Bioinformatics, Volume 32

Volume 32, Number 1, January 2016

Original Papers
Genome Analysis

• 
  Zi Yang,George Michailidis:
  A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data.1-8

Sequence Analysis

• 
  Adam Krejci,Ted R. Hupp,Matej Lexa,Borivoj Vojtesek,Petr Müller:
  Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.9-16
• 
  Paul M. Bodily,M. Stanley Fujimoto,Quinn Snell,Dan Ventura,Mark J. Clement:
  ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction.17-24

Structural Bioinformatics

• 
  Maciej Dziubinski,Pawel Daniluk,Bogdan Lesyng:
  ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins.25-34

Gene expression

• 
  Benoît Liquet,Pierre Lafaye de Micheaux,Boris P. Hejblum,Rodolphe Thiébaut:
  Group and sparse group partial least square approaches applied in genomics context.35-42
• 
  Brendan A. Veeneman,Sudhanshu Shukla,Saravana M. Dhanasekaran,Arul M. Chinnaiyan,Alexey I. Nesvizhskii:
  Two-pass alignment improves novel splice junction quantification.43-49

Genetics and Population Analysis

• 
  Kevin He,Yanming Li,Ji Zhu,Hongliang Liu,Jeffrey E. Lee,Christopher I. Amos,Terry Hyslop,Jiashun Jin,Huazhen Lin,Qinyi Wei,Yi Li:
  Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates.50-57
• 
  Paulo C. Rodrigues,Andreia Monteiro,Vanda M. Lourenço:
  A robust AMMI model for the analysis of genotype-by-environment data.58-66

Systems Biology

• 
  Qiaozi Gao,Elisabeth Ostendorf,Jeffrey A. Cruz,Rong Jin,David M. Kramer,Jin Chen:
  Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis.67-76
• 
  Begüm Genç,Ugur Dogrusoz:
  An algorithm for automated layout of process description maps drawn in SBGN.77-84
• 
  Isidro Cortes-Ciriano,Gerard J. P. van Westen,Guillaume Bouvier,Michael Nilges,John P. Overington,Andreas Bender,Thérèse E. Malliavin:
  Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.85-95
• 
  Eunjee Lee,Koichi Ito,Yong Zhao,Eric E. Schadt,Hanna Y. Irie,Jun Zhu:
  Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.96-105

Data and Text Mining

• 
  Emily K. Mallory,Ce Zhang,Christopher Ré,Russ B. Altman:
  Large-scale extraction of gene interactions from full-text literature using DeepDive.106-113

Bioimage Informatics

• 
  Wei Shao,Mingxia Liu,Daoqiang Zhang:
  Human cell structure-driven model construction for predicting protein subcellular location from biological images.114-121
• 
  Hendrik Schäfer,Tim Schäfer,Jörg Ackermann,Norbert Dichter,Claudia Döring,Sylvia Hartmann,Martin-Leo Hansmann,Ina Koch:
  CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach.122-129

Applications Notes
Genome Analysis

• 
  Utkarsh J. Dang,Geoffrey Brian Golding:
  markophylo: Markov chain analysis on phylogenetic trees.130-132
• 
  Jonathan S. Packer,Evan K. Maxwell,Colm O'Dushlaine,Alexander E. Lopez,Frederick E. Dewey,Rostislav Chernomorsky,Aris Baras,John D. Overton,Lukas Habegger,Jeffrey G. Reid:
  CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.133-135

Sequence Analysis

• 
  Karel Brinda,Valentina Boeva,Gregory Kucherov:
  RNF: a general framework to evaluate NGS read mappers.136-139
• 
  Arna Óskarsdóttir,Gísli Másson,Páll Melsted:
  BamHash: a checksum program for verifying the integrity of sequence data.140-141
• 
  Richard M. Leggett,Darren Heavens,Mario Cáccamo,Matthew D. Clark,Robert P. Davey:
  NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.142-144

Structural Bioinformatics

• 
  Ronny Lorenz,Dominik Luntzer,Ivo L. Hofacker,Peter F. Stadler,Michael T. Wolfinger:
  SHAPE directed RNA folding.145-147

Genetics and Population Analysis

• 
  Diego A. Hartasánchez,Marina Brasó-Vives,Juanma Fuentes-Díaz,Oriol Vallès-Codina,Arcadi Navarro:
  SeDuS: segmental duplication simulator.148-150
• 
  Wei-Yi Cheng,Jörg Hakenberg,Shuyu Dan Li,Rong Chen:
  DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts.151-153

Data and Text Mining

• 
  Christian Jungreuthmayer,Stefan Neubauer,Teresa Mairinger,Jürgen Zanghellini,Stephan Hann:
  ICT: isotope correction toolbox.154-156

Databases and Ontologies

• 
  Noah Fahlgren,Steven T. Hill,James C. Carrington,Alberto Carbonell:
  P-SAMS: a web site for plant artificial microRNA and synthetictrans-acting small interfering RNA design.157-158
• 
  William Gilpin:
  PyPDB: a Python API for the Protein Data Bank.159-160

Volume 32, Number 2, January 2016

Original Papers
Sequence Analysis

• 
  Jimmy Caroli,Cristian Taccioli,A. De La Fuente,P. Serafini,Silvio Bicciato:
  APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data.161-164
• 
  Van-Minh Bui,Cheng-Tsung Lu,Trang-Thi Ho,Tzong-Yi Lee:
  MDD-SOH: exploiting maximal dependence decomposition to identifyS-sulfenylation sites with substrate motifs.165-172
• 
  Zhiying Wang,Tsachy Weissman,Olgica Milenkovic:
  smallWig: parallel compression of RNA-seq WIG files.173-180

Structural Bioinformatics

• 
  Bernhard Knapp,Samuel Demharter,Charlotte M. Deane,Peter Minary:
  Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.181-186
• 
  Marcel Kucharík,Ivo L. Hofacker,Peter F. Stadler,Jing Qin:
  Pseudoknots in RNA folding landscapes.187-194

Gene expression

• 
  Thomas J. Hardcastle:
  Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.195-202

Genetics and Population Analysis

• 
  Recep Colak,TaeHyung Kim,Hilal Kazan,Yoomi Oh,Miguel Cruz,Adan Valladares-Salgado,Jesus Peralta,Jorge Escobedo,Esteban J. Parra,Philip M. Kim,Anna Goldenberg:
  JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.203-210
• 
  Shuang Wang,Yuchen Zhang,Wenrui Dai,Kristin E. Lauter,Miran Kim,Yuzhe Richard Tang,Hongkai Xiong,Xiaoqian Jiang:
  HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS.211-218

Systems Biology

• 
  Miquel Marin-Riera,Miguel Brun-Usan,Roland Zimm,Tommi Välikangas,Isaac Salazar-Ciudad:
  Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model.219-225
• 
  Yong-Cui Wang,Shi-Long Chen,Nai-Yang Deng,Yong Wang:
  Computational probing protein-protein interactions targeting small molecules.226-234
• 
  Francesco Napolitano,Francesco Sirci,Diego Carrella,Diego di Bernardo:
  Drug-set enrichment analysis: a novel tool to investigate drug mode of action.235-241
• 
  Allison N. Tegge,Nicholas Sharp,T. M. Murali:
  Xtalk: a path-based approach for identifying crosstalk between signaling pathways.242-251
• 
  Pengyi Yang,Sean J. Humphrey,David E. James,Yee Hwa Yang,Raja Jothi:
  Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data.252-259
• 
  Jiyang Yu,José Silva,Andrea Califano:
  ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.260-267

Data and Text Mining

• 
  Nathaniel G. Mahieu,Jonathan L. Spalding,Gary J. Patti:
  Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis.268-275
• 
  Suwisa Kaewphan,Sofie Van Landeghem,Tomoko Ohta,Yves Van de Peer,Filip Ginter,Sampo Pyysalo:
  Cell line name recognition in support of the identification of synthetic lethality in cancer from text.276-282

Applications Notes
Genome Analysis

• 
  Tomaz Berisa,Joseph K. Pickrell:
  Approximately independent linkage disequilibrium blocks in human populations.283-285
• 
  Belinda Phipson,Jovana Maksimovic,Alicia Oshlack:
  missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.286-288
• 
  Bernat Gel,Anna Díez-Villanueva,Eduard Serra,Marcus Buschbeck,Miguel A. Peinado,Roberto Malinverni:
  regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.289-291
• 
  Konstantin Okonechnikov,Ana Conesa,Fernando García-Alcalde:
  Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.292-294
• 
  Donghyung Lee,Vernell S. Williamson,T. Bernard Bigdeli,Brien P. Riley,Bradley Todd Webb,Ayman H. Fanous,Kenneth S. Kendler,Vladimir I. Vladimirov,Silviu-Alin Bacanu:
  JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.295-297

Sequence Analysis

• 
  James Dunbar,Charlotte M. Deane:
  ANARCI: antigen receptor numbering and receptor classification.298-300
• 
  Paul Hodor,Amandeep Chawla,Andrew Clark,Lauren Neal:
  cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.301-303
• 
  Sergey Sheetlin,Yonil Park,Martin C. Frith,John L. Spouge:
  ALP & FALP: C++ libraries for pairwise local alignmentE-values.304-305

Systems Biology

• 
  Devin K. Schweppe,Juan D. Chavez,James E. Bruce:
  XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.306-308

Data and Text Mining

• 
  Max Franz,Christian Tannus Lopes,Gerardo Huck,Yue Dong,Selçuk Onur Sümer,Gary D. Bader:
  Cytoscape.js: a graph theory library for visualisation and analysis.309-311

Databases and Ontologies

• 
  James M. Melott,John N. Weinstein,Bradley M. Broom:
  PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.312-314

Bioimage Informatics

• 
  Andreas Bartschat,Eduard Hübner,Markus Reischl,Ralf Mikut,Johannes Stegmaier:
  XPIWIT - an XML pipeline wrapper for the Insight Toolkit.315-317
• 
  Pavel Krízek,Tomás Lukes,Martin Ovesný,Karel Fliegel,Guy M. Hagen:
  SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.318-320

Volume 32, Number 3, February 2016

Discovery note
Genome Analysis

• 
  Ka-Chun Wong,Yue Li,Chengbin Peng:
  Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells.321-324

Sequence Analysis

• 
  Michael Knudsen,Dan Søndergaard,Claus Tofting-Olesen,Frederik T. Hansen,Ditlev Egeskov Brodersen,Christian N. S. Pedersen:
  Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases.325-329

Original Papers
Genome Analysis

• 
  Shaolong Cao,Huaizhen Qin,Alexej Gossmann,Hong-Wen Deng,Yu-Ping Wang:
  Unified tests for fine-scale mapping and identifying sparse high-dimensional sequence associations.330-337

Sequence Analysis

• 
  Swati Kaushik,Anu G. Nair,Eshita Mutt,Hari Prasanna Subramanian,Ramanathan Sowdhamini:
  Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.338-344
• 
  Juliana S. Bernardes,Fabio R. J. Vieira,Gerson Zaverucha,Alessandra Carbone:
  A multi-objective optimization approach accurately resolves protein domain architectures.345-353
• 
  Genivaldo Gueiros Z. Silva,Kevin T. Green,Bas E. Dutilh,Robert A. Edwards:
  SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.354-361
• 
  Bin Liu,Longyun Fang,Ren Long,Xun Lan,Kuo-Chen Chou:
  iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudok-tuple nucleotide composition.362-369

Structural Bioinformatics

• 
  Peter Brown,Wayne Pullan,Yuedong Yang,Yaoqi Zhou:
  Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.370-377
• 
  Haiyou Deng,Ya Jia,Yang Zhang:
  3DRobot: automated generation of diverse and well-packed protein structure decoys.378-387

Gene expression

• 
  Isik Baris Fidaner,Ayca Cankorur-Cetinkaya,Duygu Dikicioglu,Betül Kirdar,Ali Taylan Cemgil,Stephen G. Oliver:
  CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.388-397

Systems Biology

• 
  Mehrshad Khosraviani,Morteza Saheb Zamani,Gholamreza Bidkhori:
  FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction.398-408
• 
  Tin Chi Nguyen,Rebecca Tagett,Michele Donato,Cristina Mitrea,Sorin Draghici:
  A novel bi-level meta-analysis approach: applied to biological pathway analysis.409-416
• 
  Jeremy Hyrkas,Sophie Clayton,Francois Ribalet,Daniel Halperin,E. Virginia Armbrust,Bill Howe:
  Scalable clustering algorithms for continuous environmental flow cytometry.417-423
• 
  Marcel Mischnik,Francesca Sacco,Jürgen Cox,Hans-Christoph Schneider,Matthias Schäfer,Manfred Hendlich,Daniel Crowther,Matthias Mann,Thomas Klabunde:
  IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data.424-431

Data and Text Mining

• 
  Simon Baker,Ilona Silins,Yufan Guo,Imran Ali,Johan Högberg,Ulla Stenius,Anna Korhonen:
  Automatic semantic classification of scientific literature according to the hallmarks of cancer.432-440

Applications Notes
Genome Analysis

• 
  Mitchell J. Sullivan,Nathan L. Bachmann,Peter Timms,Adam Polkinghorne:
  HapFlow: visualizing haplotypes in sequencing data.441-443

Sequence Analysis

• 
  Johannes Köster:
  Rust-Bio: a fast and safe bioinformatics library.444-446
• 
  Ibrahim Tanyalcin,Carla Al Assaf,Alexander Gheldof,Katrien Stouffs,Willy Lissens,Anna C. Jansen:
  I-PV: a CIRCOS module for interactive protein sequence visualization.447-449
• 
  Parth Patel,S. Deepthi Ramachandruni,Atul Kakrana,Mayumi Nakano,Blake C. Meyers:
  miTRATA: a web-based tool formicroRNATruncationandTailingAnalysis.450-452
• 
  Ivan Borozan,Vincent Ferretti:
  CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.453-455
• 
  Jérôme Mariette,Frédéric Escudié,Philippe Bardou,Nabihoudine Ibouniyamine,Céline Noirot,Marie-Stéphane Trotard,Christine Gaspin,Christophe Klopp:
  Jflow: a workflow management system for web applications.456-458

Structural Bioinformatics

• 
  Danny Incarnato,Francesco Neri,Francesca Anselmi,Salvatore Oliviero:
  RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.459-461
• 
  Chao Wang,Haicang Zhang,Wei-Mou Zheng,Dong Xu,Jianwei Zhu,Bing Wang,Kang Ning,Shiwei Sun,Shuai Cheng Li,Dongbo Bu:
  FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.462-464

Gene expression

• 
  Christoph Müssel,Florian Schmid,Tamara J. Blätte,Martin Hopfensitz,Ludwig Lausser,Hans A. Kestler:
  BiTrinA - multiscale binarization and trinarization with quality analysis.465-468

Genetics and Population Analysis

• 
  Jun Chen,Allan C. Just,Joel Schwartz,Lifang Hou,Nadereh Jafari,Zhifu Sun,Jean-Pierre A. Kocher,Andrea A. Baccarelli,Xihong Lin:
  CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies.469-471

Systems Biology

• 
  Weizhong Tu,Haoran Zhang,Juan Liu,Qian-Nan Hu:
  BioSynther: a customized biosynthetic potential explorer.472-473

Databases and Ontologies

• 
  Tim Schäfer,Andreas Scheck,Daniel Bruneß,Patrick May,Ina Koch:
  The new protein topology graph library web server.474-476
• 
  Gaston K. Mazandu,Emile R. Chimusa,Mamana Mbiyavanga,Nicola J. Mulder:
  A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.477-479

Volume 32, Number 4, February 2016

Review
Structural Bioinformatics

• 
  Guido Capitani,Jose M. Duarte,Kumaran Baskaran,Spencer Bliven,Joseph C. Somody:
  Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.481-489

Original Papers
Genome Analysis

• 
  Haoyang Zeng,Tatsunori B. Hashimoto,Daniel D. Kang,David K. Gifford:
  GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.490-496
• 
  Uwe Baier,Timo Beller,Enno Ohlebusch:
  Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform.497-504

Sequence Analysis

• 
  M. Kroon,Eric-Wubbo Lameijer,N. Lakenberg,Jayne Y. Hehir-Kwa,D. T. Thung,P. Eline Slagboom,Joost N. Kok,Kai Ye:
  Detecting dispersed duplications in high-throughput sequencing data using a database-free approach.505-510
• 
  Massimo Andreatta,Morten Nielsen:
  Gapped sequence alignment using artificial neural networks: application to the MHC class I system.511-517

Phylogenetics

• 
  Sarah Bastkowski,Vincent Moulton,Andreas Spillner,Taoyang Wu:
  The minimum evolution problem is hard: a link between tree inference and graph clustering problems.518-522

Gene expression

• 
  Alex Lewin,Habib Saadi,James E. Peters,Aida Moreno-Moral,James C. Lee,Kenneth G. C. Smith,Enrico Petretto,Leonardo Bottolo,Sylvia Richardson:
  MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.523-532
• 
  Sheida Nabavi,Daniel Schmolze,Mayinuer Maitituoheti,Sadhika Malladi,Andrew H. Beck:
  EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.533-541

Genetics and Population Analysis

• 
  Qiongshi Lu,Xinwei Yao,Yiming Hu,Hongyu Zhao:
  GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation.542-548
• 
  Emile R. Chimusa,Mamana Mbiyavanga,Gaston K. Mazandu,Nicola J. Mulder:
  ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations.549-556
• 
  Po-Ju Yao,Ren-Hua Chung:
  SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence.557-562

Systems Biology

• 
  Martin Scharm,Olaf Wolkenhauer,Dagmar Waltemath:
  An algorithm to detect and communicate the differences in computational models describing biological systems.563-570
• 
  Thorsten Will,Volkhard Helms:
  PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.571-578

Databases and Ontologies

• 
  Chen Wang,Gang Hu,Kui Wang,Michal Brylinski,Lei Xie,Lukasz A. Kurgan:
  PDID: database of molecular-level putative protein-drug interactions in the structural human proteome.579-586

