burkowski, Mu Zhu:
  Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins. 124-132
• 
  Xuefeng Cui, Hammad Naveed, Xin Gao:
  Finding optimal interaction interface alignments between biological complexes. 133-141
• 
  Yeu-Chern Harn, M. J. Powers, Elizabeth A. Shank, Vladimir Jojic:
  Deconvolving molecular signatures of interactions between microbial colonies. 142-150
• 
  Tomasz Oliwa, Yang Shen:
  cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions. 151-160

Systems

• 
  Yoshihiro Yamanishi, Yasuo Tabei, Masaaki Kotera:
  Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. 161-170
• 
  Yuriy Hulovatyy, Huili Chen, Tijana Milenkovic:
  Exploring the structure and function of temporal networks with dynamic graphlets. 171-180
• 
  Danny S. Park, Brielin Brown, Celeste Eng, Scott Huntsman, Donglei Hu, Dara G. Torgerson, Esteban Gonzàlez Burchard, Noah Zaitlen:
  Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses. 181-189
• 
  James Y. Zou, Eran Halperin, Esteban Gonzàlez Burchard, Sriram Sankararaman:
  Inferring parental genomic ancestries using pooled semi-Markov processes. 190-196
• 
  Francesca Petralia, Pei Wang, Jialiang Yang, Zhidong Tu:
  Integrative random forest for gene regulatory network inference. 197-205
• 
  Farhad Hormozdiari, Gleb Kichaev, Wen-Yun Yang, Bogdan Pasaniuc, Eleazar Eskin:
  Identification of causal genes for complex traits. 206-213
• 
  Dorothee Childs, Sergio Grimbs, Joachim Selbig:
  Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns. 214-220
• 
  Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng, Shuigeng Zhou:
  Improving compound-protein interaction prediction by building up highly credible negative samples. 221-229
• 
  Marinka Zitnik, Blaz Zupan:
  Gene network inference by fusing data from diverse distributions. 230-239
• 
  Felipe Llinares-López, Dominik G. Grimm, Dean A. Bodenham, Udo Gieraths, Mahito Sugiyama, Beth Rowan, Karsten M. Borgwardt:
  Genome-wide detection of intervals of genetic heterogeneity associated with complex traits. 240-249
• 
  Zongliang Yue, Madhura M. Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael T. Neylon, Liugen Zhu, Timothy Ratliff, Jake Yue Chen:
  PAGER: constructing PAGs and new PAG-PAG relationships for network biology. 250-257

Disease

• 
  Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
  Inferring models of multiscale copy number evolution for single-tumor phylogenetics. 258-267
• 
  Nora K. Speicher, Nico Pfeifer:
  Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery. 268-275
• 
  Yang Chen, Li Li, Guo-Qiang Zhang, Rong Xu:
  Phenome-driven disease genetics prediction toward drug discovery. 276-283
• 
  Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka:
  MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types. 284-292
• 
  A. Grant Schissler, Vincent Gardeux, Qike Li, Ikbel Achour, Haiquan Li, Walter W. Piegorsch, Yves A. Lussier:
  Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. 293-302
• 
  Damian Roqueiro, Menno J. Witteveen, Verneri Anttila, Gisela M. Terwindt, Arn M. J. M. van den Maagdenberg, Karsten M. Borgwardt:
  In silico phenotyping via co-training for improved phenotype prediction from genotype. 303-310
• 
  Amin Allahyar, Jeroen de Ridder:
  FERAL: network-based classifier with application to breast cancer outcome prediction. 311-319

Data

• 
  Alice Schoenauer Sebag, Sandra Plancade, Céline Raulet-Tomkiewicz, Robert Barouki, Jean-Philippe Vert, Thomas Walter:
  A generic methodological framework for studying single cell motility in high-throughput time-lapse data. 320-328
• 
  Mingfu Shao, Bernard M. E. Moret:
  Comparing genomes with rearrangements and segmental duplications. 329-338
• 
  Ke Liu, Shengwen Peng, Junqiu Wu, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu:
  MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence. 339-347
• 
  Davy Weissenbacher, Tasnia Tahsin, Rachel Beard, Mari Figaro, Robert Rivera, Matthew Scotch, Graciela Gonzalez:
  Knowledge-driven geospatial location resolution for phylogeographic models of virus migration. 348-356
• 
  Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng:
  Exploiting ontology graph for predicting sparsely annotated gene function. 357-364
• 
  Ramanuja Simha, Sebastian Briesemeister, Oliver Kohlbacher, Hagit Shatkay:
  Protein (multi-)location prediction: utilizing interdependencies via a generative model. 365-374
• 
  Andrew Palmer, Ekaterina Ovchinnikova, Mikael Thuné, Régis Lavigne, Blandine Guével, Andrey Dyatlov, Olga Vitek, Charles Pineau, Mats Borén, Theodore Alexandrov:
  Using collective expert judgements to evaluate quality measures of mass spectrometry images. 375-384

Original Papers
Genome Analysis

• 
  Marco Masseroli, Pietro Pinoli, Francesco Venco, Abdulrahman Kaitoua, Vahid Jalili, Fernando Palluzzi, Heiko Müller, Stefano Ceri:
  GenoMetric Query Language: a novel approach to large-scale genomic data management. 1881-1888
• 
  Li Chen, Chi Wang, Zhaohui S. Qin, Hao Wu:
  A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. 1889-1896

Sequence Analysis

• 
  Jacob Schreiber, Kevin Karplus:
  Analysis of nanopore data using hidden Markov models. 1897-1903
• 
  Manuel Holtgrewe, Léon Kuchenbecker, Knut Reinert:
  Methods for the detection and assembly of novel sequence in high-throughput sequencing data. 1904-1912
• 
  Eduard Zorita, Pol Cuscó, Guillaume J. Filion:
  Starcode: sequence clustering based on all-pairs search. 1913-1919
• 
  Carl Kingsford, Rob Patro:
  Reference-based compression of short-read sequences using path encoding. 1920-1928
• 
  Wenzhi Mao, Cihan Kaya, Anindita Dutta, Amnon Horovitz, Ivet Bahar:
  Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. 1929-1937

Structural Bioinformatics

• 
  Wei He, Zhi Liang, Maikun Teng, Liwen Niu:
  mFASD: a structure-based algorithm for discriminating different types of metal-binding sites. 1938-1944
• 
  Tobias Hamp, Burkhard Rost:
  Evolutionary profiles improve protein-protein interaction prediction from sequence. 1945-1950
• 
  Elihu C. Ihms, Mark P. Foster:
  MESMER: minimal ensemble solutions to multiple experimental restraints. 1951-1958
• 
  Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi:
  Mobility-based prediction of hydration structures of protein surfaces. 1959-1965
• 
  Jed M. Zaretzki, Michael R. Browning, Tyler B. Hughes, S. Joshua Swamidass:
  Extending P450 site-of-metabolism models with region-resolution data. 1966-1973

Gene Expression

• 
  Chen Xu, Zhengchang Su:
  Identification of cell types from single-cell transcriptomes using a novel clustering method. 1974-1980

Genetics and Population Analysis

• 
  Scott J. Hebbring, Majid Rastegar-Mojarad, Zhan Ye, John Mayer, Crystal Jacobson, Simon M. Lin:
  Application of clinical text data for phenome-wide association studies (PheWASs). 1981-1987

Systems Biology

• 
  Connor Clark, Jugal Kalita:
  A multiobjective memetic algorithm for PPI network alignment. 1988-1998
• 
  Joe Wandy, Rónán Daly, Rainer Breitling, Simon Rogers:
  Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. 1999-2006
• 
  Peng Li, Chao Huang, Yingxue Fu, Jinan Wang, Ziyin Wu, Jinlong Ru, Chunli Zheng, Zihu Guo, Xuetong Chen, Wei Zhou, Wenjuan Zhang, Yan Li, Jianxin Chen, Aiping Lu, Yonghua Wang:
  Large-scale exploration and analysis of drug combinations. 2007-2016
• 
  Igor Nikolskiy, Gary Siuzdak, Gary J. Patti:
  Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry. 2017-2023

Bioimage Informatics

• 
  Aruna Jammalamadaka, Panuakdet Suwannatat, Steven K. Fisher, B. S. Manjunath, Tobias Höllerer, Gabriel Luna:
  Characterizing spatial distributions of astrocytes in the mammalian retina. 2024-2031

Applications Notes
Genome Analysis

• 
  Artem Tarasov, Albert J. Vilella, Edwin Cuppen, Isaac J. Nijman, Pjotr Prins:
  Sambamba: fast processing of NGS alignment formats. 2032-2034

Sequence Analysis

• 
  Jared O'Connell, Ole Schulz-Trieglaff, Emma Carlson, Matthew M. Hims, Niall A. Gormley, Anthony J. Cox:
  NxTrim: optimized trimming of Illumina mate pair reads. 2035-2037
• 
  Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Mario Cáccamo:
  PolyMarker: A fast polyploid primer design pipeline. 2038-2039
• 
  Xuefeng Wang, Xiaoqing Yu, Wei Zhu, W. Richard McCombie, Eric Antoniou, R. Scott Powers, Nicholas O. Davidson, Ellen Li, Jennie Williams:
  A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. 2040-2042

Structural Bioinformatics

• 
  Felix Mueller-Planitz:
  Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkers. 2043-2045
• 
  Anastasia V. Rudik, Alexander V. Dmitriev, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov:
  SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds. 2046-2048

Systems Biology

• 
  Xian Liu, Yuan Gao, Jianlong Peng, Yuan Xu, Yulan Wang, Nannan Zhou, Jing Xing, Xiaomin Luo, Hualiang Jiang, Mingyue Zheng:
  TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds. 2049-2051