Applications Notes
Genome Analysis

• 
  Nathan C. Sheffield,Christoph Bock:
  LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.587-589
• 
  Heng Li:
  BGT: efficient and flexible genotype query across many samples.590-592
• 
  Kathleen Oros Klein,Stepan Grinek,Sasha Bernatsky,Luigi Bouchard,Antonio Ciampi,Ines Colmegna,Jean-Philippe Fortin,Long Gao,Marie-France Hivert,Marie Hudson,Michael S. Kobor,Aurélie Labbe,Julia L. MacIsaac,Michael J. Meaney,Alexander M. Morin,Kieran J. O'Donnell,Tomi Pastinen,Marinus H. Van Ijzendoorn,Gregory Voisin,Celia M. T. Greenwood:
  funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.593-595
• 
  Jeffrey Staples,Lynette Ekunwe,Ethan M. Lange,James G. Wilson,Deborah A. Nickerson,Jennifer E. Below:
  PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes.596-598
• 
  Cyril Denby Wilkes,Olivier Arnaiz,Linda Sperling:
  ParTIES: a toolbox forParamecium interspersed DNA elimination studies.599-601

Sequence Analysis

• 
  Mayya Sedova,Lukasz Jaroszewski,Adam Godzik:
  Protael: protein data visualization library for the web.602-604
• 
  Yu-Wei Wu,Blake A. Simmons,Steven W. Singer:
  MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.605-607

Phylogenetics

• 
  François Chevenet,Jean-Philippe Doyon,Céline Scornavacca,Edwin Jacox,Emmanuelle Jousselin,Vincent Berry:
  SylvX: a viewer for phylogenetic tree reconciliations.608-610

Structural Bioinformatics

• 
  Hyojung Ryu,Gyutae Lim,Bong Hyun Sung,Jinhyuk Lee:
  NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.611-613
• 
  Lin Wang,Min Zhang,Emil Alexov:
  DelPhiPKa web server: predicting pK_a of proteins, RNAs and DNAs.614-615
• 
  Alexey G. Kikhney,Alejandro Panjkovich,Anna V. Sokolova,Dmitri I. Svergun:
  DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data.616-618
• 
  Hirofumi Suzuki,Takeshi Kawabata,Haruki Nakamura:
  Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.619-620
• 
  Matthieu Chartier,Etienne Adriansen,Rafael Najmanovich:
  IsoMIF Finder: online detection of binding site molecular interaction field similarities.621-623

Genetics and Population Analysis

• 
  Ming-Huei Chen,Qiong Yang:
  RVFam: an R package for rare variant association analysis with family data.624-626
• 
  António Múrias dos Santos,Maria Pilar Cabezas,Ana Isabel Tavares,Raquel Xavier,Madalena Branco:
  tcsBU: a tool to extend TCS network layout and visualization.627-628

Systems Biology

• 
  Bruce E. Shapiro,Eric Mjolsness:
  Pycellerator: an arrow-based reaction-like modelling language for biological simulations.629-631
• 
  Jan Winter,Marco Breinig,Florian Heigwer,Dirk Brügemann,Svenja Leible,Oliver Pelz,Tianzuo Zhan,Michael Boutros:
  caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens.632-634

Data and Text Mining

• 
  Juan J. Diaz-Montana,Owen J. L. Rackham,Norberto Díaz-Díaz,Enrico Petretto:
  Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data.635-637

Databases and Ontologies

• 
  Caterina Barillari,Diana S. M. Ottoz,Juan Mariano Fuentes-Serna,Chandrasekhar Ramakrishnan,Bernd Rinn,Fabian Rudolf:
  openBIS ELN-LIMS: an open-source database for academic laboratories.638-640

Volume 32, Number 5, March 2016

Original Papers
Genome Analysis

• 
  Feng Liu,Chao Ren,Hao Li,Pingkun Zhou,Xiaochen Bo,Wenjie Shu:
  De novo identification of replication-timing domains in the human genome by deep learning.641-649
• 
  Zheng Xu,Guosheng Zhang,Fulai Jin,Mengjie Chen,Terrence S. Furey,Patrick F. Sullivan,Zhaohui S. Qin,Ming Hu,Yun Li:
  A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.650-656
• 
  Tomasz Konopka,Sebastian M. B. Nijman:
  Comparison of genetic variants in matched samples using thesaurus annotation.657-663
• 
  Wonyul Lee,Jeffrey S. Morris:
  Identification of differentially methylated loci using wavelet-based functional mixed models.664-672

Sequence Analysis

• 
  Lorena Pantano,Marc R. Friedländer,Geòrgia Escaramís,Esther Lizano,Joan Pallarès-Albanell,Isidre Ferrer,Xavier Estivill,Eulalia Martí:
  Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.673-681

Gene expression

• 
  Ben Li,Zhaonan Sun,Qing He,Yu Zhu,Zhaohui S. Qin:
  Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes.682-689
• 
  Charlotte Siska,Russell Bowler,Katerina J. Kechris:
  The discordant method: a novel approach for differential correlation.690-696
• 
  Valerio Cestarelli,Giulia Fiscon,Giovanni Felici,Paola Bertolazzi,Emanuel Weitschek:
  CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules.697-704
• 
  Qi Shen,Jiyuan Hu,Ning Jiang,Xiaohua Hu,Zewei Luo,Hong Zhang:
  contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples.705-712

Genetics and Population Analysis

• 
  Wei Hao,Minsun Song,John D. Storey:
  Probabilistic models of genetic variation in structured populations applied to global human studies.713-721

Systems Biology

• 
  Eduardo Palma,Lilian Salinas,Julio Aracena:
  Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks.722-729
• 
  Matthias P. Gerstl,Steffen Klamt,Christian Jungreuthmayer,Jürgen Zanghellini:
  Exact quantification of cellular robustness in genome-scale metabolic networks.730-737
• 
  Marie Denis,Mahlet G. Tadesse:
  Evaluation of hierarchical models for integrative genomic analyses.738-746

Bioimage Informatics

• 
  A. Mazouchi,Joshua N. Milstein:
  Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy.747-754
• 
  Hao-Chih Lee,Tao Liao,Yongjie Jessica Zhang,Ge Yang:
  Shape component analysis: structure-preserving dimension reduction on biological shape spaces.755-763

Applications Notes
Genome Analysis

• 
  Minh Duc Cao,Devika Ganesamoorthy,Matthew A. Cooper,Lachlan J. M. Coin:
  Realtime analysis and visualization of MinION sequencing data with npReader.764-766
• 
  Katharina Jasmin Hoff,Simone Lange,Alexandre Lomsadze,Mark Borodovsky,Mario Stanke:
  BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.767-769

Sequence Analysis

• 
  André Kahles,Jonas Behr,Gunnar Rätsch:
  MMR: a tool for read multi-mapper resolution.770-772
• 
  Carmen Maria Livi,Petr Klus,Riccardo Delli Ponti,Gian Gaetano Tartaglia:
  catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions.773-775
• 
  Sumit Mukherjee,Supratim Sengupta:
  Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences.776-778
• 
  Sneha Mitra,Leelavati Narlikar:
  No Promoter Left Behind (NPLB): learnde novo promoter architectures from genome-wide transcription start sites.779-781
• 
  Dietmar Rieder,Thomas Amort,Elisabeth Kugler,Alexandra Lusser,Zlatko Trajanoski:
  meRanTK: methylated RNA analysis ToolKit.782-785

Phylogenetics

• 
  Brant C. Faircloth:
  PHYLUCE is a software package for the analysis of conserved genomic loci.786-788
• 
  Sebastian Höhna,Michael R. May,Brian R. Moore:
  TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.789-791

Structural Bioinformatics

• 
  Florian Kaiser,Alexander Eisold,Sebastian Bittrich,Dirk Labudde:
  Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data.792-794

Genetics and Population Analysis

• 
  Matthias Steinrücken,Ethan M. Jewett,Yun S. Song:
  SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes.795-797

Systems Biology

• 
  Brandon R. Thomas,Lily A. Chylek,Joshua Colvin,Suman Sirimulla,Andrew H. A. Clayton,William S. Hlavacek,Richard G. Posner:
  BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.798-800

Volume 32, Number 6, March 2016

Original Papers
Genome Analysis

• 
  Mookyung Cheon,Choongrak Kim,Iksoo Chang:
  Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector.801-807
• 
  Kyle S. Smith,Vinod Kumar Yadav,Shanshan Pei,Daniel A. Pollyea,Craig T. Jordan,Subhajyoti De:
  SomVarIUS: somatic variant identification from unpaired tissue samples.808-813

Sequence Analysis

• 
  Gearoid Fox,Fabian Sievers,Desmond G. Higgins:
  Usingde novo protein structure predictions to measure the quality of very large multiple sequence alignments.814-820
• 
  Enrique Audain,Yassel Ramos,Henning Hermjakob,Darren R. Flower,Yasset Pérez-Riverol:
  Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.821-827
• 
  Goro Terai,Satoshi Kamegai,Kiyoshi Asai:
  CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.828-834
• 
  Filippo Utro,Valeria Di Benedetto,Davide F. V. Corona,Raffaele Giancarlo:
  The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes.835-842

Structural Bioinformatics

• 
  Rhys Heffernan,Abdollah Dehzangi,James G. Lyons,Kuldip K. Paliwal,Alok Sharma,Jihua Wang,Abdul Sattar,Yaoqi Zhou,Yuedong Yang:
  Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.843-849

Genetics and Population Analysis

• 
  Sangjin Kim,Paul Schliekelman:
  Prioritizing hypothesis tests for high throughput data.850-858
• 
  Pierre Pudlo,Jean-Michel Marin,Arnaud Estoup,Jean-Marie Cornuet,Mathieu Gautier,Christian P. Robert:
  Reliable ABC model choice via random forests.859-866

Systems Biology

• 
  Matthew B. Biggs,Jason A. Papin:
  Metabolic network-guided binning of metagenomic sequence fragments.867-874
• 
  S. M. Minhaz Ud-Dean,Rudiyanto Gunawan:
  Optimal design of gene knockout experiments for gene regulatory network inference.875-883
• 
  Aristidis G. Vrahatis,Konstantina Dimitrakopoulou,Panos Balomenos,Athanasios K. Tsakalidis,Anastasios Bezerianos:
  CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis.884-892
• 
  Martin Pirkl,Elisabeth Hand,Dieter Kube,Rainer Spang:
  Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.893-900

Data and Text Mining

• 
  Yusuke Komiyama,Masaki Banno,Kokoro Ueki,Gul Saad,Kentaro Shimizu:
  Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.901-907
• 
  Goksel Misirli,Matteo Cavaliere,William Waites,Matthew R. Pocock,Curtis Madsen,Owen Gilfellon,Ricardo Honorato-Zimmer,Paolo Zuliani,Vincent Danos,Anil Wipat:
  Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.908-917

Databases and Ontologies

• 
  Samuel Croset,Joachim Rupp,Martin Romacker:
  Flexible data integration and curation using a graph-based approach.918-925

Applications Notes
Genome Analysis

• 
  Xuefeng Wang,Mengjie Chen,Xiaoqing Yu,Natapol Pornputtapong,Hao Chen,Nancy Ruonan Zhang,R. Scott Powers,Michael Krauthammer:
  Global copy number profiling of cancer genomes.926-928
• 
  Michael Richter,Ramon Rosselló-Mora,Frank Oliver Glöckner,Jörg Peplies:
  JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.929-931

Sequence Analysis

• 
  Joanna Lange,Lucjan Stanislaw Wyrwicz,Gert Vriend:
  KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.932-936
• 
  Kun Yang,Giovanni Stracquadanio,Jingchuan Luo,Jef D. Boeke,Joel S. Bader:
  BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.937-939

Structural Bioinformatics

• 
  Nan Li,Richard I. Ainsworth,Meixin Wu,Bo Ding,Wei Wang:
  MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.940-942

Gene expression

• 
  Wentao Yang,Katja Dierking,Hinrich Schulenburg:
  WormExp: a web-based application for aCaenorhabditis elegans-specific gene expression enrichment analysis.943-945

Genetics and Population Analysis

• 
  Yan Wen,Wenyu Wang,Xiong Guo,Feng Zhang:
  PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries.946-948
• 
  Tokhir Dadaev,Daniel A. Leongamornlert,Edward J. Saunders,Rosalind A. Eeles,Zsofia Kote-Jarai:
  LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.949-951

Data and Text Mining

• 
  Ying-Wooi Wan,Genevera I. Allen,Zhandong Liu:
  TCGA2STAT: simple TCGA data access for integrated statistical analysis in R.952-954

Bioimage Informatics

• 
  Filippo Piccinini,Alexa Kiss,Péter Horváth:
  CellTracker (not only) for dummies.955-957
• 
  Dominic Waithe,Mathias P. Clausen,Erdinc Sezgin,Christian Eggeling:
  FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting.958-960

Volume 32, Number 7, April 2016

Recomb-Seq/RECOMB-CBB
Genome Analysis

• 
  Birte Kehr,Páll Melsted,Bjarni V. Halldórsson:
  PopIns: population-scale detection of novel sequence insertions.961-967
• 
  Simona Constantinescu,Ewa Szczurek,Pejman Mohammadi,Jörg Rahnenführer,Niko Beerenwinkel:
  TiMEx: a waiting time model for mutually exclusive cancer alterations.968-975
• 
  Monica Golumbeanu,Pejman Mohammadi,Niko Beerenwinkel:
  BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.976-983
• 
  Daria Iakovishina,Isabelle Janoueix-Lerosey,Emmanuel Barillot,Mireille Régnier,Valentina Boeva:
  SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.984-992

Sequence Analysis

• 
  Jie Ren,Kai Song,Minghua Deng,Gesine Reinert,Charles H. Cannon,Fengzhu Sun:
  Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.993-1000
• 
  Yuzhen Ye,Haixu Tang:
  Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.1001-1008

Original Papers
Genome Analysis

• 
  Dmitry Antipov,Anton I. Korobeynikov,Jeffrey S. McLean,Pavel A. Pevzner:
  hybridSPAdes: an algorithm for hybrid assembly of short and long reads.1009-1015
• 
  Lee Mendelowitz,David C. Schwartz,Mihai Pop:
  Maligner: a fast ordered restriction map aligner.1016-1022

Sequence Analysis

• 
  Kevin Vervier,Pierre Mahé,Maud Tournoud,Jean-Baptiste Veyrieras,Jean-Philippe Vert:
  Large-scale machine learning for metagenomics sequence classification.1023-1032

Structural Bioinformatics

• 
  Laura DiChiacchio,Michael F. Sloma,David H. Mathews:
  AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.1033-1039

Gene expression

• 
  Martina Fischer,Bernhard Y. Renard:
  iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification.1040-1047

Genetics and Population Analysis

• 
  Anna Paola Carrieri,Filippo Utro,Laxmi Parida:
  Sampling ARG of multiple populations under complex configurations of subdivision and admixture.1048-1056

Systems Biology

• 
  Zhanchao Li,Meng-Hua Huang,Wen-Qian Zhong,Zhi-Qing Liu,Yun Xie,Zong Dai,Xiaoyong Zou:
  Identification of drug-target interaction from interactome network with 'guilt-by-association' principle and topology features.1057-1064

Data and Text Mining

• 
  Wim Verleyen,Sara Ballouz,Jesse A. Gillis:
  Positive and negative forms of replicability in gene network analysis.1065-1073

Databases and Ontologies

• 
  Suzanne M. Paley,Markus Krummenacker,Peter D. Karp:
  Representation and inference of cellular architecture for metabolic reconstruction and modeling.1074-1079

Applications Notes
Genome Analysis

• 
  Nour-al-dain Marzouka,Jessica Nordlund,Christofer L. Bäcklin,Gudmar Lönnerholm,Ann-Christine Syvänen,Jonas Carlsson Almlöf:
  CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.1080-1082
• 
  Thomas Lacroix,Sylvie Thérond,Marc Rugeri,Pierre Nicolas,Annie Gendrault,Valentin Loux,Jean-François Gibrat:
  Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.1083-1084
• 
  Andrea Franceschini,Jianyi Lin,Christian von Mering,Lars Juhl Jensen:
  SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.1085-1087
• 
  Alla Mikheenko,Vladislav Saveliev,Alexey A. Gurevich:
  MetaQUAST: evaluation of metagenome assemblies.1088-1090
• 
  Denis Seyres,Elodie Darbo,Laurent Perrin,Carl Herrmann,Aitor González:
  LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.1091-1093

Sequence Analysis

• 
  Jun Cheng,Franziska Metge,Christoph Dieterich:
  Specific identification and quantification of circular RNAs from sequencing data.1094-1096

Gene expression

• 
  Deena M. A. Gendoo,Natchar Ratanasirigulchai,Markus S. Schröder,Laia Paré,Joel S. Parker,Aleix Prat,Benjamin Haibe-Kains:
  Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.1097-1099
• 
  Chee Lee,Snehal Patil,Maureen A. Sartor:
  RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power.1100-1102

Genetics and Population Analysis

• 
  Rongfeng Cui,Molly Schumer,Gil G. Rosenthal:
  Admix'em: a flexible framework for forward-time simulations of hybrid populations with selection and mate choice.1103-1105
• 
  Gilles Guillot,Hákon Jónsson,Antoine Hinge,Nabil Manchih,Ludovic Orlando:
  Accurate continuous geographic assignment from low- to high-density SNP data.1106-1108

Systems Biology

• 
  Lars Barquist,Matthew Mayho,Carla A. Cummins,Amy K. Cain,Christine J. Boinett,Andrew J. Page,Gemma C. Langridge,Michael A. Quail,Jacqueline A. Keane,Julian Parkhill:
  The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.1109-1111

Bioimage Informatics

• 
  Christopher Schmied,Peter Steinbach,Tobias Pietzsch,Stephan Preibisch,Pavel Tomancak:
  An automated workflow for parallel processing of large multiview SPIM recordings.1112-1114

Letters to the Editor
Sequence Analysis

• 
  Sebastian Deorowicz,Szymon Grabowski,Idoia Ochoa,Mikel Hernaez,Tsachy Weissman:
  Comment on: 'ERGC: an efficient referential genome compression algorithm'.1115-1117
• 
  Subrata Saha,Sanguthevar Rajasekaran:
  Authors' response to 'Comment on: ERGC: An efficient Referential Genome Compression Algorithm'.1118-1119

Corrigendum
Sequence Analysis

• 
  Paulo Gaspar,José Luís Oliveira,Jörg Frommlet,Manuel A. S. Santos,Gabriela R. Moura:
  Corrigendum: EuGene: maximizing synthetic gene design for heterologous expression.1120

Volume 32, Number 8, April 2016

Original Papers
Genome Analysis

• 
  Yoli Shavit,Barnabas James Walker,Pietro Liò:
  Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration.1121-1129

Sequence Analysis

• 
  Yongzhuang Liu,Jian Liu,Jianguo Lu,Jiajie Peng,Liran Juan,Xiaolin Zhu,Bingshan Li,Yadong Wang:
  Joint detection of copy number variations in parent-offspring trios.1130-1137
• 
  Thomas Wolf,Vladimir Shelest,Neetika Nath,Ekaterina Shelest:
  CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes.1138-1143
• 
  Fatma-Elzahraa Eid,Mahmoud ElHefnawi,Lenwood S. Heath:
  DeNovo: virus-host sequence-based protein-protein interaction prediction.1144-1150
• 
  Hwee Kim,Yo-Sub Han:
  OMPPM: online multiple palindrome pattern matching.1151-1157

Structural Bioinformatics

• 
  Christoph Peters,Konstantinos D. Tsirigos,Nanjiang Shu,Arne Elofsson:
  Improved topology prediction using the terminal hydrophobic helices rule.1158-1162
• 
  Edoardo Milanetti,Domenico Raimondo,Anna Tramontano:
  Prediction of the permeability of neutral drugs inferred from their solvation properties.1163-1169

Gene expression

• 
  Jiao Yuan,Peng Zhang,Ya Cui,Jiajia Wang,Geir Skogerbø,Da-Wei Huang,Runsheng Chen,Shunmin He:
  Computational identification of piRNA targets on mouse mRNAs.1170-1177

Genetics and Population Analysis

• 
  Il-Youp Kwak,Wei Pan:
  Adaptive gene- and pathway-trait association testing with GWAS summary statistics.1178-1184

Systems Biology

• 
  Jiajie Peng,Tao Wang,Jixuan Wang,Yadong Wang,Jin Chen:
  Extending gene ontology with gene association networks.1185-1194
• 
  Vladimir Gligorijevic,Noël Malod-Dognin,Natasa Przulj:
  Fuse: multiple network alignment via data fusion.1195-1203
• 
  Helge Hass,Clemens Kreutz,Jens Timmer,Daniel Kaschek:
  Fast integration-based prediction bands for ordinary differential equation models.1204-1210

Applications Notes
Genome Analysis

• 
  Tsu-Pei Chiu,Federico Comoglio,Tianyin Zhou,Lin Yang,Renato Paro,Remo Rohs:
  DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.1211-1213
• 
  Li Chen,Zhaohui S. Qin:
  traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.1214-1216
• 
  Charles E. Grant,James Johnson,Timothy L. Bailey,William Stafford Noble:
  MCAST: scanning forcis-regulatory motif clusters.1217-1219

Sequence Analysis

• 
  Xiaoyu Chen,Ole Schulz-Trieglaff,Richard Shaw,Bret Barnes,Felix Schlesinger,Morten Källberg,Anthony J. Cox,Semyon Kruglyak,Christopher T. Saunders:
  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.1220-1222
• 
  Sandeep Kumar Kushwaha,Pallavi Chauhan,Katarina Hedlund,Dag G. Ahrén:
  NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction.1223-1225
• 
  Youri Hoogstrate,René Böttcher,Saskia D. Hiltemann,Peter J. van der Spek,Guido Jenster,Andrew Stubbs:
  FuMa: reporting overlap in RNA-seq detected fusion genes.1226-1228
• 
  R. Gonzalo Parra,Cristian Oscar Rohr,Daniel Koile,Carolina Perez-Castro,Patricio Yankilevich:
  INSECT 2.0: a web-server for genome-widecis-regulatory modules prediction.1229-1231
• 
  Robert T. Good,Temi Varghese,John Golz,Derek A. Russell,Alexie Papanicolaou,Owain Edwards,Charles Robin:
  OfftargetFinder: a web tool for species-specific RNAi design.1232-1234

Structural Bioinformatics

• 
  Leandro E. Lombardi,Marcelo A. Marti,Luciana Capece:
  CG2AA: backmapping protein coarse-grained structures.1235-1237
• 
  Daniel Sundfeld,Jakob Hull Havgaard,Alba Cristina Magalhaes Alves de Melo,Jan Gorodkin:
  Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.1238-1240

Gene expression

• 
  Philipp Angerer,Laleh Haghverdi,Maren Büttner,Fabian J. Theis,Carsten Marr,Florian A. Büttner:
  destiny: diffusion maps for large-scale single-cell data in R.1241-1243
• 
  Petr Smirnov,Zhaleh Safikhani,Nehme Hachem,Dong Wang,Adrian She,Catharina Olsen,Mark Freeman,Heather Marie Selby,Deena M. A. Gendoo,Patrick Grossmann,Andrew H. Beck,Hugo J. W. L. Aerts,Mathieu Lupien,Anna Goldenberg,Benjamin Haibe-Kains:
  PharmacoGx: an R package for analysis of large pharmacogenomic datasets.1244-1246

Genetics and Population Analysis

• 
  Gilderlanio S. Araújo,Lucas Henrique C. Lima,Silvana Schneider,Thiago P. Leal,Ana Paula Couto da Silva,Pedro O. S. Vaz de Melo,Eduardo Tarazona-Santos,Marília O. Scliar,Maíra R. Rodrigues:
  Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks).1247-1249
• 
  Michael Matschiner:
  Fitchi: haplotype genealogy graphs based on the Fitch algorithm.1250-1252
• 
  Daniel Bottomly,Shannon K. McWeeney,Beth Wilmot:
  HitWalker2: visual analytics for precision medicine and beyond.1253-1255

Systems Biology

• 
  Ahmadreza Ghaffarizadeh,Samuel H. Friedman,Paul Macklin:
  BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.1256-1258
• 
  Maximilian Malek,Rashid Ibragimov,Mario Albrecht,Jan Baumbach:
  CytoGEDEVO - global alignment of biological networks with Cytoscape.1259-1261
• 
  Augustin Luna,Özgün Babur,Bülent Arman Aksoy,Emek Demir,Chris Sander:
  PaxtoolsR: pathway analysis in R using Pathway Commons.1262-1264
• 
  Jan Bert Van Klinken,Ko Willems van Dijk:
  FluxModeCalculator: an efficient tool for large-scale flux mode computation.1265-1266

Data and Text Mining

• 
  Alastair P. Droop:
  qsubsec: a lightweight template system for defining sun grid engine workflows.1267-1268
• 
  Dennis Goldfarb,Wei Wang,Michael B. Major:
  MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.1269-1271

Databases and Ontologies

• 
  Augustin Luna,Vinodh N. Rajapakse,Fabricio G. Sousa,Jianjiong Gao,Nikolaus Schultz,Sudhir Varma,William C. Reinhold,Chris Sander,Yves Pommier:
  rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R.1272-1274
• 
  Damion M. Dooley,Aaron J. Petkau,Gary H. Van Domselaar,William W. L. Hsiao:
  Sequence database versioning for command line and Galaxy bioinformatics servers.1275-1277

Bioimage Informatics

• 
  Zsuzsanna Püspöki,Daniel Sage,John Paul Ward,Michael Unser:
  SpotCaliper: fast wavelet-based spot detection with accurate size estimation.1278-1280

Volume 32, Number 9, May 2016

Discovery note
Phylogenetics

• 
  Sebastián Duchêne,Charles S. P. Foster,Simon Y. W. Ho:
  Estimating the number and assignment of clock models in analyses of multigene datasets.1281-1285

Original Papers
Genome Analysis

• 
  Tuan Trieu,Jianlin Cheng:
  MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data.1286-1292
• 
  Sean Simmons,Bonnie Berger:
  Realizing privacy preserving genome-wide association studies.1293-1300
• 
  Yao-Ting Huang,Chen-Fu Liao:
  Integration of string and de Bruijn graphs for genome assembly.1301-1307

Sequence Analysis

• 
  Tanzy M. T. Love,Sung Yong Park,Elena E. Giorgi,Wendy J. Mack,Alan S. Perelson,Ha Youn Lee:
  SPMM: estimating infection duration of multivariant HIV-1 infections.1308-1315
• 
  Xiaowei Wang:
  Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies.1316-1322
• 
  Maria Hauser,Martin Steinegger,Johannes Söding:
  MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.1323-1330

Phylogenetics

• 
  Diego Darriba,Michael Weiß,Alexandros Stamatakis:
  Prediction of missing sequences and branch lengths in phylogenomic data.1331-1337

Structural Bioinformatics

• 
  Amir Nikooienejad,Wenyi Wang,Valen E. Johnson:
  Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors.1338-1345

Gene expression

• 
  Antti Häkkinen,Andre S. Ribeiro:
  Characterizing rate limiting steps in transcription from RNA production times in live cells.1346-1352
• 
  Michal P. Switnicki,Malene Juul,Tobias Madsen,Karina D. Sørensen,Jakob Skou Pedersen:
  PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification.1353-1365

Genetics and Population Analysis

• 
  Dmitry Prokopenko,Julian Hecker,Edwin K. Silverman,Marcello Pagano,Markus M. Nöthen,Christian Dina,Christoph Lange,Heide Loehlein Fier:
  Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project.1366-1372

Systems Biology

• 
  Jonathan H. Young,Michael Peyton,Hyun Seok Kim,Elizabeth McMillan,John D. Minna,Michael A. White,Edward M. Marcotte:
  Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer.1373-1379

Data and Text Mining

• 
  Ahmad Pesaranghader,Stan Matwin,Marina Sokolova,Robert G. Beiko:
  simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.1380-1387
• 
  Paul Blomstedt,Ritabrata Dutta,Sohan Seth,Alvis Brazma,Samuel Kaski:
  Modelling-based experiment retrieval: a case study with gene expression clustering.1388-1394

Bioimage Informatics

• 
  Raphaël Marée,Loic Rollus,Benjamin Stevens,Renaud Hoyoux,Gilles Louppe,Remy Vandaele,Jean-Michel Begon,Philipp Kainz,Pierre Geurts,Louis Wehenkel:
  Collaborative analysis of multi-gigapixel imaging data using Cytomine.1395-1401

Applications Notes
Genome Analysis

• 
  Frederic Commo,Justin Guinney,Charles Ferté,Brian M. Bot,Celine Lefebvre,Jean-Charles Soria,Fabrice André:
  rCGH: a comprehensive array-based genomic profile platform for precision medicine.1402-1404

Sequence Analysis

• 
  Clovis Galiez,Christophe N. Magnan,François Coste,Pierre Baldi:
  VIRALpro: a tool to identify viral capsid and tail sequences.1405-1407
• 
  Ning Leng,Jeea Choi,Li-Fang Chu,James A. Thomson,Christina Kendziorski,Ron M. Stewart:
  OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.1408-1410

Structural Bioinformatics

• 
  Karolis Uziela,Björn Wallner:
  ProQ2: estimation of model accuracy implemented in Rosetta.1411-1413
• 
  Josef Laimer,Julia Hiebl-Flach,Daniel Lengauer,Peter Lackner:
  MAESTROweb: a web server for structure-based protein stability prediction.1414-1416

Gene expression

• 
  Tikira Temu,Matthias Mann,Markus Räschle,Jürgen Cox:
  Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry.1417-1419

Genetics and Population Analysis

• 
  Seung Hwan Lee,Julius H. J. Van der Werf:
  MTG2: an efficient algorithm for multivariate linear mixed model analysis based on genomic information.1420-1422
• 
  Xiaowei Zhan,Youna Hu,Bingshan Li,Gonçalo R. Abecasis,Dajiang J. Liu:
  RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.1423-1426

Systems Biology

• 
  Oliver Philipp,Heinz D. Osiewacz,Ina Koch:
  Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.1427-1429

Data and Text Mining

• 
  Angie S. Hinrichs,Brian J. Raney,Matthew L. Speir,Brooke L. Rhead,Jonathan Casper,Donna Karolchik,Robert M. Kuhn,Kate R. Rosenbloom,Ann S. Zweig,David Haussler,W. James Kent:
  UCSC Data Integrator and Variant Annotation Integrator.1430-1432

Databases and Ontologies

• 
  Jian Yang,Gaofeng Deng,Haoyang Cai:
  ChromothripsisDB: a curated database of chromothripsis.1433-1435
• 
  Catherine Mooney,Brett A. Becker,Rana Raoof,David C. Henshall:
  EpimiRBase: a comprehensive database of microRNA-epilepsy associations.1436-1438

Bioimage Informatics

• 
  Andrea Vargas,Marc Angeli,Chiara Pastrello,Rosanne McQuaid,Han Li,Andrea Jurisicova,Igor Jurisica:
  Robust quantitative scratch assay.1439-1440

Volume 32, Number 10, May 2016

Discovery note
Sequence Analysis

• 
  Luis Sánchez-Pulido,Chris P. Ponting:
  Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad.1441-1445

Original Papers
Genome Analysis

• 
  Yongseok Park,Hao Wu:
  Differential methylation analysis for BS-seq data under general experimental design.1446-1453

Structural Bioinformatics

• 
  Christian D. Schenkelberg,Christopher Bystroff:
  Protein backbone ensemble generation explores the local structural space of unseen natural homologs.1454-1461
• 
  Benjamin Thomas Viart,Camila Dias-Lopes,Edgar Ernesto Gonzalez Kozlova,C. F. B. Oliveira,C. Nguyen,G. Neshich,Carlos Chávez-Olórtegui,F. Molina,Liza Figueredo Felicori:
  EPI-peptide designer: a tool for designing peptide ligand libraries based on epitope-paratope interactions.1462-1470
• 
  Sanjay Agravat,Xuezheng Song,Teerapat Rojsajjakul,Richard D. Cummings,David F. Smith:
  Computational approaches to define a human milk metaglycome.1471-1478

Gene expression

• 
  Halit Ongen,Alfonso Buil,Andrew Anand Brown,Emmanouil T. Dermitzakis,Olivier Delaneau:
  Fast and efficient QTL mapper for thousands of molecular phenotypes.1479-1485

Genetics and Population Analysis

• 
  Gabriel H. Murillo,Na You,Xiaoquan Su,Wei Cui,Muredach P. Reilly,Mingyao Li,Kang Ning,Xinping Cui:
  MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data.1486-1492
• 
  Christian Benner,Chris C. A. Spencer,Aki S. Havulinna,Veikko Salomaa,Samuli Ripatti,Matti Pirinen:
  FINEMAP: efficient variable selection using summary data from genome-wide association studies.1493-1501

Systems Biology

• 
  Daniel Stöckel,Tim Kehl,Patrick Trampert,Lara Schneider,Christina Backes,Nicole Ludwig,Andreas Gerasch,Michael Kaufmann,Manfred Gessler,Norbert M. Graf,Eckart Meese,Andreas Keller,Hans-Peter Lenhof:
  Multi-omics enrichment analysis using the GeneTrail2 web service.1502-1508
• 
  Zhen Niu,Deborah Chasman,Amie J. Eisfeld,Yoshihiro Kawaoka,Sushmita Roy:
  Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions.1509-1517
• 
  Muaaz Gul Awan,Fahad Saeed:
  MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing.1518-1526

Data and Text Mining

• 
  Martin Strazar,Marinka Zitnik,Blaz Zupan,Jernej Ule,Tomaz Curk:
  Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins.1527-1535

Databases and Ontologies

• 
  Raymond G. Cavalcante,Snehal Patil,Terry E. Weymouth,Kestutis G. Bendinskas,Alla Karnovsky,Maureen A. Sartor:
  ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts.1536-1543

Bioimage Informatics

• 
  Lei Du,Heng Huang,Jingwen Yan,Sungeun Kim,Shannon L. Risacher,Mark Inlow,Jason H. Moore,Andrew J. Saykin,Li Shen:
  Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method.1544-1551

Applications Notes
Genome Analysis

• 
  Ahmad Vaez,Peter J. van der Most,Bram P. Prins,Harold Snieder,Edwin R. van den Heuvel,Behrooz Z. Alizadeh,Ilja M. Nolte:
  lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection.1552-1554
• 
  Ge Tan,Boris Lenhard:
  TFBSTools: an R/bioconductor package for transcription factor binding site analysis.1555-1556
• 
  Karl W. Kroll,Ann-Katherin Eisfeld,Gerard Lozanski,Clara D. Bloomfield,John C. Byrd,James S. Blachly:
  MuCor: mutation aggregation and correlation.1557-1558

Sequence Analysis

• 
  Monica-Andreea Dragan,Ismail Moghul,Anurag Priyam,Claudio Bustos,Yannick Wurm:
  GeneValidator: identify problems with protein-coding gene predictions.1559-1561
• 
  Jorge González-Domínguez,Bertil Schmidt:
  ParDRe: faster parallel duplicated reads removal tool for sequencing studies.1562-1564
• 
  Erik Scott Wright,Kalin H. Vetsigian:
  DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures.1565-1567

Structural Bioinformatics

• 
  Matías R. Machado,Sergio Pantano:
  SIRAH tools: mapping, backmapping and visualization of coarse-grained models.1568-1570
• 
  Sikander Hayat,Christoph Peters,Nanjiang Shu,Konstantinos D. Tsirigos,Arne Elofsson:
  Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.1571-1573
• 
  Shuai Li,Qiancheng Shen,Minyi Su,Xinyi Liu,Shaoyong Lu,Zhongjie Chen,Renxiao Wang,Jian Zhang:
  Alloscore: a method for predicting allosteric ligand-protein interactions.1574-1576