Data and Text Mining

• 
  Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José María Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. G. Ranea, Christine A. Orengo:
  FUN-L: gene prioritization for RNAi screens. 2052-2053
• 
  Görel Sundström, Neda Zamani, Manfred G. Grabherr, Evan Mauceli:
  Whiteboard: a framework for the programmatic visualization of complex biological analyses. 2054-2055

Databases and Ontologies

• 
  David Fenyö, Ronald C. Beavis:
  The GPMDB REST interface. 2056-2058

Message from ISCB
Databases and Ontologies

• 
  Christiana N. Fogg, Diane E. Kovats:
  Message from ISCB: Outstanding contributions to ISCB award. 2059-2060

Volume 31, Number 13, July 2015

Discovery note
Phylogenetics

• 
  Sebastián Duchêne, Simon Y. W. Ho:
  Mammalian genome evolution is governed by multiple pacemakers. 2061-2065

Original Papers
Genome Analysis

• 
  Kyung-Ah Sohn, Joshua Wing Kei Ho, Djordje Djordjevic, Hyun-hwan Jeong, Peter J. Park, Ju Han Kim:
  hiHMM: Bayesian non-parametric joint inference of chromatin state maps. 2066-2074
• 
  David C. Ream, Asma R. Bankapur, Iddo Friedberg:
  An event-driven approach for studying gene block evolution in bacteria. 2075-2083

Sequence Analysis

• 
  Derek M. Bickhart, Jana L. Hutchison, Lingyang Xu, Robert D. Schnabel, Jeremy F. Taylor, James M. Reecy, Steven G. Schroeder, Curtis P. Van Tassell, Tad S. Sonstegard, George E. Liu:
  RAPTR-SV: a hybrid method for the detection of structural variants. 2084-2090

Structural Bioinformatics

• 
  Priyashree Chaudhary, Athi N. Naganathan, M. Michael Gromiha:
  Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations. 2091-2097
• 
  Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
  AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. 2098-2105
• 
  John Lhota, Ruth Hauptman, Thomas Hart, Clara Ng, Lei Xie:
  A new method to improve network topological similarity search: applied to fold recognition. 2106-2114

Gene Expression

• 
  Diana M. Hendrickx, Danyel G. J. Jennen, Jacob J. Briedé, Rachel Cavill, Theo M. de Kok, Jos C. S. Kleinjans:
  Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study. 2115-2122
• 
  Sara Ballouz, Wim Verleyen, Jesse A. Gillis:
  Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. 2123-2130
• 
  Sam Benidt, Dan Nettleton:
  SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. 2131-2140

Genetics and Population Analysis

• 
  Ofer Isakov, Antonio V. Bordería, David Golan, Amir Hamenahem, Gershon Celniker, Liron Yoffe, Hervé Blanc, Marco Vignuzzi, Noam Shomron:
  Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum. 2141-2150

Systems Biology

• 
  Yi-Hsiung Chen, Chi-Dung Yang, Ching-Ping Tseng, Hsien-Da Huang, Shinn-Ying Ho:
  GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes. 2151-2158
• 
  Abdelmoneim Amer Desouki, Florian Jarre, Gabriel Gelius-Dietrich, Martin J. Lercher:
  CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions. 2159-2165
• 
  David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos:
  Detection of significant protein coevolution. 2166-2173
• 
  Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen:
  Automated benchmarking of peptide-MHC class I binding predictions. 2174-2181
• 
  Noël Malod-Dognin, Natasa Przulj:
  L-GRAAL: Lagrangian graphlet-based network aligner. 2182-2189

Bioimage Informatics

• 
  Murad Megjhani, Nicolas Rey-Villamizar, Amine Merouane, Yanbin Lu, Amit Mukherjee, Kristen Trett, Peter H. J. Chong, Carolyn Harris, William Shain, Badrinath Roysam:
  Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors. 2190-2198

Applications Notes
Sequence Analysis

• 
  Francesco Musacchia, Swaraj Basu, Giuseppe Petrosino, Marco Salvemini, Remo Sanges:
  Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs. 2199-2201
• 
  Adrian Tan, Gonçalo R. Abecasis, Hyun Min Kang:
  Unified representation of genetic variants. 2202-2204
• 
  Vincenzo Capece, Julio C. Garcia Vizcaino, Ramon Vidal, Raza-Ur Rahman, Tonatiuh Pena Centeno, Orr Shomroni, Irantzu Suberviola, André Fischer, Stefan Bonn:
  Oasis: online analysis of small RNA deep sequencing data. 2205-2207
• 
  Ioannis Kirmitzoglou, Vasilis J. Promponas:
  LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences. 2208-2210
• 
  Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges, Oliver Kohlbacher:
  EpiToolKit - a web-based workbench for vaccine design. 2211-2213

Structural Bioinformatics

• 
  Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, Chee Keong Kwoh:
  Fast, accurate, and reliable molecular docking with QuickVina 2. 2214-2216
• 
  Kentaro Morimoto, Takashi Nishikaze, Akiyasu C. Yoshizawa, Shigeki Kajihara, Ken Aoshima, Yoshiya Oda, Koichi Tanaka:
  GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry. 2217-2219
• 
  Fergal J. Duffy, Pauline M. Rudd:
  GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data. 2220-2221

Gene Expression

• 
  Yang Shi, Arul M. Chinnaiyan, Hui Jiang:
  rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data. 2222-2224
• 
  Bo Ding, Lina Zheng, Yun Zhu, Nan Li, Haiyang Jia, Rizi Ai, Andre Wildberg, Wei Wang:
  Normalization and noise reduction for single cell RNA-seq experiments. 2225-2227

Systems Biology

• 
  Christian Panse, Christian Trachsel, Jonas Grossmann, Ralph Schlapbach:
  specL - an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. 2228-2231
• 
  Matthias P. Gerstl, Christian Jungreuthmayer, Jürgen Zanghellini:
  tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks. 2232-2234
• 
  Enrico Glaab, Reinhard Schneider:
  RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis. 2235-2237

Message from the ISCB
Systems Biology

• 
  Christiana N. Fogg, Diane E. Kovats:
  Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia. 2238-2239

Corrigendum
Systems Biology

• 
  Daniel G. Hurley, Joseph Cursons, Yi Kan Wang, David M. Budden, Cristin G. Print, Edmund J. Crampin:
  NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. 2015-2240

Volume 31, Number 14, July 2015

Review
Genome Analysis

• 
  Saakshi Jalali, Shruti Kapoor, Ambily Sivadas, Deeksha Bhartiya, Vinod Scaria:
  Computational approaches towards understanding human long non-coding RNA biology. 2241-2251

Discovery Notes
Sequence Analysis

• 
  João Miguel Freire, Susana Almeida Dias, Luís Flores, Ana Salomé Veiga, Miguel A. R. B. Castanho:
  Mining viral proteins for antimicrobial and cell-penetrating drug delivery peptides. 2252-2256
• 
  Federico Abascal, Michael L. Tress, Alfonso Valencia:
  Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. 2257-2261

Original Papers
Genome Analysis

• 
  Liran Juan, Yongzhuang Liu, Yongtian Wang, Mingxiang Teng, Tianyi Zang, Yadong Wang:
  Family genome browser: visualizing genomes with pedigree information. 2262-2268
• 
  Michael B. Sohn, Ruofei Du, Lingling An:
  A robust approach for identifying differentially abundant features in metagenomic samples. 2269-2275

Sequence Analysis

• 
  Fábio Madeira, Michele Tinti, Gavuthami Murugesan, Emily Berrett, Margaret Stafford, Rachel Toth, Christian Cole, Carol MacKintosh, Geoffrey J. Barton:
  14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. 2276-2283
• 
  Nicolas Palopoli, Kieren T. Lythgow, Richard J. Edwards:
  QSLiMFinder: improved short linear motif prediction using specific query protein data. 2284-2293

Structural Bioinformatics

• 
  Mohamed Raef Smaoui, Henri Orland, Jérôme Waldispühl:
  Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes. 2294-2302

Gene Expression

• 
  Isaac Dialsingh, Stefanie R. Austin, Naomi S. Altman:
  Estimating the proportion of true null hypotheses when the statistics are discrete. 2303-2309
• 
  Andreas Gleiss, Mohammed Dakna, Harald Mischak, Georg Heinze:
  Two-group comparisons of zero-inflated intensity values: the choice of test statistic matters. 2310-2317
• 
  Prasad Patil, Pierre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T. Leek:
  Test set bias affects reproducibility of gene signatures. 2318-2323

Systems Biology

• 
  Cheng Zhang, Boyang Ji, Adil Mardinoglu, Jens Nielsen, Qiang Hua:
  Logical transformation of genome-scale metabolic models for gene level applications and analysis. 2324-2331
• 
  Dimitrios Kleftogiannis, Limsoon Wong, John A. C. Archer, Panos Kalnis:
  Hi-Jack: a novel computational framework for pathway-based inference of host-pathogen interactions. 2332-2339
• 
  Simon Tanaka, David Sichau, Dagmar Iber:
  LBIBCell: a cell-based simulation environment for morphogenetic problems. 2340-2347
• 
  Cheng Liang, Yue Li, Jiawei Luo, Zhaolei Zhang:
  A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. 2348-2355
• 
  Ferhat Alkan, Cesim Erten:
  SiPAN: simultaneous prediction and alignment of protein-protein interaction networks. 2356-2363

Bioimage Informatics

• 
  Luís Pedro Coelho, Catarina Pato, Ana Friães, Ariane Neumann, Maren von Köckritz-Blickwede, Mário Ramirez, João André Carriço:
  Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images. 2364-2370