Gene expression

• 
  Michael Turewicz,Maike Ahrens,Caroline May,Katrin Marcus,Martin Eisenacher:
  PAA: an R/bioconductor package for biomarker discovery with protein microarrays.1577-1579

Genetics and Population Analysis

• 
  Kelly M. Burkett,Brad McNeney,Jinko Graham:
  Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data.1580-1582
• 
  Johannes Rainer,Daniel Taliun,Yuri D'Elia,Cristian Pattaro,Francisco S. Domingues,Christian X. Weichenberger:
  FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees.1583-1585

Systems Biology

• 
  Frank T. Bergmann,Sven Sahle,Christoph Zimmer:
  Piecewise parameter estimation for stochastic models in COPASI.1586-1588
• 
  Daniel K. Witvliet,Alexey Strokach,Andrés Felipe Giraldo-Forero,Joan Teyra,Recep Colak,Philip M. Kim:
  ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity.1589-1591

Data and Text Mining

• 
  Magnus D. Vigeland,Kristina S. Gjøtterud,Kaja K. Selmer:
  FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector.1592-1594

Databases and Ontologies

• 
  Yining Liu,Min Zhao:
  lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes.1595-1597
• 
  Michael J. Meyer,Philip Geske,Haiyuan Yu:
  BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.1598-1600

Volume 32, Number 11, June 2016

Hitseq Papers
Genome Analysis

• 
  Caleb Weinreb,Benjamin J. Raphael:
  Identification of hierarchical chromatin domains.1601-1609
• 
  Yuri Pirola,Simone Zaccaria,Riccardo Dondi,Gunnar W. Klau,Nadia Pisanti,Paola Bonizzoni:
  HapCol: accurate and memory-efficient haplotype assembly from long reads.1610-1617
• 
  Faezeh Dorri,Lee Mendelowitz,Héctor Corrada Bravo:
  methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.1618-1624

Sequence Analysis

• 
  Bo Liu,Dengfeng Guan,Mingxiang Teng,Yadong Wang:
  rHAT: fast alignment of noisy long reads with regional hashing.1625-1631
• 
  Hongyi Xin,Sunny Nahar,Richard L. Zhu,John Emmons,Gennady Pekhimenko,Carl Kingsford,Can Alkan,Onur Mutlu:
  Optimal seed solver: optimizing seed selection in read mapping.1632-1642
• 
  Sunho Park,Seung-Jun Kim,Donghyeon Yu,Samuel Peña-Llopis,Jianjiong Gao,Jinsuk Park,Beibei Chen,Jessie Norris,Xinlei Wang,Min Chen,Min-Su Kim,Jeongsik Yong,Zabi Wardak,Kevin Choe,Michael Story,Timothy K. Starr,Jae-Ho Cheong,TaeHyun Hwang:
  An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types.1643-1651
• 
  Kana Shimizu,Koji Nuida,Gunnar Rätsch:
  Efficient privacy-preserving string search and an application in genomics.1652-1661
• 
  Aryan Arbabi,Ladislav Rampásek,Michael Brudno:
  Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.1662-1669
• 
  Dilip A. Durai,Marcel H. Schulz:
  Informedkmer selection forde novo transcriptome assembly.1670-1677

Gene expression

• 
  Ali May,Bernd W. Brandt,Mohammed El-Kebir,Gunnar W. Klau,Egija Zaura,Wim Crielaard,Jaap Heringa,Sanne Abeln:
  metaModules identifies key functional subnetworks in microbiome-related disease.1678-1685

Genetics and Population Analysis

• 
  Lin Huang,Bo Wang,Ruitang Chen,Sivan Bercovici,Serafim Batzoglou:
  Reveel: large-scale population genotyping using low-coverage sequencing data.1686-1696

Discovery note
Genome Analysis

• 
  Anna Hakobyan,Lilit Nersisyan,Arsen Arakelyan:
  Quantitative trait association study for mean telomere length in the South Asian genomes.1697-1700

Original Papers
Genome Analysis

• 
  Fangfang Liu,Chong Wang,Zuowei Wu,Qijing Zhang,Peng Liu:
  A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data.1701-1708

Structural Bioinformatics

• 
  Seungpyo Hong,Dongsup Kim:
  Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds.1709-1715

Gene expression

• 
  Vered Madar,Sandra Batista:
  FastLSU: a more practical approach for the Benjamini-Hochberg FDR controlling procedure for huge-scale testing problems.1716-1723
• 
  Jinyu Chen,Shihua Zhang:
  Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data.1724-1732

Systems Biology

• 
  Mattia Zampieri,Uwe Sauer:
  Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems.1733-1739

Applications Notes
Genome Analysis

• 
  Ya Cui,Xiaowei Chen,Huaxia Luo,Zhen Fan,Jianjun Luo,Shunmin He,Haiyan Yue,Peng Zhang,Runsheng Chen:
  BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.1740-1742
• 
  Claus Børnich,Ivar Grytten,Eivind Hovig,Jonas Paulsen,Martin Cech,Geir Kjetil Sandve:
  Galaxy Portal: interacting with the galaxy platform through mobile devices.1743-1745

Gene expression

• 
  Bart Mesuere,Toon Willems,Felix Van der Jeugt,Bart Devreese,Peter Vandamme,Peter Dawyndt:
  Unipept web services for metaproteomics analysis.1746-1748

Genetics and Population Analysis

• 
  Vagheesh Narasimhan,Petr Danecek,Aylwyn Scally,Yali Xue,Chris Tyler-Smith,Richard Durbin:
  BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.1749-1751

Databases and Ontologies

• 
  Zhihong Liu,Peng Ding,Xin Yan,Minghao Zheng,Huihao Zhou,Yuehua Xu,Yunfei Du,Qiong Gu,Jun Xu:
  ASDB: a resource for probing protein functions with small molecules.1752-1754
• 
  Javier Otegui,Robert P. Guralnick:
  The geospatial data quality REST API for primary biodiversity data.1755-1757

Message from the ISCB
Databases and Ontologies

• 
  Christiana N. Fogg,Diane E. Kovats:
  Message from the ISCB: 2016 ISCB Accomplishment by a Senior Scientist Award Given to Søren Brunak.1758-1759
• 
  Christiana N. Fogg,Diane E. Kovats:
  Message from the ISCB: 2016 Outstanding Contributions to ISCB Award: Burkhard Rost.1760

Volume 32, Number 12, June 2016

Ismb 2016 Proceedings July 8 to July 12, 2016, Orlando, Florida
Editorial

• 
  Pierre Baldi,Teresa M. Przytycka:
  ISMB 2016 Proceedings.1-2

Applied Bioinformatics

• 
  Forest Agostinelli,Nicholas Ceglia,Babak Shahbaba,Paolo Sassone-Corsi,Pierre Baldi:
  What time is it? Deep learning approaches for circadian rhythms.8-17
• 
  Qingjun Yuan,Junning Gao,Dongliang Wu,Shihua Zhang,Hiroshi Mamitsuka,Shanfeng Zhu:
  DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.18-27
• 
  Céline Brouard,Huibin Shen,Kai Dührkop,Florence d'Alché-Buc,Sebastian Böcker,Juho Rousu:
  Fast metabolite identification with Input Output Kernel Regression.28-36
• 
  Dan He,David Kuhn,Laxmi Parida:
  Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction.37-43

Bioimaging

• 
  Yue Deng,Steven J. Altschuler,Lani F. Wu:
  PHOCOS: inferring multi-feature phenotypic crosstalk networks.44-51
• 
  Oren Z. Kraus,Lei Jimmy Ba,Brendan J. Frey:
  Classifying and segmenting microscopy images with deep multiple instance learning.52-59

Databases, Ontologies & Text Mining

• 
  Reza Haydarlou,Annika Jacobsen,Nicola Bonzanni,K. Anton Feenstra,Sanne Abeln,Jaap Heringa:
  BioASF: a framework for automatically generating executable pathway models specified in BioPAX.60-69
• 
  Shengwen Peng,Ronghui You,Hongning Wang,Chengxiang Zhai,Hiroshi Mamitsuka,Shanfeng Zhu:
  DeepMeSH: deep semantic representation for improving large-scale MeSH indexing.70-79

Disease Models & Epidemiology

• 
  A. Grant Schissler,Qike Li,James L. Chen,Colleen Kenost,Ikbel Achour,Dean Billheimer,Haiquan Li,Walter W. Piegorsch,Yves A. Lussier:
  Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells.80-89
• 
  Marinka Zitnik,Blaz Zupan:
  Jumping across biomedical contexts using compressive data fusion.90-100
• 
  Benjamin S. Glicksberg,Li Li,Marcus A. Badgeley,Khader Shameer,Roman Kosoy,Noam D. Beckmann,Nam Pho,Jörg Hakenberg,Meng Ma,Kristin L. Ayers,Gabriel E. Hoffman,Shuyu Dan Li,Eric E. Schadt,Chirag J. Patel,Rong Chen,Joel T. Dudley:
  Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.101-110

Gene regulation

• 
  Xihao Hu,Christina Huan Shi,Kevin Y. Yip:
  A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps.111-120
• 
  Haoyang Zeng,Matthew D. Edwards,Ge Liu,David K. Gifford:
  Convolutional neural network architectures for predicting DNA-protein binding.121-127
• 
  Kyuri Jo,Inuk Jung,Ji Hwan Moon,Sun Kim:
  Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways.128-136
• 
  Jiangwen Sun,Zongliang Jiang,Xiuchun Tian,Jinbo Bi:
  A cross-species bi-clustering approach to identifying conserved co-regulated genes.137-146
• 
  Hande Topa,Antti Honkela:
  Analysis of differential splicing suggests different modes of short-term splicing regulation.147-155
• 
  Dat Duong,Jennifer Zou,Farhad Hormozdiari,Jae Hoon Sul,Jason Ernst,Buhm Han,Eleazar Eskin:
  Using genomic annotations increases statistical power to detect eGenes.156-163
• 
  Seunghak Lee,Soonho Kong,Eric P. Xing:
  A network-driven approach for genome-wide association mapping.164-173

Gene / protein sequence Analysis

• 
  Bo Liu,Dixian Zhu,Yadong Wang:
  deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding.174-182
• 
  Tzu-Yu Liu,Yun S. Song:
  Prediction of ribosome footprint profile shapes from transcript sequences.183-191
• 
  Avi Srivastava,Hirak Sarkar,Nitish Gupta,Rob Patro:
  RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.192-200
• 
  Rayan Chikhi,Antoine Limasset,Paul Medvedev:
  Compacting de Bruijn graphs from sequencing data quickly and in low memory.201-208
• 
  Carly E. Schaeffer,Nathaniel D. Figueroa,Xiaolin Liu,John E. Karro:
  phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.209-215
• 
  Volodymyr Kuleshov,Michael P. Snyder,Serafim Batzoglou:
  Genome assembly from synthetic long read clouds.216-224

Population genomics

• 
  Yufeng Wu:
  An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.225-233
• 
  Shilpa Garg,Marcel Martin,Tobias Marschall:
  Read-based phasing of related individuals.234-242

Protein Interactions & molecular Networks

• 
  Shahin Mohammadi,Ananth Grama:
  A convex optimization approach for identification of human tissue-specific interactomes.243-252
• 
  Siddhartha Jain,Joel Arrais,Narasimhan J. Venkatachari,Velpandi Ayyavoo,Ziv Bar-Joseph:
  Reconstructing the temporal progression of HIV-1 immune response pathways.253-261
• 
  Sankar Basu,Björn Wallner:
  Finding correct protein-protein docking models using ProQDock.262-270
• 
  Arnon Mazza,Konrad Klockmeier,Erich E. Wanker,Roded Sharan:
  An integer programming framework for inferring disease complexes from network data.271-277
• 
  Yasuo Tabei,Yoshihiro Yamanishi,Masaaki Kotera:
  Simultaneous prediction of enzyme orthologs from chemical transformation patterns forde novo metabolic pathway reconstruction.278-287
• 
  Jukka Intosalmi,Kari Nousiainen,Helena Ahlfors,Harri Lähdesmäki:
  Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks.288-296
• 
  Ewa Szczurek,Niko Beerenwinkel:
  Linear effects models of signaling pathways from combinatorial perturbation data.297-305

Protein Structure & Function

• 
  Alvin Farrel,Jonathan Murphy,Jun-tao Guo:
  Structure-based prediction of transcription factor binding specificity using an integrative energy function.306-313
• 
  Michal Jamróz,Andrzej Kolinski,Daisuke Kihara:
  Ensemble-based evaluation for protein structure models.314-321
• 
  Shengjie Wang,John T. Halloran,Jeff A. Bilmes,William S. Noble:
  Faster and more accurate graphical model identification of tandem mass spectra using trellises.322-331
• 
  Xuefeng Cui,Zhiwu Lu,Sheng Wang,Jim Jing-Yan Wang,Xin Gao:
  CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.332-340
• 
  Fanchi Meng,Lukasz A. Kurgan:
  DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences.341-350

Rna Bioinformatics

• 
  Yaron Orenstein,Yuhao Wang,Bonnie Berger:
  RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.351-359
• 
  Juan Antonio García-Martín,Iván Dotú,Javier Fernandez-Chamorro,Gloria Lozano,Jorge Ramajo,Encarnacion Martinez-Salas,Peter Clote:
  RNAiFold2T: Constraint Programming design of thermo-IRES switches.360-368
• 
  Mariko Tsuchiya,Kojiro Amano,Masaya Abe,Misato Seki,Sumitaka Hase,Kengo Sato,Yasubumi Sakakibara:
  SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.369-377
• 
  Xiaodong Cui,Jia Meng,Shaowu Zhang,Yidong Chen,Yufei Huang:
  A novel algorithm for calling mRNA m⁶A peaks by modeling biological variances in MeRIP-seq data.378-385

Discovery note
Systems Biology

• 
  Monica Chagoyen,Florencio Pazos:
  Characterization of clinical signs in the human interactome.1761-1765

Original Papers
Genome Analysis

• 
  Yingying Wei,Hao Wu:
  Measuring the spatial correlations of protein binding sites.1766-1772
• 
  Shicai Fan,Chengzhe Li,Rizi Ai,Mengchi Wang,Gary S. Firestein,Wei Wang:
  Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis.1773-1778

Sequence Analysis

• 
  Magali Jaillard,Maud Tournoud,Faustine Meynier,Jean-Baptiste Veyrieras:
  Optimization of alignment-based methods for taxonomic binning of metagenomics reads.1779-1787
• 
  Zhen Zhang,Jianxin Wang,Junwei Luo,Xiaojun Ding,Jiancheng Zhong,Jun Wang,Fang-Xiang Wu,Yi Pan:
  Sprites: detection of deletions from sequencing data by re-aligning split reads.1788-1796
• 
  Daniele Raimondi,Andrea M. Gazzo,Marianne Rooman,Tom Lenaerts,Wim F. Vranken:
  Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects.1797-1804

Structural Bioinformatics

• 
  Juan P. Bustamante,María E. Szretter,Mariela Sued,Marcelo A. Marti,Dario A. Estrin,Leonardo Boechi:
  A quantitative model for oxygen uptake and release in a family of hemeproteins.1805-1813

Gene expression

• 
  Victor L. Jong,Putri W. Novianti,Kit C. B. Roes,Marinus J. C. Eijkemans:
  Selecting a classification function for class prediction with gene expression data.1814-1822
• 
  Jie Zhang,Zhi Wei:
  An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing.1823-1831
• 
  Yifei Chen,Yi Li,Rajiv Narayan,Aravind Subramanian,Xiaohui Xie:
  Gene expression inference with deep learning.1832-1839
• 
  André Kahles,Cheng Soon Ong,Yi Zhong,Gunnar Rätsch:
  SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.1840-1847

Genetics and Population Analysis

• 
  Pei-Yuan Sung,Yi-Ting Wang,Ya-Wen Yu,Ren-Hua Chung:
  An efficient gene-gene interaction test for genome-wide association studies in trio families.1848-1855
• 
  Jin Liu,Xiang Wan,Shuangge Ma,Can Yang:
  EPS: an empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes.1856-1864

Systems Biology

• 
  Shobhit Jain,Gary D. Bader:
  Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.1865-1872

Data and Text Mining

• 
  Justin Wagner,Joseph N. Paulson,Xiao Wang,Bobby Bhattacharjee,Héctor Corrada Bravo:
  Privacy-preserving microbiome analysis using secure computation.1873-1879

Applications Notes
Sequence Analysis

• 
  Hao Wang,Joel McManus,Carl Kingsford:
  Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.1880-1882
• 
  Alastair P. Droop:
  fqtools: an efficient software suite for modern FASTQ file manipulation.1883-1884

Structural Bioinformatics

• 
  José Augusto Salim,Luiz C. Borro,Ivan Mazoni,Inácio Yano,José G. Jardine,Goran Neshich:
  Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.1885-1887
• 
  Sabine C. Mueller,Christina Backes,Alexander Greß,Nina Baumgarten,Olga V. Kalinina,Andreas Moll,Oliver Kohlbacher,Eckart Meese,Andreas Keller:
  BALL-SNPgp - from genetic variants toward computational diagnostics.1888-1890

Gene expression

• 
  Florian Schmid,Matthias Schmid,Christoph Müssel,J. Eric Sträng,Christian Buske,Lars Bullinger,Johann M. Kraus,Hans A. Kestler:
  GiANT: gene set uncertainty in enrichment analysis.1891-1894

Genetics and Population Analysis

• 
  Michael Degiorgio,Christian D. Huber,Melissa J. Hubisz,Ines Hellmann,Rasmus Nielsen:
  SweepFinder2: increased sensitivity, robustness and flexibility.1895-1897
• 
  Luke Jostins,Gilean McVean:
  Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes.1898-1900
• 
  Andrey Ziyatdinov,Helena Brunel,Angel Martinez-Perez,Alfonso Buil,Alexandre Perera,José Manuel Soria:
  solarius: an R interface to SOLAR for variance component analysis in pedigrees.1901-1902
• 
  Paul R. Staab,Dirk Metzler:
  Coala: an R framework for coalescent simulation.1903-1904

Systems Biology

• 
  Harold F. Gómez,Michael Hucka,Sarah M. Keating,German Nudelman,Dagmar Iber,Stuart C. Sealfon:
  MOCCASIN: converting MATLAB ODE models to SBML.1905-1906

Data and Text Mining

• 
  Chih-Hsuan Wei,Robert Leaman,Zhiyong Lu:
  Beyond accuracy: creating interoperable and scalable text-mining web services.1907-1910
• 
  Luca De Sano,Giulio Caravagna,Daniele Ramazzotti,Alex Graudenzi,Giancarlo Mauri,Bud Mishra,Marco Antoniotti:
  TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.1911-1913

Database and Ontologies

• 
  Pengbo Wen,Peng Xiao,Junfeng Xia:
  dbDSM: a manually curated database for deleterious synonymous mutations.1914-1916

Bioimage Informatics

• 
  Jonathan W. Armond,Elina Vladimirou,Andrew D. McAinsh,Nigel J. Burroughs:
  KiT: a MATLAB package for kinetochore tracking.1917-1919

Volume 32, Number 13, July 2016

Discovery note
Genome Analysis

• 
  Volkan Sevim,Ali Bashir,Chen-Shan Chin,Karen H. Miga:
  Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing.1921-1924

Original Papers
Genome Analysis

• 
  Kristoffer Sahlin,Rayan Chikhi,Lars Arvestad:
  Assembly scaffolding with PE-contaminated mate-pair libraries.1925-1932

Sequence Analysis

• 
  Kazutaka Katoh,Daron M. Standley:
  A simple method to control over-alignment in the MAFFT multiple sequence alignment program.1933-1942
• 
  Yuval Elhanati,Quentin Marcou,Thierry Mora,Aleksandra M. Walczak:
  repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.1943-1951
• 
  François D. Richard,Ronnie Alves,Andrey V. Kajava:
  Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences.1952-1958

Gene expression

• 
  Alexander Lachmann,Federico M. Giorgi,Mariano J. Alvarez,Andrea Califano:
  Detection and removal of spatial bias in multiwell assays.1959-1965
• 
  Sunghwan Kim,Chien-Wei Lin,George C. Tseng:
  MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis.1966-1973

Genetics and Population Analysis

• 
  Kevin Sharp,Warren Kretzschmar,Olivier Delaneau,Jonathan Marchini:
  Phasing for medical sequencing using rare variants and large haplotype reference panels.1974-1980
• 
  Anna Cichonska,Juho Rousu,Pekka Marttinen,Antti J. Kangas,Pasi Soininen,Terho Lehtimäki,Olli T. Raitakari,Marjo-Riitta Järvelin,Veikko Salomaa,Mika Ala-Korpela,Samuli Ripatti,Matti Pirinen:
  metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.1981-1989
• 
  Laura Buzdugan,Markus Kalisch,Arcadi Navarro,Daniel Schunk,Ernst Fehr,Peter Bühlmann:
  Assessing statistical significance in multivariable genome wide association analysis.1990-2000

Systems Biology

• 
  Luis Tobalina,Jon Pey,Francisco J. Planes:
  Direct calculation of minimal cut sets involving a specific reaction knock-out.2001-2007
• 
  Alexander Eng,Elhanan Borenstein:
  An algorithm for designing minimal microbial communities with desired metabolic capacities.2008-2016

Databases and Ontologies

• 
  Jeongbin Park,Jin-Soo Kim,Sangsu Bae:
  Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9.2017-2023

Applications Notes
Genome Analysis

• 
  Kenneth A. Watanabe,Kaiwang Ma,Arielle Homayouni,Paul J. Rushton,Qingxi J. Shen:
  Transcript structure and domain display: a customizable transcript visualization tool.2024-2025
• 
  James G. Lamine,Randall J. DeJong,Serita M. Nelesen:
  PhamDB: a web-based application for building Phamerator databases.2026-2028
• 
  Jeremiah A. Wala,Cheng-Zhong Zhang,Matthew Meyerson,Rameen Beroukhim:
  VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.2029-2031

Sequence Analysis

• 
  Yang Yang,Abhishek Niroula,Bairong Shen,Mauno Vihinen:
  PON-Sol: prediction of effects of amino acid substitutions on protein solubility.2032-2034
• 
  Susan K. Van Riper,LeeAnn Higgins,John V. Carlis,Timothy J. Griffin:
  RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification.2035-2037
• 
  Federico Mattiello,Bie M. P. Verbist,Karoline Faust,Jeroen Raes,William D. Shannon,Luc Bijnens,Olivier Thas:
  A web application for sample size and power calculation in case-control microbiome studies.2038-2040
• 
  Chuming Chen,Hongzhan Huang,Raja Mazumder,Darren A. Natale,Peter B. McGarvey,Jian Zhang,Shawn W. Polson,Yuqi Wang,Cathy H. Wu:
  Computational clustering for viral reference proteomes.2041-2043
• 
  Benjamin Schubert,Mathias Walzer,Hans-Philipp Brachvogel,András Szolek,Christopher Mohr,Oliver Kohlbacher:
  FRED 2: an immunoinformatics framework for Python.2044-2046
• 
  Samuel M. Nicholls,Amanda Clare,Joshua C. Randall:
  Goldilocks: a tool for identifying genomic regions that are 'just right'.2047-2049
• 
  Baekdoo Kim,Thahmina Ali,Samuel Hosmer,Konstantinos Krampis:
  Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.2050-2052
• 
  Alexander Ekstrom,Yanbin Yin:
  ORFanFinder: automated identification of taxonomically restricted orphan genes.2053-2055

Phylogenetics

• 
  Edwin Jacox,Cédric Chauve,Gergely J. Szöllosi,Yann Ponty,Céline Scornavacca:
  ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.2056-2058

Structural Bioinformatics

• 
  Debswapna Bhattacharya,Badri Adhikari,Jilong Li,Jianlin Cheng:
  FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.2059-2061
• 
  Alejandro Panjkovich,Dmitri I. Svergun:
  SASpy: a PyMOL plugin for manipulation and refinement of hybrid models against small angle X-ray scattering data.2062-2064

Systems Biology

• 
  Syed Asad Rahman,Gilliean Torrance,Lorenzo Baldacci,Sergio Martínez Cuesta,Franz Fenninger,Nimish Gopal,Saket Choudhary,John W. May,Gemma L. Holliday,Christoph Steinbeck,Janet M. Thornton:
  Reaction Decoder Tool (RDT): extracting features from chemical reactions.2065-2066
• 
  Ahmed Mohamed,Canh Hao Nguyen,Hiroshi Mamitsuka:
  NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.2067-2068

Data and Text Mining

• 
  Yuanwei Zhang,Qiguang Zang,Bo Xu,Wei Zheng,Rongjun Ban,Huan Zhang,Yifan Yang,QiaoMei Hao,Furhan Iqbal,Ao Li,Qinghua Shi:
  IsomiR Bank: a research resource for tracking IsomiRs.2069-2071
• 
  Karthik Gangavarapu,Vyshakh Babji,Tobias Meißner,Andrew I. Su,Benjamin M. Good:
  Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.2072-2074

Bioimage Informatics

• 
  Laurent Gole,Kok Haur Ong,Thomas Boudier,Weimiao Yu,Sohail Ahmed:
  OpenSegSPIM: a user-friendly segmentation tool for SPIM data.2075-2077

Data and Text Mining

• 
  Ognjen Arandjelovic:
  On the discovery of hospital admission patterns - a clarification.2078
• 
  Guillermo López-Campos,Fernando José Martín-Sánchez,Kathleen Gray:
  Comment on 'Discovering hospital admission patterns using models learnt from electronic hospital records'. The importance of using the right codes.2079-2080

Corrigendum
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.2081

Volume 32, Number 14, July 2016

Discovery note
Systems Biology

• 
  Yuta Narushima,Hiroko Kozuka-Hata,Kouhei Tsumoto,Jun-Ichiro Inoue,Masaaki Oyama:
  Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome analysis.2083-2088

Original Papers
Genome Analysis

• 
  Nowlan H. Freese,David C. Norris,Ann E. Loraine:
  Integrated genome browser: visual analytics platform for genomics.2089-2095
• 
  Filipe G. Vieira,Anders Albrechtsen,Rasmus Nielsen:
  Estimating IBD tracts from low coverage NGS data.2096-2102

Sequence Analysis

• 
  Heng Li:
  Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.2103-2110

Genome expression

• 
  Yann Christinat,Rafal Pawlowski,Wilhelm Krek:
  jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data.2111-2119
• 
  Heeju Noh,Rudiyanto Gunawan:
  Inferring gene targets of drugs and chemical compounds from gene expression profiles.2120-2127
• 
  Trung-Nghia Vu,Quin F. Wills,Krishna R. Kalari,Nifang Niu,Liewei Wang,Mattias Rantalainen,Yudi Pawitan:
  Beta-Poisson model for single-cell RNA-seq data analyses.2128-2135

Genetics and Population Analysis

• 
  André Lacour,David Ellinghaus,Stefan Schreiber,Andre Franke,Tim Becker:
  Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci.2136-2142

Systems Biology

• 
  Pei Chen,Rui Liu,Yongjun Li,Luonan Chen:
  Detecting critical state before phase transition of complex biological systems by hidden Markov model.2143-2150
• 
  Jie Chen,Alfred O. Hero III,Indika Rajapakse:
  Spectral identification of topological domains.2151-2158
• 
  Vincenzo Bonnici,Federico Busato,Giovanni Micale,Nicola Bombieri,Alfredo Pulvirenti,Rosalba Giugno:
  APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks.2159-2166

Data and Text Mining

• 
  Charles Blatti,Saurabh Sinha:
  Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.2167-2175

Databases and Ontologies

• 
  Chao Pang,David van Enckevort,Mark de Haan,Fleur D. L. Kelpin,Jonathan Jetten,Dennis Hendriksen,Tommy de Boer,Bart Charbon,Erwin Winder,K. Joeri van der Velde,Dany Doiron,Isabel Fortier,Hans L. Hillege,Morris A. Swertz:
  MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.2176-2183

Bioimage Informatics

• 
  Ying-Ying Xu,Fan Yang,Hong-Bin Shen:
  Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.2184-2192

Applications Notes
Genome Analysis

• 
  Anestis Touloumis,John C. Marioni,Simon Tavaré:
  HDTD: analyzing multi-tissue gene expression data.2193-2195

Sequence Analysis

• 
  Dongwon Lee:
  LS-GKM: a new gkm-SVM for large-scale datasets.2196-2198
• 
  Andreas Bremges,Esther Singer,Tanja Woyke,Alexander Sczyrba:
  MeCorS: Metagenome-enabled error correction of single cell sequencing reads.2199-2201
• 
  Birte Kehr,Páll Melsted:
  chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts.2202-2204
• 
  Mahmoud Ghandi,Morteza Mohammad Noori,Narges Ghareghani,Dongwon Lee,Levi A. Garraway,Michael A. Beer:
  gkmSVM: an R package for gapped-kmer SVM.2205-2207
• 
  Christopher J. R. Illingworth:
  SAMFIRE: multi-locus variant calling for time-resolved sequence data.2208-2209
• 
  Elena Bushmanova,Dmitry Antipov,Alla L. Lapidus,Vladimir Suvorov,Andrey D. Prjibelski:
  rnaQUAST: a quality assessment tool forde novo transcriptome assemblies.2210-2212

Structural Bioinformatics

• 
  Oz Solomon,Eran Eyal,Ninette Amariglio,Ron Unger,Gidi Rechavi:
  e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures.2213-2215
• 
  Hui Liu,Tingjun Hou:
  CaFE: a tool for binding affinity prediction using end-point free energy methods.2216-2218

Gene expression

• 
  Aaron Diaz,Siyuan J. Liu,Carmen Sandoval,Alex A. Pollen,Tom J. Nowakowski,Daniel A. Lim,Arnold Kriegstein:
  SCell: integrated analysis of single-cell RNA-seq data.2219-2220
• 
  Xiao Huo,Sheng'en Hu,Chengchen Zhao,Yong Zhang:
  Dr.seq: a quality control and analysis pipeline for droplet sequencing.2221-2223

Genetics and Population Analysis

• 
  Sophie Limou,Andrew M. Taverner,Cheryl A. Winkler:
  Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project.2224-2226
• 
  Qian S. Zhang,Brian L. Browning,Sharon R. Browning:
  ASAFE: ancestry-specific allele frequency estimation.2227-2229
• 
  Haiming Tang,Paul D. Thomas:
  PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.2230-2232

Systems Biology

• 
  Alexander Lachmann,Federico M. Giorgi,Gonzalo López,Andrea Califano:
  ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.2233-2235

Databases and Ontologies

• 
  Núria Queralt-Rosinach,Janet Piñero González,Àlex Bravo,Ferran Sanz,Laura I. Furlong:
  DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.2236-2238

Bioimage Informatics

• 
  Leonid Andronov,Yves Lutz,Jean-Luc Vonesch,Bruno P. Klaholz:
  SharpViSu: integrated analysis and segmentation of super-resolution microscopy data.2239-2241

Corrigendum

• 
  Brendan O'Fallon:
  TreesimJ: a flexible, forward time population genetic simulator.2242

Volume 32, Number 15, August 2016

Discovery note
Sequence Analysis

• 
  Can Firtina,Can Alkan:
  On genomic repeats and reproducibility.2243-2247

Original Papers
Genome Analysis

• 
  Yusuke Matsui,Masahiro Mizuta,Satoshi Ito,Satoru Miyano,Teppei Shimamura:
  D³M: detection of differential distributions of methylation levels.2248-2255
• 
  Mikhail G. Dozmorov,Lukas R. Cara,Cory B. Giles,Jonathan D. Wren:
  GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.2256-2263

Sequence Analysis

• 
  Tunca Dogan,Alistair MacDougall,Rabie Saidi,Diego Poggioli,Alex Bateman,Claire O'Donovan,Maria Jesus Martin:
  UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.2264-2271
• 
  Vitor Piro,Martin S. Lindner,Bernhard Y. Renard:
  DUDes: a top-down taxonomic profiler for metagenomics.2272-2280
• 
  Ishita K. Khan,Daisuke Kihara:
  Genome-scale prediction of moonlighting proteins using diverse protein association information.2281-2288

Structural Bioinformatics

• 
  Daniel Zaidman,Haim J. Wolfson:
  PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm.2289-2296
• 
  Sumanta Mukherjee,Chiranjib Bhattacharyya,Nagasuma Chandra:
  HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials.2297-2305

Genetics and Population Analysis

• 
  Rudy Arthur,Jared O'Connell,Ole Schulz-Trieglaff,Anthony J. Cox:
  Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.2306-2312

Systems Biology

• 
  Hao Zhu,Markus R. Owen,Yanlan Mao:
  The spatiotemporal order of signaling events unveils the logic of development signaling.2313-2320
• 
  Sabrina Hross,Jan Hasenauer:
  Analysis of CFSE time-series data using division-, age- and label-structured population models.2321-2329
• 
  Pedro A. Saa,Lars Keld Nielsen:
  ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks.2330-2337
• 
  Zichen Wang,Neil R. Clark,Avi Ma'ayan:
  Drug-induced adverse events prediction with the LINCS L1000 data.2338-2345

Data and Text Mining

• 
  Ying Yang,Xiaotao Jiang,Benli Chai,Liping Ma,Bing Li,Anni Zhang,James R. Cole,James M. Tiedje,Tong Zhang:
  ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database.2346-2351

Bioimage Informatics

• 
  Ahmed Fakhry,Hanchuan Peng,Shuiwang Ji:
  Deep models for brain EM image segmentation: novel insights and improved performance.2352-2358

Applications Notes
Genome Analysis

• 
  Christian Arnold,Pooja Bhat,Judith B. Zaugg:
  SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.2359-2360
• 
  Mariusz Butkiewicz,Jessica Cooke Bailey,Alex T. Frase,Scott M. Dudek,Brian L. Yaspan,Marylyn D. Ritchie,Sarah A. Pendergrass,Jonathan L. Haines:
  Pathway analysis by randomization incorporating structure - PARIS: an update.2361-2363
• 
  Joshua Millstein,Gary K. Chen,Carrie V. Breton:
  cit: hypothesis testing software for mediation analysis in genomic applications.2364-2365
• 
  Karen Y. Oróstica,Ricardo A. Verdugo:
  chromPlot: visualization of genomic data in chromosomal context.2366-2368
• 
  Yun Heo,Anand Ramachandran,Wen-mei W. Hwu,Jian Ma,Deming Chen:
  BLESS 2: accurate, memory-efficient and fast error correction method.2369-2371
• 
  Zuguang Gu,Roland Eils,Matthias Schlesner:
  HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.2372-2374
• 
  Eric Roller,Sergii Ivakhno,Steve Lee,Thomas Royce,Stephen Tanner:
  Canvas: versatile and scalable detection of copy number variants.2375-2377
• 
  Dan Vanderkam,Bülent Arman Aksoy,Isaac Hodes,Jaclyn Perrone,Jeff Hammerbacher:
  pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.2378-2379

Sequence Analysis

• 
  Vladimir Novichkov,Anna Kaznadzey,Natalia Alexandrova,Denis Kaznadzey:
  NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy.2380-2381
• 
  Yi Wang,Vijay K. Tiwari,Nidhi Rawat,Bikram S. Gill,Naxin Huo,Frank M. You,Devin Coleman-Derr,Yong Qiang Gu:
  GSP: a web-based platform for designing genome-specific primers in polyploids.2382-2383
• 
  Christian Haider,Marina Kavic,Erik L. L. Sonnhammer:
  TreeDom: a graphical web tool for analysing domain architecture evolution.2384-2385