Applications Notes
Genome Analysis

• 
  Owen J. L. Rackham, Petros Dellaportas, Enrico Petretto, Leonardo Bottolo:
  WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools. 2371-2373
• 
  Martin Hunt, Astrid Gall, Swee Hoe Ong, Jacqui Brener, Bridget Ferns, Philip J. R. Goulder, Eleni Nastouli, Jacqueline A. Keane, Paul Kellam, Thomas D. Otto:
  IVA: accurate de novo assembly of RNA virus genomes. 2374-2376
• 
  Matthew A. Field, Vicky Cho, Matthew C. Cook, Anselm Enders, Carola G. Vinuesa, Belinda Whittle, T. Daniel Andrews, Chris C. Goodnow:
  Reducing the search space for causal genetic variants with VASP. 2377-2379
• 
  Stefano Capomaccio, Marco Milanesi, L. Bomba, E. Vajana, Paolo Ajmone-Marsan:
  MUGBAS: a species free gene-based programme suite for post-GWAS analysis. 2380-2381
• 
  Guangchuang Yu, Li-Gen Wang, Qing-Yu He:
  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. 2382-2383
• 
  Sung-Hwan Kim, Onyeka Ezenwoye, Hwan-Gue Cho, Keith D. Robertson, Jeong-Hyeon Choi:
  iTagPlot: an accurate computation and interactive drawing tool for tag density plot. 2384-2387

Sequence Analysis

• 
  Kristen Marciniuk, Brett Trost, Scott Napper:
  EpIC: a rational pipeline for epitope immunogenicity characterization. 2388-2390

Phylogenetics

• 
  Daniel Money, Simon Whelan:
  GeLL: a generalized likelihood library for phylogenetic models. 2391-2393

Structural Bioinformatics

• 
  Prakash Chandra Rathi, Daniel Mulnaes, Holger Gohlke:
  VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability. 2394-2396
• 
  Miguel Vazquez, Alfonso Valencia, Tirso Pons:
  Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. 2397-2399

Gene Expression

• 
  Yarden Katz, Eric T. Wang, Jacob Silterra, Schraga Schwartz, Bang Wong, Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, Edoardo M. Airoldi, Christopher B. Burge:
  Quantitative visualization of alternative exon expression from RNA-seq data. 2400-2402

Systems Biology

• 
  Anindya Bhattacharya, Yan Cui:
  miR2GO: comparative functional analysis for microRNAs. 2403-2405
• 
  Martin Robinson, Steven S. Andrews, Radek Erban:
  Multiscale reaction-diffusion simulations with Smoldyn. 2406-2408
• 
  Vipin Vijayan, Vikram Saraph, Tijana Milenkovic:
  MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation. 2409-2411

Data and Text Mining

• 
  Xu Shi, Robert O. Barnes, Li Chen, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Yue Joseph Wang, Jianhua Xuan:
  BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. 2412-2414
• 
  Hannes L. Röst, George Rosenberger, Ruedi Aebersold, Lars Malmström:
  Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. 2415-2417

Bioimage Informatics

• 
  Kyle D. Bemis, April Harry, Livia S. Eberlin, Christina Ferreira, Stephanie M. van de Ven, Parag Mallick, Mark L. Stolowitz, Olga Vitek:
  Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. 2418-2420

Volume 31, Number 15, August 2015

Discovery note
Genome Analysis

• 
  Raquel M. Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, Paulo Jorge S. G. Ferreira:
  Three minimal sequences found in Ebola virus genomes and absent from human DNA. 2421-2425

Original Papers
Genome Analysis

• 
  Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai:
  Learning chromatin states with factorized information criteria. 2426-2433
• 
  Zheng Xu, Qing Duan, Song Yan, Wei Chen, Mingyao Li, Ethan M. Lange, Yun Li:
  DISSCO: direct imputation of summary statistics allowing covariates. 2434-2442
• 
  Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Liò, Pierluigi Crescenzi, Renato Fani, Marco Fondi:
  MeDuSa: a multi-draft based scaffolder. 2443-2451
• 
  Bayarbaatar Amgalan, Hyunju Lee:
  DEOD: uncovering dominant effects of cancer-driver genes based on a partial covariance selection method. 2452-2460
• 
  Brendan J. Kelly, Robert Gross, Kyle Bittinger, Scott A. Sherrill-Mix, James D. Lewis, Ronald G. Collman, Frederic D. Bushman, Hongzhe Li:
  Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. 2461-2468

Sequence Analysis

• 
  Amit K. Chattopadhyay, Diar Nasiev, Darren R. Flower:
  A statistical physics perspective on alignment-independent protein sequence comparison. 2469-2474
• 
  Quan Zou, Qinghua Hu, Maozu Guo, Guohua Wang:
  HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy. 2475-2481
• 
  Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier:
  Halvade: scalable sequence analysis with MapReduce. 2482-2488
• 
  Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen:
  SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. 2489-2496

Gene expression

• 
  Matti Pirinen, Tuuli Lappalainen, Noah A. Zaitlen, Emmanouil T. Dermitzakis, Peter Donnelly, Mark I. McCarthy, Manuel A. Rivas:
  Assessing allele-specific expression across multiple tissues from RNA-seq read data. 2497-2504
• 
  Swapna Agarwal, Pradip Ghanty, Nikhil R. Pal:
  Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer's disease. 2505-2513

Systems Biology

• 
  Francesca Gullo, Mark van der Garde, Giulia Russo, Marzio Pennisi, Santo Motta, Francesco Pappalardo, Suzanne Watt:
  Computational modeling of the expansion of human cord blood CD133⁺ hematopoietic stem/progenitor cells with different cytokine combinations. 2514-2522
• 
  Songpeng Zu, Ting Chen, Shao Li:
  Global optimization-based inference of chemogenomic features from drug-target interactions. 2523-2529
• 
  Yawwani Gunawardana, Shuhei Fujiwara, Akiko Takeda, Jeongmin Woo, Christopher H. Woelk, Mahesan Niranjan:
  Outlier detection at the transcriptome-proteome interface. 2530-2536
• 
  Fan Zhu, Lihong Shi, James Douglas Engel, Yuanfang Guan:
  Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. 2537-2544
• 
  Joan Segura, Carlos Oscar Sánchez Sorzano, Jesús Cuenca Alba, Patrick Aloy, José María Carazo:
  Using neighborhood cohesiveness to infer interactions between protein domains. 2545-2552

Data and Text Mining

• 
  Longendri Aguilera-Mendoza, Yovani Marrero-Ponce, Roberto Tellez-Ibarra, Monica T. Llorente-Quesada, Jesús Salgado, Stephen J. Barigye, Jun Liu:
  Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences. 2553-2559

Databases and Ontologies

• 
  Li Teng, Bing He, Jiahui Wang, Kai Tan:
  4DGenome: a comprehensive database of chromatin interactions. 2560-2564

Applications Notes
Genome Analysis

• 
  Graham J. Etherington, Ricardo H. Ramirez-Gonzalez, Dan MacLean:
  bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. 2565-2567
• 
  Shahar Alon, Muhammad Erew, Eli Eisenberg:
  DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data. 2568-2570

Sequence Analysis

• 
  Bachir Balech, Saverio Vicario, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo, Graziano Pesole:
  MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information. 2571-2573
• 
  Johannes Palme, Sepp Hochreiter, Ulrich Bodenhofer:
  KeBABS: an R package for kernel-based analysis of biological sequences. 2574-2576

Phylogenetics

• 
  Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis:
  ExaML version 3: a tool for phylogenomic analyses on supercomputers. 2577-2579

Structural Bioinformatics

• 
  Greet De Baets, Joost J. J. van Durme, Rob van der Kant, Joost Schymkowitz, Frederic Rousseau:
  Solubis: optimize your protein. 2580-2582
• 
  Rajendra Kumar, Helmut Grubmüller:
  do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations. 2583-2585

Gene expression

• 
  Rachel Legendre, Agnès Baudin-Baillieu, Isabelle Hatin, Olivier Namy:
  RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis. 2586-2588
• 
  Emmanuel Dimont, Jiantao Shi, Rory D. Kirchner, Winston Hide:
  edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test. 2589-2590

Genetics and Population Analysis

• 
  Quan Wang, Hui Yu, Zhongming Zhao, Peilin Jia:
  EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles. 2591-2594

Data and Text Mining

• 
  Jan Grau, Ivo Grosse, Jens Keilwagen:
  PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R. 2595-2597

Databases and Ontologies

• 
  Wenkang Huang, Guanqiao Wang, Qiancheng Shen, Xinyi Liu, Shaoyong Lu, Lv Geng, Zhimin Huang, Jian Zhang:
  ASBench: benchmarking sets for allosteric discovery. 2598-2600

Volume 31, Number 16, August 2015

Original Papers
Genome Analysis

• 
  Ellen M. Schmidt, Ji Zhang, Wei Zhou, Jin Chen, Karen L. Mohlke, Y. Eugene Chen, Cristen J. Willer:
  GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach. 2601-2606

Sequence Analysis

• 
  Chen Suo, Olga Hrydziuszko, Donghwan Lee, Setia Pramana, Dhany Saputra, Himanshu Joshi, Stefano Calza, Yudi Pawitan:
  Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival. 2607-2613
• 
  Ning Leng, Yuan Li, Brian E. McIntosh, Bao Kim Nguyen, Bret Duffin, Shulan Tian, James A. Thomson, Colin N. Dewey, Ron M. Stewart, Christina Kendziorski:
  EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. 2614-2622
• 
  Nicolò Colombo, Nikos Vlassis:
  FastMotif: spectral sequence motif discovery. 2623-2631
• 
  Igor Mandric, Alex Zelikovsky:
  ScaffMatch: scaffolding algorithm based on maximum weight matching. 2632-2638
• 
  Xiao Wang, Weiwei Zhang, Qiuwen Zhang, Guo-Zheng Li:
  MultiP-SChlo: multi-label protein subchloroplast localization prediction with Chou's pseudo amino acid composition and a novel multi-label classifier. 2639-2645