Structural Bioinformatics

• 
  Erney Ramírez-Aportela,José Ramón López-Blanco,Pablo Chacón:
  FRODOCK 2.0: fast protein-protein docking server.2386-2388

Genetics and Population Analysis

• 
  Lyndal Henden,David Wakeham,Melanie Bahlo:
  XIBD: software for inferring pairwise identity by descent on the X chromosome.2389-2391
• 
  Nadezhda M. Belonogova,Gulnara R. Svishcheva,Tatiana I. Axenovich:
  FREGAT: an R package for region-based association analysis.2392-2393

Systems Biology

• 
  Martin Lindén,Vladimir Curic,Alexis Boucharin,David Fange,Johan Elf:
  Simulated single molecule microscopy with SMeagol.2394-2395
• 
  Abdelrahman Hosny,Paola Vera-Licona,Reinhard C. Laubenbacher,Thibauld Favre:
  AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.2396-2398
• 
  Sufang Wang,Michael Gribskov,Tony R. Hazbun,Pete E. Pascuzzi:
  CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data.2399-2401

Corrigendum

• 
  Yuriy Hulovatyy,Huili Chen,Tijana Milenkovic:
  Exploring the structure and function of temporal networks with dynamic graphlets.2402

Volume 32, Number 16, August 2016

Originals Papers
Genome Analysis

• 
  Xu Hua,Luxiao Chen,Jin Wang,Jie Li,Edgar Wingender:
  Identifying cell-specific microRNA transcriptional start sites.2403-2410

Sequence Analysis

• 
  Bin Liu,Ren Long,Kuo-Chen Chou:
  iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.2411-2418
• 
  Aleksander Jankowski,Jerzy Tiuryn,Shyam Prabhakar:
  Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.2419-2426
• 
  En-Shiun Annie Lee,Fiona J. Whelan,Dawn M. E. Bowdish,Andrew K. C. Wong:
  Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters.2427-2434

Structural Bioinformatics

• 
  Jing Yang,Qi-Yu Jin,Biao Zhang,Hong-Bin Shen:
  R₂C: improvingab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter.2435-2443
• 
  Naama Hurwitz,Dina Schneidman-Duhovny,Haim J. Wolfson:
  Memdock: an α-helical membrane protein docking algorithm.2444-2450
• 
  Daisuke Kuroda,Jeffrey J. Gray:
  Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.2451-2456

Genetics and Population Analysis

• 
  Kerstin Bunte,Eemeli Leppäaho,Inka Saarinen,Samuel Kaski:
  Sparse group factor analysis for biclustering of multiple data sources.2457-2463

Systems Biology

• 
  Eva-Maria Geissen,Jan Hasenauer,Stephanie Heinrich,Silke Hauf,Fabian J. Theis,Nicole Radde:
  MEMO: multi-experiment mixture model analysis of censored data.2464-2472

Data and Text Mining

• 
  Gianni Monaco,Hao Chen,Michael Poidinger,Jinmiao Chen,João Pedro de Magalhães,Anis Larbi:
  flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.2473-2480

Databases and Ontologies

• 
  Venetia Pliatsika,Phillipe Loher,Aristeidis G. Telonis,Isidore Rigoutsos:
  MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.2481-2489

Bioimage Informatics

• 
  Subhadip Basu,Dariusz Plewczynski,Satadal Saha,Matylda Roszkowska,Marta Magnowska,Ewa Baczynska,Jakub Wlodarczyk:
  2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity.2490-2498

Applications Notes
Genome Analysis

• 
  Tarun Mall,John Eckstein,David C. Norris,Hiral Vora,Nowlan H. Freese,Ann E. Loraine:
  ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.2499-2501
• 
  Hyungro Lee,Min Su Lee,Wazim Mohammed Ismail,Mina Rho,Geoffrey C. Fox,Sangyoon Oh,Haixu Tang:
  MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.2502-2504
• 
  Eugene Andres Houseman,Kevin C. Johnson,Brock C. Christensen:
  OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA.2505-2507
• 
  William Chow,Kim Brügger,Mario Cáccamo,Ian Sealy,James W. Torrance,Kerstin Howe:
  gEVAL - a web-based browser for evaluating genome assemblies.2508-2510
• 
  E. C. Schofield,Tim Carver,Premanand Achuthan,P. Freire-Pritchett,Mikhail Spivakov,John A. Todd,Oliver S. Burren:
  CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.2511-2513
• 
  Peng Jiang,James A. Thomson,Ron M. Stewart:
  Quality control of single-cell RNA-seq by SinQC.2514-2516
• 
  Alexander J. Titus,Eugene Andres Houseman,Kevin C. Johnson,Brock C. Christensen:
  methyLiftover: cross-platform DNA methylation data integration.2517-2519
• 
  Jens Roat Kultima,Luís Pedro Coelho,Kristoffer Forslund,Jaime Huerta-Cepas,Simone S. Li,Marja Driessen,Anita Yvonne Voigt,Georg Zeller,Shinichi Sunagawa,Peer Bork:
  MOCAT2: a metagenomic assembly, annotation and profiling framework.2520-2523
• 
  Miguel Pignatelli:
  TnT: a set of libraries for visualizing trees and track-based annotations for the web.2524-2525

Sequence Analysis

• 
  Yousong Peng,Lei Yang,Honglei Li,Yuanqiang Zou,Lizong Deng,Aiping Wu,Xiangjun Du,Dayan Wang,Yuelong Shu,Taijiao Jiang:
  PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences.2526-2527
• 
  Romain Fenouil,Nicolas Descostes,Lionel Spinelli,Frederic Koch,Muhammad Ahmad Maqbool,Touati Benoukraf,Pierre Cauchy,Charlène Innocenti,Pierre Ferrier,Jean-Christophe Andrau:
  Pasha: a versatile R package for piling chromatin HTS data.2528-2530

Structural Bioinformatics

• 
  Kota Kasahara,Neetha Mohan,Ikuo Fukuda,Haruki Nakamura:
  mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.2531-2533
• 
  Hui-Chun Lu,Julián Herrera Braga,Franca Fraternali:
  PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.2534-2536
• 
  Jimmy C. F. Ngai,Pui-In Mak,Shirley W. I. Siu:
  ProtPOS: a python package for the prediction of protein preferred orientation on a surface.2537-2538
• 
  Erik Walinda,Daichi Morimoto,Mayu Nishizawa,Masahiro Shirakawa,Kenji Sugase:
  Efficient identification and analysis of chemical exchange in biomolecules byR_1ρ relaxation dispersion withAmaterasu.2539-2541
• 
  Castrense Savojardo,Piero Fariselli,Pier Luigi Martelli,Rita Casadio:
  INPS-MD: a web server to predict stability of protein variants from sequence and structure.2542-2544
• 
  Zachary Ziegler,Molly Schmidt,Thomas Gurry,Virginia Burger,Collin M. Stultz:
  Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins.2545-2547
• 
  Guillaume Postic,Yassine Ghouzam,Jean-Christophe Gelly:
  OREMPRO web server: orientation and assessment of atomistic and coarse-grained structures of membrane proteins.2548-2550

Gene expression

• 
  Abhinav Nellore,Christopher Wilks,Kasper D. Hansen,Jeffrey T. Leek,Ben Langmead:
  Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.2551-2553

Genetics and Population Analysis

• 
  Linda Odenthal-Hesse,Julien Y. Dutheil,Fabian Klötzl,Bernhard Haubold:
  hotspot: software to support sperm-typing for investigating recombination hotspots.2554-2555
• 
  Christine B. Peterson,M. Bogomolov,Yoav Benjamini,Chiara Sabatti:
  TreeQTL: hierarchical error control for eQTL findings.2556-2558

Systems Biology

• 
  Timo Lubitz,Jens Hahn,Frank T. Bergmann,Elad Noor,Edda Klipp,Wolfram Liebermeister:
  SBtab: a flexible table format for data exchange in systems biology.2559-2561

Data and Text Mining

• 
  Petar Velickovic,Pietro Liò:
  Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types.2562-2564

Corrigendum

• 
  Marta Rosikiewicz,Marc Robinson-Rechavi:
  IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.2565

Volume 32, Number 17, September 2016

ECCB 2016:The 15th European Conference on Computational Biology
Editorial

• 
  Jaap Heringa,Marcel J. T. Reinders,Sanne Abeln,Jeroen de Ridder:
  ECCB 2016: The 15th European Conference on Computational Biology.389-392

Data

• 
  Michael Lenz,Nadia J. T. Roumans,Roel G. Vink,Marleen A. van Baak,Edwin C. M. Mariman,Ilja C. W. Arts,Theo M. de Kok,Gökhan Ertaylan:
  Estimating real cell size distribution from cross-section microscopy imaging.396-404
• 
  Chantriolnt-Andreas Kapourani,Guido Sanguinetti:
  Higher order methylation features for clustering and prediction in epigenomic studies.405-412
• 
  Nanne Aben,Daniel J. Vis,Magali Michaut,Lodewyk F. A. Wessels:
  TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.413-420
• 
  Charles J. Labuzzetta,Margaret L. Antonio,Patricia M. Watson,Robert C. Wilson,Lauren A. Laboissonniere,Jeffrey M. Trimarchi,Baris Genc,P. Hande Ozdinler,Dennis K. Watson,Paul E. Anderson:
  Complementary feature selection from alternative splicing events and gene expression for phenotype prediction.421-429
• 
  William Poole,David L. Gibbs,Ilya Shmulevich,Brady Bernard,Theo A. Knijnenburg:
  Combining dependentP-values with an empirical adaptation of Brown's method.430-436
• 
  Sunjoo Bang,Jae-Hoon Kim,Hyunjung Shin:
  Causality modeling for directed disease network.437-444
• 
  Thanh Le Van,Matthijs van Leeuwen,Ana Carolina Fierro,Dries De Maeyer,Jimmy Van den Eynden,Lieven P. C. Verbeke,Luc De Raedt,Kathleen Marchal,Siegfried Nijssen:
  Simultaneous discovery of cancer subtypes and subtype features by molecular data integration.445-454
• 
  Muhammad Ammad-ud-din,Suleiman A. Khan,Disha Malani,Astrid Murumägi,Olli-P. Kallioniemi,Tero Aittokallio,Samuel Kaski:
  Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization.455-463
• 
  Dalia Cohn-Alperovich,Alona Rabner,Ilona Kifer,Yael Mandel-Gutfreund,Zohar Yakhini:
  Mutual enrichment in aggregated ranked lists with applications to gene expression regulation.464-472
• 
  Georg Summer,Thomas Kelder,Marijana Radonjic,Marc van Bilsen,Suzan Wopereis,Stephane Heymans:
  The Network Library: a framework to rapidly integrate network biology resources.473-478
• 
  Kedar Tatwawadi,Mikel Hernaez,Idoia Ochoa,Tsachy Weissman:
  GTRAC: fast retrieval from compressed collections of genomic variants.479-486

Genome

• 
  Siavash Sheikhizadeh,M. Eric Schranz,Mehmet Akdel,Dick de Ridder,Sandra Smit:
  PanTools: representation, storage and exploration of pan-genomic data.487-493
• 
  Ilan Shomorony,Samuel H. Kim,Thomas A. Courtade,David N. C. Tse:
  Information-optimal genome assembly via sparse read-overlap graphs.494-502
• 
  Andreas D. M. Gunawan,Bingxin Lu,Louxin Zhang:
  A program for verification of phylogenetic network models.503-510
• 
  Tarmo Äijö,Xiaojing Yue,Anjana Rao,Harri Lähdesmäki:
  LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs.511-519
• 
  Jikai Lei,Yanni Sun:
  Assemble CRISPRs from metagenomic sequencing data.520-528
• 
  Nan Du,Yanni Sun:
  Improve homology search sensitivity of PacBio data by correcting frameshifts.529-537
• 
  Ariya Shajii,Deniz Yörükoglu,Yun William Yu,Bonnie Berger:
  Fast genotyping of known SNPs through approximatek-mer matching.538-544
• 
  Ehsan Haghshenas,Faraz Hach,Süleyman Cenk Sahinalp,Cédric Chauve:
  CoLoRMap: Correcting Long Reads by Mapping short reads.545-551
• 
  Olga V. Matveeva,Yury D. Nechipurenko,Evgeniy Riabenko,Chikako Ragan,Nafisa N. Nazipova,Aleksey Y. Ogurtsov,Svetlana A. Shabalina:
  Optimization of signal-to-noise ratio for efficient microarray probe design.552-558
• 
  Shay Ben-Elazar,Benny Chor,Zohar Yakhini:
  Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data.559-566
• 
  Samuele Girotto,Cinzia Pizzi,Matteo Comin:
  MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.567-575
• 
  Omer S. Alkhnbashi,Shiraz A. Shah,Roger A. Garrett,Sita J. Saunders,Fabrizio Costa,Rolf Backofen:
  Characterizing leader sequences of CRISPR loci.576-585

Genes

• 
  Sungyoung Lee,Sungkyoung Choi,Young Jin Kim,Bong-Jo Kim,Heungsun Hwang,Taesung Park:
  Pathway-based approach using hierarchical components of collapsed rare variants.586-594
• 
  Kathrin Trappe,Tobias Marschall,Bernhard Y. Renard:
  Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.595-604
• 
  Wenbao Yu,Seungyeoun Lee,Taesung Park:
  A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions.605-610
• 
  Jaehoon Lee,Young Jin Kim,Juyoung Lee,Bong-Jo Kim,Seungyeoun Lee,Taesung Park:
  Gene-set association tests for next-generation sequencing data.611-619
• 
  Djordje Djordjevic,Kenro Kusumi,Joshua Wing Kei Ho:
  XGSA: A statistical method for cross-species gene set analysis.620-628
• 
  Tuomo Hartonen,Biswajyoti Sahu,Kashyap Dave,Teemu Kivioja,Jussi Taipale:
  PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments.629-638
• 
  Ritambhara Singh,Jack Lanchantin,Gabriel Robins,Yanjun Qi:
  DeepChrome: deep-learning for predicting gene expression from histone modifications.639-648
• 
  I. Gregor,Alexander Schönhuth,Alice Carolyn McHardy:
  Snowball: strain aware gene assembly of metagenomes.649-657

Proteins

• 
  Somaye Hashemifar,Jianzhu Ma,Hammad Naveed,Stefan Canzar,Jinbo Xu:
  ModuleAlign: module-based global alignment of protein-protein interaction networks.658-664
• 
  Konstantinos D. Tsirigos,Arne Elofsson,Pantelis G. Bagos:
  PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins.665-671
• 
  Sheng Wang,Jianzhu Ma,Jinbo Xu:
  AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.672-679
• 
  Robert Vaser,Dario Pavlovic,Mile Sikic:
  SWORD - a highly efficient protein database search.680-684
• 
  Olga S. Voitenko,Andi Dhroso,Anna Feldmann,Dmitry Korkin,Olga V. Kalinina:
  Patterns of amino acid conservation in human and animal immunodeficiency viruses.685-692
• 
  Émilie Neveu,David W. Ritchie,Petr Popov,Sergei Grudinin:
  PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation.693-701
• 
  Thang V. Pham,Connie R. Jimenez:
  Simulated linear test applied to quantitative proteomics.702-709
• 
  Thach Nguyen,Michael Habeck:
  A probabilistic model for detecting rigid domains in protein structures.710-717

Systems

• 
  Bernhard Steiert,Jens Timmer,Clemens Kreutz:
  L₁ regularization facilitates detection of cell type-specific parameters in dynamical systems.718-726
• 
  Hesam Montazeri,Jack Kuipers,Roger D. Kouyos,Jürg Böni,Sabine Yerly,Thomas Klimkait,Vincent Aubert,Huldrych F. Günthard,Niko Beerenwinkel,The Swiss Hiv Cohort Study:
  Large-scale inference of conjunctive Bayesian networks.727-735
• 
  Mark D. M. Leiserson,Matthew A. Reyna,Benjamin J. Raphael:
  A weighted exact test for mutually exclusive mutations in cancer.736-745
• 
  Matthew Ruffalo,Ziv Bar-Joseph:
  Genome wide predictions of miRNA regulation by transcription factors.746-754
• 
  Max Sajitz-Hermstein,Nadine Töpfer,Sabrina Kleessen,Alisdair R. Fernie,Zoran Nikoloski:
  iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models.755-762
• 
  Hung-Cuong Trinh,Yung-Keun Kwon:
  Edge-based sensitivity analysis of signaling networks by using Boolean dynamics.763-771
• 
  Pauline Traynard,Adrien Fauré,François Fages,Denis Thieffry:
  Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation.772-780
• 
  Konstantinos Koutroumpas,Paolo Ballarini,Irene Votsi,Paul-Henry Cournède:
  Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach.781-789
• 
  Daniel Sánchez-Taltavull,Matthew MacLeod,Theodore J. Perkins:
  On cross-conditional and fluctuation correlations in competitive RNA networks.790-797

Original Papers
Genome Analysis

• 
  Jiarui Ding,Sohrab P. Shah,Anne Condon:
  densityCut: an efficient and versatile topological approach for automatic clustering of biological data.2567-2576
• 
  Elias Dohmen,Lukas P. M. Kremer,Erich Bornberg-Bauer,Carsten Kemena:
  DOGMA: domain-based transcriptome and proteome quality assessment.2577-2581
• 
  Ivan Sovic,Kresimir Krizanovic,Karolj Skala,Mile Sikic:
  Evaluation of hybrid and non-hybrid methods forde novo assembly of nanopore reads.2582-2589
• 
  Liam Harold Childs,Soulafa Mamlouk,Jörgen Brandt,Christine Sers,Ulf Leser:
  SoFIA: a data integration framework for annotating high-throughput datasets.2590-2597
• 
  T. Bernard Bigdeli,Donghyung Lee,Bradley Todd Webb,Brien P. Riley,Vladimir I. Vladimirov,Ayman H. Fanous,Kenneth S. Kendler,Silviu-Alin Bacanu:
  A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans.2598-2603
• 
  Raivo Kolde,Kaspar Märtens,Kaie Lokk,Sven Laur,Jaak Vilo:
  seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.2604-2610
• 
  Eric Z. Chen,Hongzhe Li:
  A two-part mixed-effects model for analyzing longitudinal microbiome compositional data.2611-2617
• 
  Zheng-Zheng Tang,Guanhua Chen,Alexander V. Alekseyenko:
  PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances.2618-2625

Sequence Analysis

• 
  Sudhakar Sahoo,Michal P. Switnicki,Jakob Skou Pedersen:
  ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.2626-2635
• 
  Ganapathi Varma Saripella,Erik L. L. Sonnhammer,Kristoffer Forslund:
  Benchmarking the next generation of homology inference tools.2636-2641

Structural Bioinformatics

• 
  Gelio Alves,Yi-Kuo Yu:
  Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution.2642-2649
• 
  David W. Ritchie:
  Calculating and scoring high quality multiple flexible protein structure alignments.2650-2658

Gene expression

• 
  Liang Niu,Zongli Xu,Jack A. Taylor:
  RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.2659-2663

Systems Biology

• 
  Huimin Luo,Jianxin Wang,Min Li,Junwei Luo,Xiaoqing Peng,Fang-Xiang Wu,Yi Pan:
  Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm.2664-2671
• 
  Francesco Pappalardo,Epifanio Fichera,Nicoletta Paparone,Alessandro Lombardo,Marzio Pennisi,Giulia Russo,Marco Leotta,Alessandro Pedretti,Francesco De Fiore,Santo Motta:
  A computational model to predict the immune system activation by citrus-derived vaccine adjuvants.2672-2680
• 
  Daniel Lobo,Junji Morokuma,Michael Levin:
  Computational discovery andin vivo validation ofhnf4 as a regulatory gene in planarian regeneration.2681-2685

Data and Text Mining

• 
  Jonathan D. Wren:
  Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.2686-2691

Applications Notes
Genome Analysis

• 
  Zheng Xu,Guosheng Zhang,Cong Wu,Yun Li,Ming Hu:
  FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data.2692-2695

Sequence Analysis

• 
  Elena Yavorska Harris,Rachid Ounit,Stefano Lonardi:
  BRAT-nova: fast and accurate mapping of bisulfite-treated reads.2696-2698
• 
  Paul P. S. Wang,Wendy T. Parker,Susan Branford,Andreas W. Schreiber:
  BAM-matcher: a tool for rapid NGS sample matching.2699-2701
• 
  Ben J. Woodcroft,Joel A. Boyd,Gene W. Tyson:
  OrfM: a fast open reading frame predictor for metagenomic data.2702-2703
• 
  Bianca K. Stöcker,Johannes Köster,Sven Rahmann:
  SimLoRD: Simulation of Long Read Data.2704-2706
• 
  Brandon D. Pickett,S. M. Karlinsey,C. E. Penrod,Michael J. Cormier,Mark T. W. Ebbert,Dennis K. Shiozawa,C. J. Whipple,Perry G. Ridge:
  SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.2707-2709

Structural Bioinformatics

• 
  Marianna Sakka,Grigorios Tzortzis,Michalis D. Mantzaris,Nick Bekas,Tahsin F. Kellici,Aristidis Likas,Dimitrios Galaris,Ioannis P. Gerothanassis,Andreas G. Tzakos:
  PRESS: PRotEin S-Sulfenylation server.2710-2712

Systems Biology

• 
  Ivan H. Goenawan,Kenneth Bryan,David J. Lynn:
  DyNet: visualization and analysis of dynamic molecular interaction networks.2713-2715
• 
  Devin K. Schweppe,Chunxiang Zheng,Juan D. Chavez,Arti T. Navare,Xia Wu,Jimmy K. Eng,James E. Bruce:
  XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.2716-2718

Databases and Ontologies

• 
  Maciej J. Swat,Pierre Grenon,Sarala M. Wimalaratne:
  ProbOnto: ontology and knowledge base of probability distributions.2719-2721
• 
  Anna Lukasik,Maciej Wójcikowski,Piotr Zielenkiewicz:
  Tools4miRs - one place to gather all the tools for miRNA analysis.2722-2724
• 
  Julia Varga,László Dobson,Gábor E. Tusnády:
  TOPDOM: database of conservatively located domains and motifs in proteins.2725-2726

Corrigendum

• 
  Li Teng,Bing He,Jiahui Wang,Kai Tan:
  4DGenome: a comprehensive database of chromatin interactions.2727

Volume 32, Number 18, September 2016

Original Papers
Genome Analysis

• 
  Mulin Jun Li,Zhicheng Pan,Zipeng Liu,Jiexing Wu,Panwen Wang,Yun Zhu,Feng Xu,Zhengyuan Xia,Pak Chung Sham,Jean-Pierre A. Kocher,Miao-Xin Li,Jun S. Liu,Junwen Wang:
  Predicting regulatory variants with composite statistic.2729-2736
• 
  Xiaonan Hu,Wei Zhang,Sanguo Zhang,Shuangge Ma,Qizhai Li:
  Group-combinedP-values with applications to genetic association studies.2737-2743

Sequence Analysis

• 
  Mindaugas Margelevicius:
  Bayesian nonparametrics in protein remote homology search.2744-2752
• 
  Kira Vyatkina,Si Wu,Lennard J. Dekker,Martijn M. VanDuijn,Xiaowen Liu,Nikola Tolic,Theo M. Luider,Ljiljana Pasa-Tolic,Pavel A. Pevzner:
  Top-down analysis of protein samples byde novo sequencing techniques.2753-2759
• 
  Vladimir Ulyantsev,Sergey Kazakov,Veronika B. Dubinkina,Alexander V. Tyakht,Dmitry G. Alexeev:
  MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.2760-2767
• 
  Jun Ding,Xiaoman Li,Haiyan Hu:
  TarPmiR: a new approach for microRNA target site prediction.2768-2775
• 
  Thomas Hrabe,Lukasz Jaroszewski,Adam Godzik:
  Revealing aperiodic aspects of solenoid proteins from sequence information.2776-2782
• 
  Abdullah-Al Mamun,Soumitra Pal,Sanguthevar Rajasekaran:
  KCMBT: ak-mer Counter based on Multiple Burst Trees.2783-2790

Structural Bioinformatics

• 
  Debswapna Bhattacharya,Renzhi Cao,Jianlin Cheng:
  UniCon3D:de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.2791-2799

Gene expression

• 
  Paul Florian Thaben,Pål O. Westermark:
  Differential rhythmicity: detecting altered rhythmicity in biological data.2800-2808
• 
  Francisco García-García,Joaquin Panadero,Joaquín Dopazo,David Montaner:
  Integrated gene set analysis for microRNA studies.2809-2816

Genetics and Population Analysis

• 
  Aaron A. Behr,Katherine Z. Liu,Gracie Liu-Fang,Priyanka Nakka,Sohini Ramachandran:
  pong: fast analysis and visualization of latent clusters in population genetic data.2817-2823

Systems Biology

• 
  Jung Eun Shim,Insuk Lee:
  Weighted mutual information analysis substantially improves domain-based functional network models.2824-2830
• 
  Hongyi Zhou,Jeffrey Skolnick:
  A knowledge-based approach for predicting gene-disease associations.2831-2838

Data and Text Mining

• 
  Robert Leaman,Zhiyong Lu:
  TaggerOne: joint named entity recognition and normalization with semi-Markov Models.2839-2846

Applications Notes
Genome Analysis

• 
  Zuguang Gu,Roland Eils,Matthias Schlesner:
  Complex heatmaps reveal patterns and correlations in multidimensional genomic data.2847-2849

Sequence Analysis

• 
  Yana Valasatava,Antonio Rosato,Lucia Banci,Claudia Andreini:
  MetalPredator: a web server to predict iron-sulfur cluster binding proteomes.2850-2852

Structural Bioinformatics

• 
  Shravan Sukumar,Xiaolei Zhu,Spencer S. Ericksen,Julie C. Mitchell:
  DBSI server: DNA binding site identifier.2853-2855

Gene expression

• 
  Umesh K. Nandal,Antoine H. C. van Kampen,Perry D. Moerland:
  compendiumdb: an R package for retrieval and storage of functional genomics data.2856-2857
• 
  David J. Arenillas,Alistair R. R. Forrest,Hideya Kawaji,Timo Lassmann,Wyeth W. Wasserman,Anthony Mathelier:
  CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.2858-2860

Genetics and Population Analysis

• 
  Yuri Tani Utsunomiya,Marco Milanesi,Adam T. H. Utsunomiya,Paolo Ajmone-Marsan,José Fernando Garcia:
  GHap: an R package for genome-wide haplotyping.2861-2862

Systems Biology

• 
  Sisi Fan,Quentin Geissmann,Eszter Lakatos,Saulius Lukauskas,Angelique Ale,Ann C. Babtie,Paul D. W. Kirk,Michael P. H. Stumpf:
  MEANS: python package for Moment Expansion Approximation, iNference and Simulation.2863-2865
• 
  Giovanni Y. Di Veroli,Chiara Fornari,Dennis Wang,Séverine Mollard,Jo L. Bramhall,Frances M. Richards,Duncan I. Jodrell:
  Combenefit: an interactive platform for the analysis and visualization of drug combinations.2866-2868
• 
  Samy Deghou,Georg Zeller,Murat Iskar,Marja Driessen,Mercedes Castillo,Vera van Noort,Peer Bork:
  CART - a chemical annotation retrieval toolkit.2869-2871
• 
  Giorgio Valentini,Giuliano Armano,Marco Frasca,Jianyi Lin,Marco Mesiti,Matteo Re:
  RANKS: a flexible tool for node label ranking and classification in biological networks.2872-2874
• 
  Daniel Weindl,André Wegner,Karsten Hiller:
  MIA: non-targeted mass isotopolome analysis.2875-2876
• 
  Michael J. O'Connell,Eric F. Lock:
  R.JIVE for exploration of multi-source molecular data.2877-2879
• 
  James C. Schaff,Dan Vasilescu,Ion I. Moraru,Leslie M. Loew,Michael L. Blinov:
  Rule-based modeling with Virtual Cell.2880-2882

Data and Text Mining

• 
  Philippe Thomas,Tim Rocktäschel,Jörg Hakenberg,Yvonne Lichtblau,Ulf Leser:
  SETH detects and normalizes genetic variants in text.2883-2885
• 
  Kyubum Lee,Won-Ho Shin,Byounggun Kim,Sunwon Lee,Yonghwa Choi,Sunkyu Kim,Minji Jeon,Aik Choon Tan,Jaewoo Kang:
  HiPub: translating PubMed and PMC texts to networks for knowledge discovery.2886-2888

Corrigendum

• 
  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.2889

Volume 32, Number 19, October 2016

Discovery Note
Systems Biology

• 
  Zijian Ding,Songpeng Zu,Jin Gu:
  Evaluating the molecule-based prediction of clinical drug responses in cancer.2891-2895

Original Papers
Genome Analysis

• 
  Pol Cuscó,Guillaume J. Filion:
  Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control.2896-2902
• 
  Micol Marchetti-Bowick,Junming Yin,Judie A. Howrylak,Eric P. Xing:
  A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits.2903-2910
• 
  Yuta Suzuki,Jonas Korlach,Stephen W. Turner,Tatsuya Tsukahara,Junko Taniguchi,Wei Qu,Kazuki Ichikawa,Jun Yoshimura,Hideaki Yurino,Yuji Takahashi,Jun Mitsui,Hiroyuki Ishiura,Shoji Tsuji,Hiroyuki Takeda,Shinichi Morishita:
  AgIn: measuring the landscape of CpG methylation of individual repetitive elements.2911-2919

Sequence Analysis

• 
  Panu Somervuo,Sonja Koskela,Juho Pennanen,R. Henrik Nilsson,Otso Ovaskainen:
  Unbiased probabilistic taxonomic classification for DNA barcoding.2920-2927

Structural Bioinformatics

• 
  Markus Fricke,Manja Marz:
  Prediction of conserved long-range RNA-RNA interactions in full viral genomes.2928-2935
• 
  Lijun Quan,Qiang Lv,Yang Zhang:
  STRUM: structure-based prediction of protein stability changes upon single-point mutation.2936-2946
• 
  Nouf S. Al-Numair,Luis Lopes,Petros Syrris,Lorenzo Monserrat,Perry Elliott,Andrew C. R. Martin:
  The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants.2947-2955

Gene expression

• 
  Jing Yang,Christopher A. Penfold,Murray R. Grant,Magnus Rattray:
  Inferring the perturbation time from biological time course data.2956-2964
• 
  Yuanhua Huang,Guido Sanguinetti:
  Statistical modeling of isoform splicing dynamics from RNA-seq time series data.2965-2972
• 
  John E. Reid,Lorenz Wernisch:
  Pseudotime estimation: deconfounding single cell time series.2973-2980

Data and Text Mining

• 
  Kun Ming Kenneth Lim,Chenhao Li,Kern Rei Chng,Niranjan Nagarajan:
  @MInter: automated text-mining of microbial interactions.2981-2987
• 
  Fabio Fabris,Alex Alves Freitas:
  New KEGG pathway-based interpretable features for classifying ageing-related mouse proteins.2988-2995
• 
  Guangyuan Fu,Jun Wang,Bo Yang,Guo-Xian Yu:
  NegGOA: negative GO annotations selection using ontology structure.2996-3004

Databases and Ontologies

• 
  Christopher B. Barnett,Kiyoko F. Aoki-Kinoshita,Kevin J. Naidoo:
  The Glycome Analytics Platform: an integrative framework for glycobioinformatics.3005-3011

Applications Notes
Genome Analysis

• 
  Zachary L. Skidmore,Alex H. Wagner,Robert Lesurf,Katie M. Campbell,Jason Kunisaki,Obi L. Griffith,Malachi Griffith:
  GenVisR: Genomic Visualizations in R.3012-3014
• 
  F. Anthony San Lucas,Smruthy Sivakumar,Selina Vattathil,Jerry Fowler,Eduardo Vilar,Paul Scheet:
  Rapid and powerful detection of subtle allelic imbalance from exome sequencing data withhapLOHseq.3015-3017
• 
  Tomasz Stokowy,Mateusz Garbulowski,Torunn Fiskerstrand,Rita Holdhus,Kornel Labun,Pawel Sztromwasser,Christian Gilissen,Alexander Hoischen,Gunnar Houge,Kjell Petersen,Inge Jonassen,Vidar M. Steen:
  RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.3018-3020
• 
  Maria Nattestad,Michael C. Schatz:
  Assemblytics: a web analytics tool for the detection of variants from an assembly.3021-3023

Sequence Analysis

• 
  Zhong Wang,André L. Martins,Charles G. Danko:
  RTFBSDB: an integrated framework for transcription factor binding site analysis.3024-3026

Phylogenetics

• 
  Astrid Cruaud,Mathieu Gautier,Jean-Pierre Rossi,Jean-Yves Rasplus,Jérôme Gouzy:
  RADIS: analysis ofRAD-seq data for interspecific phylogeny.3027-3028

Gene expression

• 
  Billy Heung Wing Chang,Weidong Tian:
  GSA-Lightning: ultra-fast permutation-based gene set analysis.3029-3031

Genetics and Population Analysis

• 
  Pier Francesco Palamara:
  ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process.3032-3034
• 
  Russell Corbett-Detig,Matt Jones:
  SELAM: simulation of epistasis and local adaptation during admixture with mate choice.3035-3037
• 
  Daniel Edsgärd,Björn Reinius,Rickard Sandberg:
  scphaser: haplotype inference using single-cell RNA-seq data.3038-3040

Systems Biology

• 
  Francisco Salavert,Luz Garcia-Alonso,Rubén Sánchez,Roberto Alonso,Marta Bleda,Ignacio Medina,Joaquín Dopazo:
  Web-based network analysis and visualization using CellMaps.3041-3043

Data and Text Mining

• 
  Sun Kim,Lana Yeganova,W. John Wilbur:
  Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.3044-3046
• 
  Philip Ewels,Måns Magnusson,Sverker Lundin,Max Käller:
  MultiQC: summarize analysis results for multiple tools and samples in a single report.3047-3048

Databases and Ontologies

• 
  Vijay Barve,Javier Otegui:
  bdvis: visualizing biodiversity data in R.3049-3050

Corrigendum

• 
  Forest Agostinelli,Nicholas Ceglia,Babak Shahbaba,Paolo Sassone-Corsi,Pierre Baldi:
  What time is it? Deep learning approaches for circadian rhythms.3051

Volume 32, Number 20, October 2016

Discovery Note
Sequence Analysis

• 
  Anna A. Deeva,Evgenia A. Temlyakova,Anatoly A. Sorokin,Elena V. Nemtseva,Valentina A. Kratasyuk:
  Structural distinctions of fast and slow bacterial luciferases revealed by phylogenetic analysis.3053-3057

Original Papers
Genome Analysis

• 
  Jianwei Zhang,Dave Kudrna,Ting Mu,Weiming Li,Dario Copetti,Yeisoo Yu,Jose Luis Goicoechea,Yang Lei,Rod A. Wing:
  Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.3058-3064
• 
  Jacob Shujui Hsu,Johnny S. H. Kwan,Zhicheng Pan,Maria-Mercè Garcia-Barcelo,Pak Chung Sham,Miao-Xin Li:
  Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes.3065-3071
• 
  Junho Kim,Ju Heon Maeng,Jae Seok Lim,Hyeonju Son,Junehawk Lee,Jeong Ho Lee,Sangwoo Kim:
  Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination.3072-3080