Structural Bioinformatics

• 
  Ke Tang, Samuel W. K. Wong, Jun S. Liu, Jinfeng Zhang, Jie Liang:
  Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method. 2646-2652
• 
  Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im:
  GS-align for glycan structure alignment and similarity measurement. 2653-2659
• 
  Liang Ding, Xingran Xue, Sal LaMarca, Mohammad Mohebbi, Abdul Samad, Russell L. Malmberg, Liming Cai:
  Accurate prediction of RNA nucleotide interactions with backbone k-tree model. 2660-2667
• 
  Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann:
  StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo. 2668-2675

Gene expression

• 
  Mohamed A. Ghadie, Nathalie Japkowicz, Theodore J. Perkins:
  Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach. 2676-2682
• 
  Martin Sill, Maral Saadati, Axel Benner:
  Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data. 2683-2690

Genetics and Population Analysis

• 
  Amadou Gaye, Thomas W. Y. Burton, Paul R. Burton:
  ESPRESSO: taking into account assessment errors on outcome and exposures in power analysis for association studies. 2691-2696

Systems Biology

• 
  Ömer Nebil Yaveroglu, Tijana Milenkovic, Natasa Przulj:
  Proper evaluation of alignment-free network comparison methods. 2697-2704
• 
  Franziska Witzel, Raphaela Fritsche-Guenther, Nadine Lehmann, Anja Sieber, Nils Blüthgen:
  Analysis of impedance-based cellular growth assays. 2705-2712

Data and Text Mining

• 
  Arief Gusnanto, Peter Tcherveniakov, Farag Shuweihdi, Manar Samman, Pamela Rabbitts, Henry M. Wood:
  Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data. 2713-2720
• 
  David Gfeller, Vincent Zoete:
  Protein homology reveals new targets for bioactive small molecules. 2721-2727

Databases and Ontologies

• 
  Agne Antanaviciute, Catherine Daly, Laura A. Crinnion, Alexander F. Markham, Christopher M. Watson, David T. Bonthron, Ian M. Carr:
  GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. 2728-2735
• 
  Catherine Kirsanova, Alvis Brazma, Gabriella Rustici, Ugis Sarkans:
  Cellular phenotype database: a repository for systems microscopy data. 2736-2740

Applications Notes
Genome Analysis

• 
  Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam:
  MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. 2741-2744

Sequence Analysis

• 
  Yongwook Choi, Agnes P. Chan:
  PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. 2745-2747
• 
  Hue Vuong, Anney Che, Sarangan Ravichandran, Brian T. Luke, Jack R. Collins, Uma S. Mudunuri:
  AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes. 2748-2750

Structural Bioinformatics

• 
  Judemir Ribeiro, Francisco Melo, Andreas Schüller:
  PDIviz: analysis and visualization of protein-DNA binding interfaces. 2751-2753

Genetics and Population Analysis

• 
  Dragana Vuckovic, Paolo Gasparini, Nicole Soranzo, Valentina Iotchkova:
  MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies. 2754-2756

Systems Biology

• 
  Dmitry Grapov, Kwanjeera Wanichthanarak, Oliver Fiehn:
  MetaMapR: pathway independent metabolomic network analysis incorporating unknowns. 2757-2760

Volume 31, Number 17, September 2015

Original Papers
Genome Analysis

• 
  Vahid Jalili, Matteo Matteucci, Marco Masseroli, Marco J. Morelli:
  Using combined evidence from replicates to evaluate ChIP-seq peaks. 2761-2769

Sequence Analysis

• 
  Rob Patro, Carl Kingsford:
  Data-dependent bucketing improves reference-free compression of sequencing reads. 2770-2777
• 
  Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek:
  Polyester: simulating RNA-seq datasets with differential transcript expression. 2778-2784
• 
  Yuting He, Fan Zhang, Patrick Flaherty:
  RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. 2785-2793

Phylogenetics

• 
  Emily Jane McTavish, Cody E. Hinchliff, James F. Allman, Joseph W. Brown, Karen Cranston, Mark T. Holder, Jonathan Rees, Stephen A. Smith:
  Phylesystem: a git-based data store for community-curated phylogenetic estimates. 2794-2800

Structural Bioinformatics

• 
  Naama Amir, Dan Cohen, Haim J. Wolfson:
  DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes. 2801-2807
• 
  Seungmyung Lee, Hanjoo Kim, Siqi Tian, Taehoon Lee, Sungroh Yoon, Rhiju Das:
  Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles. 2808-2815
• 
  Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio:
  INPS: predicting the impact of non-synonymous variations on protein stability from sequence. 2816-2821

Gene expression

• 
  Ellis Patrick, Michael J. Buckley, Samuel Müller, David M. Lin, Jean Yee Hwa Yang:
  Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data. 2822-2828
• 
  Stefano de Pretis, Theresia Kress, Marco J. Morelli, Giorgio E. M. Melloni, Laura Riva, Bruno Amati, Mattia Pelizzola:
  INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. 2829-2835

Systems Biology

• 
  Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner:
  Addressing false discoveries in network inference. 2836-2843
• 
  Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt:
  Genome-scale strain designs based on regulatory minimal cut sets. 2844-2851
• 
  Juhani Kähärä, Harri Lähdesmäki:
  BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data. 2852-2859

Databases and Ontologies

• 
  Lucila Aimo, Robin Liechti, Nevila Hyka-Nouspikel, Anne Niknejad, Anne Gleizes, Lou Götz, Dmitry Kuznetsov, Fabrice P. A. David, F. Gisou van der Goot, Howard Riezman, Lydie Bougueleret, Ioannis Xenarios, Alan J. Bridge:
  The SwissLipids knowledgebase for lipid biology. 2860-2866

Applications Notes
Genome Analysis

• 
  Lex Overmars, Sacha A. F. T. van Hijum, Roland J. Siezen, Christof Francke:
  CiVi: circular genome visualization with unique features to analyze sequence elements. 2867-2869
• 
  Adrian Baez-Ortega, Fabian Lorenzo-Diaz, Mariano Hernandez, Carlos Ignacio Gonzalez-Vila, José Luis Roda García, Marcos Colebrook, Carlos Flores:
  IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data. 2870-2873
• 
  Scott Newman:
  Interactive analysis of large cancer copy number studies with Copy Number Explorer. 2874-2876

Sequence Analysis

• 
  Shea N. Gardner, Tom Slezak, Barry G. Hall:
  kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. 2877-2878
• 
  Hamed Shateri Najafabadi, Mihai Albu, Timothy R. Hughes:
  Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. 2879-2881
• 
  Kathrin Petra Aßhauer, Bernd Wemheuer, Rolf Daniel, Peter Meinicke:
  Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. 2882-2884
• 
  Heng Li:
  BFC: correcting Illumina sequencing errors. 2885-2887

Phylogenetics

• 
  William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Anthony R. Ives, Caroline M. Tucker, Steve C. Walker, Matthew R. Helmus:
  pez: phylogenetics for the environmental sciences. 2888-2890

Structural Bioinformatics

• 
  Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan:
  iFoldRNA v2: folding RNA with constraints. 2891-2893
• 
  Wellisson R. S. Gonçalves, Valdete M. Gonçalves-Almeida, Aleksander L. Arruda, Wagner Meira Jr., Carlos Henrique da Silveira, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi:
  PDBest: a user-friendly platform for manipulating and enhancing protein structures. 2894-2896
• 
  Christopher J. Knight, Jochen S. Hub:
  MemGen: a general web server for the setup of lipid membrane simulation systems. 2897-2899

Gene expression

• 
  Stefan Rödiger, Michal Burdukiewicz, Peter Schierack:
  chipPCR: an R package to pre-process raw data of amplification curves. 2900-2902

Systems Biology

• 
  Yasset Pérez-Riverol, Julian Uszkoreit, Aniel Sánchez, Tobias Ternent, Noemi del-Toro, Henning Hermjakob, Juan Antonio Vizcaíno, Rui Wang:
  ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. 2903-2905
• 
  Ozan Kahramanogullari, Luca Cardelli:
  Gener: a minimal programming module for chemical controllers based on DNA strand displacement. 2906-2908

Data and Text Mining

• 
  Zachary Charlop-Powers, Sean F. Brady:
  phylogeo: an R package for geographic analysis and visualization of microbiome data. 2909-2911
• 
  Wencke Walter, Fátima Sánchez-Cabo, Mercedes Ricote:
  GOplot: an R package for visually combining expression data with functional analysis. 2912-2914

Databases and Ontologies

• 
  Bruno Reis Dotto, Evelise Leis Carvalho, Alexandre Freitas Silva, Luiz Fernando Duarte Silva, Paulo Marcos Pinto, Mauro Freitas Ortiz, Gabriel da Luz Wallau:
  HTT-DB: Horizontally transferred transposable elements database. 2915-2917

Bioimage Informatics

• 
  Alejandro Gimeno, Pablo Ares, Ignacio Horcas, Adriana Gil, José M. Gómez-Rodríguez, Jaime Colchero, Julio Gómez-Herrero:
  'Flatten plus': a recent implementation in WSxM for biological research. 2918-2920

Volume 31, Number 18, September 2015

Original Papers
Genome Analysis

• 
  Yao Lu, Yulan Lu, Jingyuan Deng, Hai Peng, Hui Lu, Long Jason Lu:
  A novel essential domain perspective for exploring gene essentiality. 2921-2929
• 
  Sofia Morfopoulou, Vincent Plagnol:
  Bayesian mixture analysis for metagenomic community profiling. 2930-2938

Sequence Analysis

• 
  Raffaele Giancarlo, Simona E. Rombo, Filippo Utro:
  Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning. 2939-2946
• 
  Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen:
  Repeat- and error-aware comparison of deletions. 2947-2954
• 
  Song Yan, Shuai Yuan, Zheng Xu, Baqun Zhang, Bo Zhang, Guolian Kang, Andrea Byrnes, Yun Li:
  Likelihood-based complex trait association testing for arbitrary depth sequencing data. 2955-2962
• 
  Léon Kuchenbecker, Mikalai Nienen, Jochen Hecht, Avidan U. Neumann, Nina Babel, Knut Reinert, Peter N. Robinson:
  IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. 2963-2971
• 
  Stefano Lonardi, Seyed Hamid Mirebrahim, Steve Wanamaker, Matthew Alpert, Gianfranco Ciardo, Denisa Duma, Timothy J. Close:
  When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. 2972-2980

Structural Bioinformatics

• 
  Piotr Klukowski, Michal J. Walczak, Adam Gonczarek, Julien Boudet, Gerhard Wider:
  Computer vision-based automated peak picking applied to protein NMR spectra. 2981-2988

Gene expression

• 
  Laleh Haghverdi, Florian Buettner, Fabian J. Theis:
  Diffusion maps for high-dimensional single-cell analysis of differentiation data. 2989-2998

Systems Biology

• 
  David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga:
  Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. 2999-3007
• 
  Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu:
  Trans-species learning of cellular signaling systems with bimodal deep belief networks. 3008-3015

Data and Text Mining

• 
  Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra:
  CAPRI: efficient inference of cancer progression models from cross-sectional data. 3016-3026

Databases and Ontologies

• 
  David E. Robillard, Phelelani T. Mpangase, Scott Hazelhurst, Frank Dehne:
  SpeeDB: fast structural protein searches. 3027-3034
• 
  Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey R. Brender, Junguk Hur, Arzucan Özgür, Yang Zhang:
  GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. 3035-3042

Applications Notes
Genome Analysis

• 
  Bin Wang, John M. Cunningham, Xinan Holly Yang:
  Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. 3043-3045
• 
  Kazumitsu Maehara, Yasuyuki Ohkawa:
  agplus: a rapid and flexible tool for aggregation plots. 3046-3047
• 
  Xinyi Shi, Jing Peng, Xiaohan Yu, Xiaohong Zhang, Dongye Li, Baohui Liu, Fanjiang Kong, Xiaohui Yuan:
  PopGeV: a web-based large-scale population genome browser. 3048-3050

Sequence Analysis

• 
  Elke Schaper, Alexander Korsunsky, Julija Pecerska, Antonio Messina, Riccardo Murri, Heinz Stockinger, Stefan Zoller, Ioannis Xenarios, Maria Anisimova:
  TRAL: tandem repeat annotation library. 3051-3053

Gene expression

• 
  Antoine Chambaz, Pierre Neuvial:
  tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation. 3054-3056
• 
  Swneke D. Bailey, Carl Virtanen, Benjamin Haibe-Kains, Mathieu Lupien:
  ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. 3057-3059

Systems Biology

• 
  Gregory W. Gundersen, Matthew R. Jones, Andrew D. Rouillard, Yan Kou, Caroline D. Monteiro, Axel S. Feldmann, Kevin S. Hu, Avi Ma'ayan:
  GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. 3060-3062
• 
  Ron Wehrens, Tom G. Bloemberg, Paul H. C. Eilers:
  Fast parametric time warping of peak lists. 3063-3065
• 
  Rémy Nicolle, François Radvanyi, Mohamed Elati:
  CoRegNet: reconstruction and integrated analysis of co-regulatory networks. 3066-3068
• 
  Minjae Yoo, Jimin Shin, Jihye Kim, Karen A. Ryall, Kyubum Lee, Sunwon Lee, Minji Jeon, Jaewoo Kang, Aik Choon Tan:
  DSigDB: drug signatures database for gene set analysis. 3069-3071
• 
  Astrid Wachter, Tim Beißbarth:
  pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. 3072-3074

Databases and Ontologies

• 
  Alba Gutiérrez-Sacristán, Solène Grosdidier, Olga Valverde, Marta Torrens, Àlex Bravo, Janet Piñero González, Ferran Sanz, Laura Inés Furlong:
  PsyGeNET: a knowledge platform on psychiatric disorders and their genes. 3075-3077
• 
  Alex Hodgkins, Anna Farne, Sajith Perera, Tiago Grego, David J. Parry-Smith, William C. Skarnes, Vivek Iyer:
  WGE: a CRISPR database for genome engineering. 3078-3080

Volume 31, Number 19, October 2015

Discovery note
Genome Analysis

• 
  Wenlong Shen, Dong Wang, Bingyu Ye, Minglei Shi, Lei Ma, Yan Zhang, Zhihu Zhao:
  GC3-biased gene domains in mammalian genomes. 3081-3084

Original Papers
Genome Analysis

• 
  Felix A. Klein, Tibor Pakozdi, Simon Anders, Yad Ghavi-Helm, Eileen E. M. Furlong, Wolfgang Huber:
  FourCSeq: analysis of 4C sequencing data. 3085-3091
• 
  Douglas H. Phanstiel, Alan P. Boyle, Nastaran Heidari, Michael P. Snyder:
  Mango: a bias-correcting ChIA-PET analysis pipeline. 3092-3098
• 
  Donghyung Lee, T. Bernard Bigdeli, Vernell S. Williamson, Vladimir I. Vladimirov, Brien P. Riley, Ayman H. Fanous, Silviu-Alin Bacanu:
  DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts. 3099-3104
• 
  Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim, Doheon Lee:
  SoloDel: a probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data. 3105-3113

Sequence Analysis

• 
  Robert Kleinkauf, Martin Mann, Rolf Backofen:
  antaRNA: ant colony-based RNA sequence design. 3114-3121
• 
  Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman:
  QVZ: lossy compression of quality values. 3122-3129
• 
  Joaquín Tárraga, Mariano Pérez, Juan M. Orduña, José Duato, Ignacio Medina, Joaquín Dopazo:
  A parallel and sensitive software tool for methylation analysis on multicore platforms. 3130-3138

Structural Bioinformatics

• 
  Chunyu Zhao, Ahmet Sacan:
  UniAlign: protein structure alignment meets evolution. 3139-3146

Gene expression

• 
  Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau:
  xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. 3147-3155
• 
  Sebastian Gibb, Korbinian Strimmer:
  Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis. 3156-3162
• 
  Zi Wang, Wei Yuan, Giovanni Montana:
  Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons. 3163-3171

Systems Biology

• 
  Huaying Fang, Chengcheng Huang, Hongyu Zhao, Minghua Deng:
  CCLasso: correlation inference for compositional data through Lasso. 3172-3180
• 
  Vishal R. Patel, Nicholas Ceglia, Michael Zeller, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi:
  The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework. 3181-3188

Bioimage Informatics

• 
  Amine Merouane, Nicolas Rey-Villamizar, Yanbin Lu, Ivan Liadi, Gabrielle Romain, Jennifer Lu, Harjeet Singh, Laurence J. N. Cooper, Navin Varadarajan, Badrinath Roysam:
  Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING). 3189-3197
• 
  Chalini D. Wijetunge, Isaam Saeed, Berin A. Boughton, Jeffrey M. Spraggins, Richard M. Caprioli, Antony Bacic, Ute Roessner, Saman K. Halgamuge:
  EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data. 3198-3206

Applications Notes
Genome Analysis

• 
  Ka-Kit Lam, Kurt LaButti, Asif Khalak, David N. C. Tse:
  FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads. 3207-3209
• 
  Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, Evgeny M. Zdobnov:
  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. 3210-3212

Sequence Analysis

• 
  Yana Safonova, Alla L. Lapidus, Jennie Lill:
  IgSimulator: a versatile immunosequencing simulator. 3213-3215
• 
  Siavash Sheikhizadeh, Dick de Ridder:
  ACE: accurate correction of errors using K-mer tries. 3216-3218
• 
  Matthew C. LaFave, Gaurav K. Varshney, Shawn M. Burgess:
  GeIST: a pipeline for mapping integrated DNA elements. 3219-3221

Structural Bioinformatics

• 
  G. C. P. van Zundert, Alexandre M. J. J. Bonvin:
  DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. 3222-3224

Gene expression

• 
  Henry Löffler-Wirth, Martin Kalcher, Hans Binder:
  oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. 3225-3227
• 
  José M. Juanes, Ana Miguel, Lucas J. Morales, José E. Pérez-Ortín, Vicente Arnau:
  A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data. 3228-3230

Systems Biology

• 
  Marta R. A. Matos, Bettina Knapp, Lars Kaderali:
  lpNet: a linear programming approach to reconstruct signal transduction networks. 3231-3233
• 
  Adrian Friebel, Johannes Neitsch, Tim Johann, Seddik Hammad, Jan G. Hengstler, Dirk Drasdo, Stefan Hoehme:
  TiQuant: software for tissue analysis, quantification and surface reconstruction. 3234-3236

Database and Ontologies

• 
  Yi Shen, Fan Gao, Minghui Wang, Ao Li:
  RPdb: a database of experimentally verified cellular reprogramming records. 3237-3239

Corrigendum
Database and Ontologies

• 
  Arnold Kuzniar, Somdutta Dhir, Harm Nijveen, Sándor Pongor, Jack A. M. Leunissen:
  Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks. 3240

Volume 31, Number 20, October 2015

Review
Structural Bioinformatics

• 
  Paul R. Burton, Madeleine J. Murtagh, Andy Boyd, James B. Williams, Edward S. Dove, Susan E. Wallace, Anne-Marie Tassé, Julian Little, Rex L. Chisholm, Amadou Gaye, Kristian Hveem, Anthony J. Brookes, Pat Goodwin, Jon Fistein, Martin Bobrow, Bartha M. Knoppers:
  Data Safe Havens in health research and healthcare. 3241-3248

Discovery note
Gene Expression

• 
  Kun Zhang, Yan Fu, Wen-Feng Zeng, Kun He, Hao Chi, Chao Liu, Yan-Chang Li, Yuan Gao, Ping Xu, Si-Min He:
  A note on the false discovery rate of novel peptides in proteogenomics. 3249-3253

Original Papers
Genome Analysis

• 
  Steve Oden, Luciano Brocchieri:
  Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans. 3254-3261

Sequence Analysis

• 
  Irina Vasilinetc, Andrey D. Prjibelski, Alexey A. Gurevich, Anton I. Korobeynikov, Pavel A. Pevzner:
  Assembling short reads from jumping libraries with large insert sizes. 3262-3268
• 
  Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
  TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. 3269-3275
• 
  (Withdrawn) LFQC: a lossless compression algorithm for FASTQ files. 3276-3281

Phylogenetics

• 
  Shiwei Lan, Julia A. Palacios, Michael D. Karcher, Vladimir N. Minin, Babak Shahbaba:
  An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics. 3282-3289

Gene Expression

• 
  Holger Fröhlich:
  biRte: Bayesian inference of context-specific regulator activities and transcriptional networks. 3290-3298

Systems Biology

• 
  Aditya Pratapa, Shankar Balachandran, Karthik Raman:
  Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks. 3299-3305
• 
  Huey-Eng Chua, Sourav S. Bhowmick, Lisa Tucker-Kellogg, C. Forbes Dewey Jr.:
  TENET: topological feature-based target characterization in signalling networks. 3306-3314
• 
  Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro:
  libRoadRunner: a high performance SBML simulation and analysis library. 3315-3321
• 
  Yuguang Ban, Lingling An, Hongmei Jiang:
  Investigating microbial co-occurrence patterns based on metagenomic compositional data. 3322-3329
• 
  Meng Zou, Zhaoqi Liu, Xiang-Sun Zhang, Yong Wang:
  NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data. 3330-3338

Databases and Ontologies

• 
  Brice Beinsteiner, Jonathan Michalon, Bruno P. Klaholz:
  IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes. 3339-3344

Applications Notes
Genome Analysis

• 
  Kishori M. Konwar, Niels W. Hanson, Maya P. Bhatia, Dongjae Kim, Shang-Ju Wu, Aria S. Hahn, Connor Morgan-Lang, Hiu Kan Cheung, Steven J. Hallam:
  MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. 3345-3347
• 
  Matthew R. Laird, Morgan G. I. Langille, Fiona S. L. Brinkman:
  GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. 3348-3349
• 
  Ryan R. Wick, Mark B. Schultz, Justin Zobel, Kathryn E. Holt:
  Bandage: interactive visualization of de novo genome assemblies. 3350-3352

Sequence Analysis

• 
  Chandler Zuo, Sunyoung Shin, Sündüz Keles:
  atSNP: transcription factor binding affinity testing for regulatory SNP detection. 3353-3355
• 
  Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, Steven H. Kleinstein:
  Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. 3356-3358
• 
  Wenzhong Liu, Yubin Xie, Jiyong Ma, Xiaotong Luo, Peng Nie, Zhixiang Zuo, Urs Lahrmann, Qi Zhao, Yueyuan Zheng, Yong Zhao, Yu Xue, Jian Ren:
  IBS: an illustrator for the presentation and visualization of biological sequences. 3359-3361
• 
  Yan-Hui Li, Gaigai Zhang, Qinghua Cui:
  PPUS: a web server to predict PUS-specific pseudouridine sites. 3362-3364
• 
  Dimitrios M. Vitsios, Anton J. Enright:
  Chimira: analysis of small RNA sequencing data and microRNA modifications. 3365-3367
• 
  Stephen Nayfach, Michael A. Fischbach, Katherine S. Pollard:
  MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. 3368-3370
• 
  Owen J. Marshall, Andrea H. Brand:
  damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. 3371-3373

Structural Bioinformatics

• 
  Leonid B. Pereyaslavets, Igor V. Sokolovskiy, Oxana V. Galzitskaya:
  FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures. 3374-3376
• 
  Peter Kerpedjiev, Stefan Hammer, Ivo L. Hofacker:
  Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. 3377-3379

Gene Expression

• 
  Miguel Juliá, Amalio Telenti, Antonio Rausell:
  Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. 3380-3382

Systems Biology

• 
  Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger:
  JSBML 1.0: providing a smorgasbord of options to encode systems biology models. 3383-3386
• 
  Yang Liu, Erica Manesso, Rudiyanto Gunawan:
  REDEMPTION: reduced dimension ensemble modeling and parameter estimation. 3387-3389
• 
  Graham L. Cromar, Anthony Zhao, Alex Yang, John Parkinson:
  Hyperscape: visualization for complex biological networks. 3390-3391

Databases and Ontologies

• 
  Günter Klambauer, Martin Wischenbart, Michael Mahr, Thomas Unterthiner, Andreas Mayr, Sepp Hochreiter:
  Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map. 3392-3394
• 
  Pawel P. Wozniak, Malgorzata Kotulska:
  AmyLoad: website dedicated to amyloidogenic protein fragments. 3395-3397

Bioimage Informatics

• 
  Benjamin Schmid, Jan Huisken:
  Real-time multi-view deconvolution. 3398-3400

Volume 31, Number 21, November 2015

Discovery note
Genome Analysis

• 
  Naiqian Zhang, Hua-Jun Wu, Weiwei Zhang, Jun Wang, Hao Wu, Xiaoqi Zheng:
  Predicting tumor purity from methylation microarray data. 3401-3405

Original Papers
Genome Analysis

• 
  Abhishek Biswas, David Gauthier, Desh Ranjan, Mohammad Zubair:
  ISQuest: finding insertion sequences in prokaryotic sequence fragment data. 3406-3412
• 
  Min Jin Ha, Veerabhadran Baladandayuthapani, Kim-Anh Do:
  DINGO: differential network analysis in genomics. 3413-3420
• 
  Amin Allam, Panos Kalnis, Victor V. Solovyev:
  Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data. 3421-3428

Sequence Analysis

• 
  Dan Ofer, Michal Linial:
  ProFET: Feature engineering captures high-level protein functions. 3429-3436
• 
  Thies Gehrmann, Marcel J. T. Reinders:
  Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level. 3437-3444
• 
  Jichen Yang, Stephen A. Ramsey:
  A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. 3445-3450
• 
  Daniel K. Manter, Matthew G. Bakker:
  Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff. 3451-3459
• 
  Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo:
  Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. 3460-3467
• 
  Subrata Saha, Sanguthevar Rajasekaran:
  ERGC: an efficient referential genome compression algorithm. 3468-3475
• 
  Robert C. Edgar, Henrik Flyvbjerg:
  Error filtering, pair assembly and error correction for next-generation sequencing reads. 3476-3482
• 
  Guillaume Beauclair, Antoine Bridier-Nahmias, Jean-François Zagury, Ali Saïb, Alessia Zamborlini:
  JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs. 3483-3491
• 
  Bin Liu, Junjie Chen, Xiaolong Wang:
  Application of learning to rank to protein remote homology detection. 3492-3498

Structural Bioinformatics

• 
  Michal J. Pietal, Janusz M. Bujnicki, Lukasz Pawel Kozlowski:
  GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. 3499-3505
• 
  Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
  Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. 3506-3513

Genetics and Population Analysis

• 
  Huwenbo Shi, Bogdan Pasaniuc, Kenneth L. Lange:
  A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data. 3514-3521
• 
  Michael Correll, Adam L. Bailey, Alper Sarikaya, David H. O'Connor, Michael Gleicher:
  LayerCake: a tool for the visual comparison of viral deep sequencing data. 3522-3528

Systems Biology

• 
  Zixing Wang, Wenlong Xu, Yin Liu:
  Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions. 3529-3536

Databases and Ontologies

• 
  Tyler Weirick, David John, Stefanie Dimmeler, Shizuka Uchida:
  C-It-Loci: a knowledge database for tissue-enriched loci. 3537-3543

Applications Notes
Sequence Analysis

• 
  Ilham A. Shahmuradov, Victor V. Solovyev:
  Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements. 3544-3545

Phylogenetics

• 
  Richard A. Neher, Trevor Bedford:
  nextflu: real-time tracking of seasonal influenza virus evolution in humans. 3546-3548

Genetics and Population Analysis

• 
  Alex H. Stram, Paul Marjoram, Gary K. Chen:
  al3c: high-performance software for parameter inference using Approximate Bayesian Computation. 3549-3551
• 
  Andrei-Alin Popescu, Katharina T. Huber:
  PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS. 3552-3554
• 
  Mitchell J. Machiela, Stephen J. Chanock:
  LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. 3555-3557

Systems Biology

• 
  Andreas Raue, Bernhard Steiert, Max Schelker, Clemens Kreutz, Tim Maiwald, Helge Hass, Joep Vanlier, Christian Tönsing, Lorenz Adlung, Raphael Engesser, Wolfgang Mader, Tim Heinemann, Jan Hasenauer, Marcel Schilling, Thomas Höfer, Edda Klipp, Fabian J. Theis, Ursula Klingmüller, Birgit Schoeberl, Jens Timmer:
  Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. 3558-3560

Volume 31, Number 22, November 2015

Original Papers
Genome Analysis

• 
  Runjun D. Kumar, Adam C. Searleman, S. Joshua Swamidass, Obi L. Griffith, Ron Bose:
  Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data. 3561-3568
• 
  Adam M. Novak, Yohei Rosen, David Haussler, Benedict Paten:
  Canonical, stable, general mapping using context schemes. 3569-3576
• 
  Na Zhu, Verena Heinrich, Thorsten Dickhaus, Jochen Hecht, Peter N. Robinson, Stefan Mundlos, Tom Kamphans, Peter M. Krawitz:
  Strategies to improve the performance of rare variant association studies by optimizing the selection of controls. 3577-3583

Sequence Analysis

• 
  Karel Brinda, Maciej Sykulski, Gregory Kucherov:
  Spaced seeds improve k-mer-based metagenomic classification. 3584-3592
• 
  Ying Jin, Oliver H. Tam, Eric Paniagua, Molly Hammell:
  TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. 3593-3599

Structural Bioinformatics

• 
  Pavel P. Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein:
  High-order neural networks and kernel methods for peptide-MHC binding prediction. 3600-3607
• 
  Rajdeep Kaur Grewal, Devrani Mitra, Soumen Roy:
  Mapping networks of light-dark transition in LOV photoreceptors. 3608-3616

Gene expression

• 
  Daniel Trejo-Baños, Andrew J. Millar, Guido Sanguinetti:
  A Bayesian approach for structure learning in oscillating regulatory networks. 3617-3624
• 
  Marek Gierlinski, Christian Cole, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark L. Blaxter, Geoffrey J. Barton:
  Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. 3625-3630
• 
  Camille Stephan-Otto Attolini, Víctor Peña, David Rossell:
  Designing alternative splicing RNA-seq studies. Beyond generic guidelines. 3631-3637

Systems Biology

• 
  Yingli Lv, Shuyuan Wang, Fanlin Meng, Lei Yang, Zhifeng Wang, Jing Wang, Xiaowen Chen, Wei Jiang, Yixue Li, Xia Li:
  Identifying novel associations between small molecules and miRNAs based on integrated molecular networks. 3638-3644
• 
  Gengbo Chen, Liang Cui, Guo Shou Teo, Choon Nam Ong, Chuen Seng Tan, Hyungwon Choi:
  MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics. 3645-3652

Data and Text Mining

• 
  Sungchul Kim, Lee Sael, Hwanjo Yu:
  A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization. 3653-3659
• 
  Roger A. Morbey, Alex J. Elliot, Andre Charlett, Neville Q. Verlander, Nick Andrews, Gillian E. Smith:
  The application of a novel 'rising activity, multi-level mixed effects, indicator emphasis' (RAMMIE) method for syndromic surveillance in England. 3660-3665

Databases and Ontologies

• 
  Mumtahena Rahman, Laurie K. Jackson, W. Evan Johnson, Dean Y. Li, Andrea H. Bild, Stephen R. Piccolo:
  Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. 3666-3672

Applications Notes
Genome Analysis

• 
  Julian Gehring, Bernd Fischer, Michael F. Lawrence, Wolfgang Huber:
  SomaticSignatures: inferring mutational signatures from single-nucleotide variants. 3673-3675
• 
  Honglei Liu, Zheng Wei, Antonia Dominguez, Yanda Li, Xiaowo Wang, Lei S. Qi:
  CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. 3676-3678
• 
  Arnaud Céol, Heiko Müller:
  The MI bundle: enabling network and structural biology in genome visualization tools. 3679-3681
• 
  Christopher E. Gillies, Catherine C. Robertson, Matthew G. Sampson, Hyun Min Kang:
  GeneVetter: a web tool for quantitative monogenic assessment of rare diseases. 3682-3684
• 
  Wei-Hien Cheong, Yung-Chie Tan, Soon-Joo Yap, Kee-Peng Ng:
  ClicO FS: an interactive web-based service of Circos. 3685-3687

Sequence Analysis

• 
  Courtney E. Lane, Daniel Hulgan, Kelly O'Quinn, Michael G. Benton:
  CEMAsuite: open source degenerate PCR primer design. 3688-3690
• 
  Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill:
  Roary: rapid large-scale prokaryote pan genome analysis. 3691-3693
• 
  Heng Li:
  FermiKit: assembly-based variant calling for Illumina resequencing data. 3694-3696

Structural Bioinformatics

• 
  Elias D. López, Juan Pablo Arcon, Diego F. Gauto, Ariel A. Petruk, Carlos P. Modenutti, Victoria G. Dumas, Marcelo A. Marti, Adrian Gustavo Turjanski:
  WATCLUST: a tool for improving the design of drugs based on protein-water interactions. 3697-3699
• 
  Chengcheng Liu, Ju Xin Chin, Dong-Yup Lee:
  SynLinker: an integrated system for designing linkers and synthetic fusion proteins. 3700-3702

Gene expression

• 
  Paula Helena Reyes-Herrera, C. A. Speck-Hernandez, Carlos Andrés Sierra, S. Herrera:
  BackCLIP: a tool to identify common background presence in PAR-CLIP datasets. 3703-3705

Genetics and Population Analysis

• 
  Biao Li, Gao T. Wang, Suzanne M. Leal:
  Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits. 3706-3708
• 
  Chase W. Nelson, Louise H. Moncla, Austin L. Hughes:
  SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. 3709-3711

Systems Biology

• 
  Varun Giri, Tadi Venkata Sivakumar, Kwang Myung Cho, Tae Yong Kim, Anirban Bhaduri:
  RxnSim: a tool to compare biochemical reactions. 3712-3714

Data and Text Mining

• 
  Bugra Ozer, Mahmut Samil Sagiroglu, Hüseyin Demirci:
  GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes. 3715-3717
• 
  Tal Galili:
  dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. 3718-3720

Volume 31, Number 23, December 2015

Discovery note
Data and Text Mining

• 
  Michael E. Kurczy, Julijana Ivanisevic, Caroline H. Johnson, Winnie Uritboonthai, Linh Hoang, Mingliang Fang, Matthew Hicks, Anthony Aldebot, Duane Rinehart, Lisa J. Mellander, Ralf Tautenhahn, Gary J. Patti, Mary E. Spilker, H. Paul Benton, Gary Siuzdak:
  Determining conserved metabolic biomarkers from a million database queries. 3721-3724

Original Papers
Genome Analysis

• 
  Taj Morton, Weng-Keen Wong, Molly Megraw:
  TIPR: transcription initiation pattern recognition on a genome scale. 3725-3732
• 
  Shunichi Kosugi, Hideki Hirakawa, Satoshi Tabata:
  GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments. 3733-3741
• 
  Matthew E. Holford, Michael Krauthammer:
  Mutadelic: mutation analysis using description logic inferencing capabilities. 3742-3747

Sequence Analysis

• 
  Hao-Dong Xu, Shao-Ping Shi, Ping-Ping Wen, Jian-Ding Qiu:
  SuccFind: a novel succinylation sites online prediction tool via enhanced characteristic strategy. 3748-3750
• 
  Jonathan K. Vis, Martijn Vermaat, Peter E. M. Taschner, Joost N. Kok, Jeroen F. J. Laros:
  An efficient algorithm for the extraction of HGVS variant descriptions from sequences. 3751-3757
• 
  Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier:
  BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. 3758-3766

Structural Bioinformatics

• 
  Mario Abdel Messih, Rosalba Lepore, Anna Tramontano:
  LoopIng: a template-based tool for predicting the structure of protein loops. 3767-3772
• 
  Jing Yang, Bao-Ji He, Richard Jang, Yang Zhang, Hong-Bin Shen:
  Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins. 3773-3781
• 
  Yassine Ghouzam, Guillaume Postic, Alexandre G. de Brevern, Jean-Christophe Gelly:
  Improving protein fold recognition with hybrid profiles combining sequence and structure evolution. 3782-3789

Genetics and Population Analysis

• 
  Alejandro Q. Nato, Nicola H. Chapman, Harkirat K. Sohi, Hiep D. Nguyen, Zoran Brkanac, Ellen M. Wijsman:
  PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers. 3790-3798

Systems Biology

• 
  Karen A. Ryall, Jimin Shin, Minjae Yoo, Trista K. Hinz, Jihye Kim, Jaewoo Kang, Lynn E. Heasley, Aik Choon Tan:
  Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. 3799-3806
• 
  Franziska Taruttis, Rainer Spang, Julia C. Engelmann:
  A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA). 3807-3814

Data and Text Mining

• 
  John-Patrick Mpindi, Potdar Swapnil, Dmitrii Bychkov, Saarela Jani, Khalid Saeed, Krister Wennerberg, Tero Aittokallio, Päivi Östling, Olli-P. Kallioniemi:
  Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. 3815-3821

Databases and Ontologies

• 
  Agne Antanaviciute, Christopher M. Watson, Sally M. Harrison, Carolina Lascelles, Laura A. Crinnion, Alexander F. Markham, David T. Bonthron, Ian M. Carr:
  OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. 3822-3829

Applications Notes
Genome Analysis

• 
  Marcin Kierczak, Jagoda Jablonska, Simon K. G. Forsberg, Matteo Bianchi, Katarina Tengvall, Mats E. Pettersson, Veronika Scholz, Jennifer R. S. Meadows, Patric Jern, Örjan Carlborg, Kerstin Lindblad-Toh:
  cgmisc: enhanced genome-wide association analyses and visualization. 3830-3831
• 
  Chao He, Michael Q. Zhang, Xiaowo Wang:
  MICC: an R package for identifying chromatin interactions from ChIA-PET data. 3832-3834
• 
  Nicholas W. Wolfe, Nathan L. Clark:
  ERC analysis: web-based inference of gene function via evolutionary rate covariation. 3835-3837

Sequence Analysis

• 
  Bryson C. Gibbons, Matthew Chambers, Matthew E. Monroe, David L. Tabb, Samuel H. Payne:
  Correcting systematic bias and instrument measurement drift with mzRefinery. 3838-3840
• 
  Giuseppe Profiti, Piero Fariselli, Rita Casadio:
  AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints. 3841-3843
• 
  Vojtech Bystrý, Andreas Agathangelidis, Vasilis Bikos, Lesley Ann Sutton, Panagiotis Baliakas, Anastasia Hadzidimitriou, Kostas Stamatopoulos, Nikos Darzentas:
  ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. 3844-3846
• 
  Simon G. Coetzee, Gerhard A. Coetzee, Dennis J. Hazelett:
  motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. 3847-3849

Structural Bioinformatics

• 
  Jinchao Yu, Géraldine Picord, Pierre Tufféry, Raphaël Guérois:
  HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. 3850-3852
• 
  Iñigo Marcos-Alcalde, Javier Setoain, Jesús I. Mendieta-Moreno, Jesús Mendieta, Paulino Gómez-Puertas:
  MEPSA: minimum energy pathway analysis for energy landscapes. 3853-3855
• 
  Francis Gaudreault, Louis-Philippe Morency, Rafael J. Najmanovich:
  NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. 3856-3858

Gene expression

• 
  Adam S. Brown, Chirag J. Patel:
  aRrayLasso: a network-based approach to microarray interconversion. 3859-3861

Genetics and Population Analysis

• 
  Alencar Xavier, Shizhong Xu, William M. Muir, Katy Martin Rainey:
  NAM: association studies in multiple populations. 3862-3864

Systems Biology

• 
  Emmanuel Chaplais, Henri-Jean Garchon:
  stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation. 3865-3867
• 
  Georg Summer, Thomas Kelder, Keiichiro Ono, Marijana Radonjic, Stephane Heymans, Barry Demchak:
  cyNeo4j: connecting Neo4j and Cytoscape. 3868-3869
• 
  Jing Yang, Su-Juan Wu, Yi-Xue Li, Yuan-Yuan Li:
  DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism. 3870-3872

Data and Text Mining

• 
  Mario Di Guardo, Diego Micheletti, Luca Bianco, Herma J. J. Koehorst-van Putten, Sara Longhi, Fabrizio Costa, Maria José Aranzana, Riccardo Velasco, Pere Arús, Michela Troggio, Eric W. van de Weg:
  ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. 3873-3874
• 
  Stefan Helfrich, Charaf E. Azzouzi, Christopher Probst, Johannes Seiffarth, Alexander Grünberger, Wolfgang Wiechert, Dietrich Kohlheyer, Katharina Nöh:
  Vizardous: interactive analysis of microbial populations with single cell resolution. 3875-3877

Databases and Ontologies

• 
  Matthias Ziehm, Dobril K. Ivanov, Aditi Bhat, Linda Partridge, Janet M. Thornton:
  SurvCurv database and online survival analysis platform update. 3878-3880

Volume 31, Number 24, December 2015

Original Papers
Genome Analysis

• 
  James Hensman, Panagiotis Papastamoulis, Peter Glaus, Antti Honkela, Magnus Rattray:
  Fast and accurate approximate inference of transcript expression from RNA-seq data. 3881-3889
• 
  A. Yazdani, David B. Dunson:
  A hybrid bayesian approach for genome-wide association studies on related individuals. 3890-3896

Sequence Analysis

• 
  Rujira Achawanantakun, Jiao Chen, Yanni Sun, Yuan Zhang:
  LncRNA-ID: Long non-coding RNA IDentification using balanced random forests. 3897-3905
• 
  Jaegyoon Ahn, Xinshu Xiao:
  RASER: reads aligner for SNPs and editing sites of RNA. 3906-3913

Structural Bioinformatics

• 
  Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen:
  Pairwise RNA secondary structure alignment with conserved stem pattern. 3914-3921
• 
  Hammad Naveed, Umar S. Hameed, Deborah Harrus, William Bourguet, Stefan T. Arold, Xin Gao:
  An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. 3922-3929
• 
  Virginie Y. Martiny, Pablo Carbonell, Florent Chevillard, Gautier Moroy, Arnaud B. Nicot, Philippe Vayer, Bruno O. Villoutreix, Maria A. Miteva:
  Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6. 3930-3937

Gene expression

• 
  Katharina E. Hayer, Angel D. Pizarro, Nicholas F. Lahens, John B. Hogenesch, Gregory R. Grant:
  Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. 3938-3945

Genetics and Population Analysis

• 
  Marc Pybus, Pierre Luisi, Giovanni Marco Dall'Olio, Manu Uzkudun, Hafid Laayouni, Jaume Bertranpetit, Johannes Engelken:
  Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. 3946-3952
• 
  Bin Gao, Yuehua Cui:
  Learning directed acyclic graphical structures with genetical genomics data. 3953-3960

Systems Biology

• 
  Amit Frishberg, Yael Steuerman, Irit Gat-Viks:
  CoD: inferring immune-cell quantities related to disease states. 3961-3969

Data and Text Mining

• 
  Ognjen Arandjelovic:
  Discovering hospital admission patterns using models learnt from electronic hospital records. 3970-3976
• 
  Xingjie Shi, Qing Zhao, Jian Huang, Yang Xie, Shuangge Ma:
  Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach. 3977-3983

Applications Notes
Genome Analysis

• 
  Wenzhi Li, Guoxing Fu, Weinian Rao, Wei Xu, Li Ma, Shiwen Guo, Qing Song:
  GenomeLaser: fast and accurate haplotyping from pedigree genotypes. 3984-3987
• 
  Junwei Luo, Jianxin Wang, Weilong Li, Zhen Zhang, Fang-Xiang Wu, Min Li, Yi Pan:
  EPGA2: memory-efficient de novo assembler. 3988-3990
• 
  Li Chen, Han Liu, Jean-Pierre A. Kocher, Hongzhe Li, Jun Chen:
  glmgraph: an R package for variable selection and predictive modeling of structured genomic data. 3991-3993

Sequence Analysis

• 
  Noah Spies, Justin M. Zook, Marc Salit, Arend Sidow:
  svviz: a read viewer for validating structural variants. 3994-3996
• 
  Ulrich Bodenhofer, Enrico Bonatesta, Christoph Horejs-Kainrath, Sepp Hochreiter:
  msa: an R package for multiple sequence alignment. 3997-3999
• 
  Haisi Yi, Zhe Li, Tao Li, Jindong Zhao:
  Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences. 4000-4002
• 
  José Manuel Abuín, Juan Carlos Pichel, Tomás F. Pena, Jorge Amigo:
  BigBWA: approaching the Burrows-Wheeler aligner to Big Data technologies. 4003-4005
• 
  Shengjie Gao, Dan Zou, Likai Mao, Huayu Liu, Pengfei Song, Youguo Chen, Shancen Zhao, Changduo Gao, Xiangchun Li, Zhibo Gao, Xiaodong Fang, Huanming Yang, Torben F. Ørntoft, Karina D. Sørensen, Lars Bolund:
  BS-SNPer: SNP calling in bisulfite-seq data. 4006-4008
• 
  Thorfinn Sand Korneliussen, Ida Moltke:
  NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. 4009-4011
• 
  Pavel Beran, Ivan Mraz:
  ABIF Manager: simple reading and editing of ABIF formatted files. 4012-4013
• 
  Jeongbin Park, Sangsu Bae, Jin-Soo Kim:
  Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites. 4014-4016

Structural Bioinformatics

• 
  Craig T. Porter, Andrew C. R. Martin:
  BiopLib and BiopTools - a C programming library and toolset for manipulating protein structure. 4017-4019
• 
  Le Viet Hung, Silvia Caprari, Massimiliano Bizai, Daniele Toti, Fabio Polticelli:
  LIBRA: LIgand Binding site Recognition Application. 4020-4022
• 
  Christian D. Schenkelberg, Christopher Bystroff:
  InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite. 4023-4025

Gene expression

• 
  Hyunwoo Kim, Hosung Jo, Heejin Park, Eunok Paek:
  HiXCorr: a portable high-speed X_Corr engine for high-resolution tandem mass spectrometry. 4026-4028

Genetics and Population Analysis

• 
  Matthias Geihs, Ying Yan, Klaudia Walter, Jie Huang, Yasin Memari, Josine L. Min, Daniel Mead, Tim J. P. Hubbard, Nicholas J. Timpson, Thomas A. Down, Nicole Soranzo:
  An interactive genome browser of association results from the UK10K cohorts project. 4029-4031

Systems Biology

• 
  Mariano J. Alvarez, James C. Chen, Andrea Califano:
  DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. 4032-4034

Data and Text Mining

• 
  Min Ou, Ricky Ma, Jeanno Cheung, Katie Lo, Patrick Yee, Tewei Luo, T. L. Chan, Chun Hang Au, Ava Kwong, Ruibang Luo, Tak Wah Lam:
  database.bio: a web application for interpreting human variations. 4035-4037

Databases and Ontologies

• 
  Zhengyu Guo, Boriana Tzvetkova, Jennifer M. Bassik, Tara Bodziak, Brianna M. Wojnar, Wei Qiao, Md A. Obaida, Sacha B. Nelson, Bo Hua Hu, Peng Yu:
  RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. 4038-4040