Sequence Analysis

• 
  Hákon Guðbjartsson,Guðmundur Fr. Georgsson,Sigurjón Axel Guðjónsson,Ragnar þór Valdimarsson,Jóhann H. Sigurðsson,Sigmar K. Stefánsson,Gísli Másson,Gísli Magnússon,Vilmundur Pálmason,Kári Stefánsson:
  GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture.3081-3088
• 
  John P. Barton,Eleonora De Leonardis,Alice Coucke,Simona Cocco:
  ACE: adaptive cluster expansion for maximum entropy graphical model inference.3089-3097
• 
  Bram Gerritsen,Aridaman Pandit,Arno C. Andeweg,Rob J. De Boer:
  RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data.3098-3106
• 
  Ping-Ping Wen,Shaoping Shi,Hao-Dong Xu,Li-na Wang,Jian-Ding Qiu:
  Accuratein silico prediction of species-specific methylation sites based on information gain feature optimization.3107-3115
• 
  Wangren Qiu,Bi-Qian Sun,Xuan Xiao,Zhao-Chun Xu,Kuo-Chen Chou:
  iPTM-mLys: identifying multiple lysine PTM sites and their different types.3116-3123
• 
  Daniel L. Greenfield,Oliver Stegle,Alban Rrustemi:
  GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.3124-3132
• 
  Jianhua Jia,Liuxia Zhang,Zi Liu,Xuan Xiao,Kuo-Chen Chou:
  pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC.3133-3141

Structural Bioinformatics

• 
  Pradeep Anand Ravindranath,Michel F. Sanner:
  AutoSite: an automated approach for pseudo-ligands prediction - from ligand-binding sites identification to predicting key ligand atoms.3142-3149

Genetics and Population Analysis

• 
  Haixiang Zhang,Yinan Zheng,Zhou Zhang,Tao Gao,Brian Joyce,Grace Yoon,Wei Zhang,Joel Schwartz,Allan C. Just,Elena Colicino,Pantel Vokonas,Lihui Zhao,Jinchi Lv,Andrea A. Baccarelli,Lifang Hou,Lei Liu:
  Estimating and testing high-dimensional mediation effects in epigenetic studies.3150-3154

Systems Biology

• 
  Lei Meng,Aaron Striegel,Tijana Milenkovic:
  Local versus global biological network alignment.3155-3164
• 
  Jing Ma,Ali Shojaie,George Michailidis:
  Network-based pathway enrichment analysis with incomplete network information.3165-3174

Data and Text Mining

• 
  Dhanya Sridhar,Shobeir Fakhraei,Lise Getoor:
  A probabilistic approach for collective similarity-based drug-drug interaction prediction.3175-3182
• 
  Na Le Dang,Tyler B. Hughes,Varun Krishnamurthy,S. Joshua Swamidass:
  A simple model predicts UGT-mediated metabolism.3183-3189

Applications Notes
Genome Analysis

• 
  Kai Kruse,Clemens B. Hug,Benjamín Hernández-Rodríguez,Juan M. Vaquerizas:
  TADtool: visual parameter identification for TAD-calling algorithms.3190-3192
• 
  Bai-Han Zhu,Ying-Nan Song,Wei Xue,Gui-Cai Xu,Jun Xiao,Ming-Yuan Sun,Xiaowen Sun,Jiongtang Li:
  PEP_scaffolder: using (homologous) proteins to scaffold genomes.3193-3195

Sequence Analysis

• 
  Ewa A. Bergmann,Bo-Juen Chen,Kanika Arora,Vladimir Vacic,Michael C. Zody:
  Conpair: concordance and contamination estimator for matched tumor-normal pairs.3196-3198

Gene expression

• 
  Vittorio Fortino,Roberto Tagliaferri,Dario Greco:
  CONDOP: an R package for CONdition-Dependent Operon Predictions.3199-3200
• 
  Steffi Grote,Kay Prüfer,Janet Kelso,Michael Dannemann:
  ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.3201-3203

Genetics and Population Analysis

• 
  Simon Dellicour,Rebecca Rose,Nuno R. Faria,Philippe Lemey,Oliver G. Pybus:
  SERAPHIM: studying environmental rasters and phylogenetically informed movements.3204-3206

Databases and Ontologies

• 
  James R. Staley,James A. Blackshaw,Mihir A. Kamat,Steve Ellis,Praveen Surendran,Benjamin B. Sun,Dirk S. Paul,Daniel Freitag,Stephen Burgess,John Danesh,Robin Young,Adam S. Butterworth:
  PhenoScanner: a database of human genotype-phenotype associations.3207-3209

Bioimage Informatics

• 
  David Dao,Adam Fraser,Jane Hung,Vebjorn Ljosa,Shantanu Singh,Anne E. Carpenter:
  CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.3210-3212

Corrigendum

• 
  Vikas Bansal,Ondrej Libiger:
  A statistical method for the detection of variants from next-generation resequencing of DNA poolsA probabilistic method for the detection and genotyping of small indels from population-scale sequence data.3213

Volume 32, Number 21, November 2016

Original Papers
Genome Analysis

• 
  Sara El-Metwally,Magdi Zakaria,Taher Hamza:
  LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.3215-3223

Sequence Analysis

• 
  Bo Liu,Hongzhe Guo,Michael Brudno,Yadong Wang:
  deBGA: read alignment with de Bruijn graph-based seed and extension.3224-3232
• 
  Qamar M. Sheikh,Derek Gatherer,Pedro A. Reche,Darren R. Flower:
  Towards the knowledge-based design of universal influenza epitope ensemble vaccines.3233-3239
• 
  Gongyi Huang,Shaoli Wang,Xueqin Wang,Na You:
  An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data.3240-3245
• 
  Kazunori D. Yamada,Kentaro Tomii,Kazutaka Katoh:
  Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees.3246-3251

Structural Bioinformatics

• 
  Marco Barsacchi,Eva Maria Novoa,Manolis Kellis,Alessio Bechini:
  SwiSpot: modeling riboswitches by spotting out switching sequences.3252-3259
• 
  Xiuzhen Hu,Qiwen Dong,Jianyi Yang,Yang Zhang:
  Recognizing metal and acid radical ion-binding sites by integratingab initio modeling with template-based transferals.3260-3269
• 
  Pawel Krupa,Magdalena A. Mozolewska,Marta Wisniewska,Yanping Yin,Yi He,Adam K. Sieradzan,Robert Ganzynkowicz,Agnieszka G. Lipska,Agnieszka S. Karczynska,Magdalena Slusarz,Rafal Slusarz,Artur Gieldon,Cezary Czaplewski,Dawid Jagiela,Bartlomiej Zaborowski,Harold A. Scheraga,Adam Liwo:
  Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.3270-3278

Gene expression

• 
  Xuebei An,Jianhua Hu,Kim-Anh Do:
  SIFORM: shared informative factor models for integration of multi-platform bioinformatic data.3279-3290
• 
  Zhi Liu,Tuantuan Gui,Zhen Wang,Hong Li,Yunhe Fu,Xiao Dong,Yixue Li:
  cisASE: a likelihood-based method for detecting putativecis-regulated allele-specific expression in RNA sequencing data.3291-3297

Genetics and Population Analysis

• 
  A. Macé,M. A. Tuke,Jacques S. Beckmann,L. Lin,S. Jacquemont,Michael N. Weedon,Alexandre Reymond,Zoltán Kutalik:
  New quality measure for SNP array based CNV detection.3298-3305

Systems Biology

• 
  Yat Hin Chan,Jukka Intosalmi,Sini Rautio,Harri Lähdesmäki:
  A subpopulation model to analyze heterogeneous cell differentiation dynamics.3306-3313

Data and Text Mining

• 
  Tomer Illouz,Ravit Madar,Charlotte Clague,Kathleen J. Griffioen,Yoram Louzoun,Eitan Okun:
  Unbiased classification of spatial strategies in the Barnes maze.3314-3320

Applications Notes
Genome Analysis

• 
  Alla Mikheenko,Gleb Valin,Andrey D. Prjibelski,Vladislav Saveliev,Alexey A. Gurevich:
  Icarus: visualizer forde novo assembly evaluation.3321-3323
• 
  Hamid Younesy,Cydney B. Nielsen,Matthew C. Lorincz,Steven J. M. Jones,Mohammad M. Karimi,Torsten Möller:
  ChAsE: chromatin analysis and exploration tool.3324-3326
• 
  Thomas Weinmaier,Alexander Platzer,Jeroen Frank,Hans-Jörg Hellinger,Patrick Tischler,Thomas Rattei:
  ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.3327-3329
• 
  Jakob Dohrmann,Rahul Singh:
  The SMAL web server: global multiple network alignment from pairwise alignments.3330-3332
• 
  Mingyang Cai,Fan Gao,Wange Lu,Kai Wang:
  w4CSeq: software and web application to analyze 4C-seq data.3333-3335
• 
  Jian Ma,Johannes Köster,Qian Qin,Shengen Hu,Wei Li,Chenhao Chen,Qingyi Cao,Jinzeng Wang,Shenglin Mei,Qi Liu,Han Xu,Xiaole Shirley Liu:
  CRISPR-DO for genome-wide CRISPR design and optimization.3336-3338

Sequence Analysis

• 
  Altan Kara,Martin J. Vickers,Martin T. Swain,David E. Whitworth,Narcis Fernandez-Fuentes:
  MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins.3339-3341

Structural Bioinformatics

• 
  Bing Xia,Sandor Vajda,Dima Kozakov:
  Accounting for pairwise distance restraints in FFT-based protein-protein docking.3342-3344

Gene expression

• 
  Alexey Stupnikov,Shailesh Tripathi,Ricardo de Matos Simoes,Darragh G. McArt,Manuel Salto-Tellez,Galina V. Glazko,Matthias Dehmer,Frank Emmert-Streib:
  samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.3345-3347

Genetics and Population Analysis

• 
  Xiaoyu Wang,James Y. Dai:
  TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials.3348-3350

Systems Biology

• 
  Gang Wu,Ron C. Anafi,Michael Hughes,Karl Kornacker,John B. Hogenesch:
  MetaCycle: an integrated R package to evaluate periodicity in large scale data.3351-3353
• 
  Guillaume Devailly,Anna Mantsoki,Anagha Joshi:
  Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.3354-3356
• 
  Eva Balsa-Canto,David Henriques,Attila Gábor,Julio R. Banga:
  AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.3357-3359
• 
  Irene Otero-Muras,David Henriques,Julio R. Banga:
  SYNBADm: a tool for optimization-based automated design of synthetic gene circuits.3360-3362
• 
  David G. P. van IJzendoorn,Kimberly Glass,John Quackenbush,Marieke L. Kuijjer:
  PyPanda: a Python package for gene regulatory network reconstruction.3363-3365
• 
  Leonard A. Harris,Justin S. Hogg,José Juan Tapia,John A. P. Sekar,Sanjana Gupta,Ilya Korsunsky,Arshi Arora,Dipak Barua,Robert P. Sheehan,James R. Faeder:
  BioNetGen 2.2: advances in rule-based modeling.3366-3368
• 
  Maureen R. Smith,Redmond P. Smyth,Roland Marquet,Max von Kleist:
  MIMEAnTo: profiling functional RNA in mutational interference mapping experiments.3369-3370

Databases and Ontologies

• 
  Edgar Mixcoha,Roberto Rosende,Rebeca García-Fandiño,Ángel Piñeiro:
  Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins.3371-3373

Volume 32, Number 22, November 2016

Discovery Note
Phylogenetics

• 
  Sebastián Duchêne,Jemma L. Geoghegan,Edward C. Holmes,Simon Y. W. Ho:
  Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods.3375-3379

Original Papers
Genome Analysis

• 
  Dmitry Antipov,Nolan Hartwick,Max W. Shen,Mikhail Raiko,Alla L. Lapidus,Pavel A. Pevzner:
  plasmidSPAdes: assembling plasmids from whole genome sequencing data.3380-3387
• 
  Stefanie König,Lars Romoth,Lizzy Gerischer,Mario Stanke:
  Simultaneous gene finding in multiple genomes.3388-3395
• 
  Yalu Wen,Fushun Chen,Qingzheng Zhang,Yan Zhuang,Zhiguang Li:
  Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics.3396-3404

Sequence Analysis

• 
  Subrata Saha,Sanguthevar Rajasekaran:
  NRGC: a novel referential genome compression algorithm.3405-3412

Structural Bioinformatics

• 
  Véronique Hourdel,Stevenn Volant,Darragh P. O'Brien,Alexandre Chenal,Julia Chamot-Rooke,Marie-Agnès Dillies,Sébastien Brier:
  MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets.3413-3419
• 
  George A. Cortina,Peter M. Kasson:
  Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance.3420-3427

Gene expression

• 
  Mengyin Lu,Matthew Stephens:
  Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances.3428-3434

Systems Biology

• 
  Yun Hao,Nicholas P. Tatonetti:
  Predicting G protein-coupled receptor downstream signaling by tissue expression.3435-3443

Data and Text Mining

• 
  Zhehuan Zhao,Zhihao Yang,Ling Luo,Hongfei Lin,Jian Wang:
  Drug drug interaction extraction from biomedical literature using syntax convolutional neural network.3444-3453
• 
  Shu Tadaka,Kengo Kinoshita:
  NCMine: Core-peripheral based functional module detection using near-clique mining.3454-3460
• 
  Daniyar Bakirov,Alex Pappachen James,Amin Zollanvari:
  An efficient method to estimate the optimum regularization parameter in RLDA.3461-3468
• 
  Yi Wang,Ling Xu,Yong Qiang Gu,Devin Coleman-Derr:
  MetaCoMET: a web platform for discovery and visualization of the core microbiome.3469-3470

Databases and Ontologies

• 
  Yukako Tohsato,Kenneth H. L. Ho,Koji Kyoda,Shuichi Onami:
  SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.3471-3479

Bioimage Informatics

• 
  Jian Fang,Dongdong Lin,S. Charles Schulz,Zongben Xu,Vince D. Calhoun,Yu-Ping Wang:
  Joint sparse canonical correlation analysis for detecting differential imaging genetics modules.3480-3488

Applications Notes
Genome Analysis

• 
  Samuele Bovo,Pietro Di Lena,Pier Luigi Martelli,Piero Fariselli,Rita Casadio:
  NET-GE: a web-server for NETwork-based human gene enrichment.3489-3491

Sequence Analysis

• 
  Hamid Mohamadi,Justin Chu,Benjamin P. Vandervalk,Inanç Birol:
  ntHash: recursive nucleotide hashing.3492-3494
• 
  Qiang Kou,Likun Xun,Xiaowen Liu:
  TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.3495-3497
• 
  Chia-Hua Chang,Min-Te Chou,Yi-Chung Wu,Ting-Wei Hong,Yun-Lung Li,Chia-Hsiang Yang,Jui-Hung Hung:
  sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping.3498-3500
• 
  Guy Yachdav,Sebastian Wilzbach,Benedikt Rauscher,Robert Sheridan,Ian Sillitoe,James B. Procter,Suzanna E. Lewis,Burkhard Rost,Tatyana Goldberg:
  MSAViewer: interactive JavaScript visualization of multiple sequence alignments.3501-3503
• 
  Samuel A. Lambert,Mihai Albu,Timothy R. Hughes,Hamed Shateri Najafabadi:
  Motif comparison based on similarity of binding affinity profiles.3504-3506
• 
  Haifeng Chen,Andrew D. Smith,Ting Chen:
  WALT: fast and accurate read mapping for bisulfite sequencing.3507-3509

Structural Bioinformatics

• 
  Lars Skjærven,Shashank Jariwala,Xin-Qiu Yao,Barry J. Grant:
  Online interactive analysis of protein structure ensembles with Bio3D-web.3510-3512

Genetics and Population Analysis

• 
  Aika Terada,Ryo Yamada,Koji Tsuda,Jun Sese:
  LAMPLINK: detection of statistically significant SNP combinations from GWAS data.3513-3515
• 
  Diego Ortega-Del Vecchyo,Clare D. Marsden,Kirk E. Lohmueller:
  PReFerSim: fast simulation of demography and selection under the Poisson Random Field model.3516-3518

Systems Biology

• 
  Giovanni Stracquadanio,Kun Yang,Jef D. Boeke,Joel S. Bader:
  BioPartsDB: a synthetic biology workflow web-application for education and research.3519-3521
• 
  Tadi Venkata Sivakumar,Varun Giri,Jin Hwan Park,Tae Yong Kim,Anirban Bhaduri:
  ReactPRED: a tool to predict and analyze biochemical reactions.3522-3524

Data and Text Mining

• 
  Richard A. Schäfer,Björn Voß:
  VisualGraphX: interactive graph visualization within Galaxy.3525-3527
• 
  Li Chen,Yongyi Yu,Xinchen Zhang,Chen Liu,Chuyu Ye,Longjiang Fan:
  PcircRNA_finder: a software for circRNA prediction in plants.3528-3529

Bioimage Informatics

• 
  Mark R. Winter,Walter C. Mankowski,Eric Wait,Sally Temple,Andrew R. Cohen:
  LEVER: software tools for segmentation, tracking and lineaging of proliferating cells.3530-3531
• 
  David Legland,Ignacio Arganda-Carreras,Philippe Andrey:
  MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.3532-3534

Volume 32, Number 23, December 2016

Original Papers
Genome Analysis

• 
  Niels W. Hanson,Kishori M. Konwar,Steven J. Hallam:
  LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.3535-3542
• 
  Tianshun Gao,Bing He,Sheng Liu,Heng Zhu,Kai Tan,Jiang Qian:
  EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types.3543-3551
• 
  Alexander V. Alekseyenko:
  Multivariate Welcht-test on distances.3552-3558

Sequence Analysis

• 
  Ruoyan Chen,Yu-Lung Lau,Yan Zhang,Wanling Yang:
  SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads.3559-3565
• 
  Nicole E. Wheeler,Lars Barquist,Robert A. Kingsley,Paul P. Gardner:
  A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.3566-3574

Structural Bioinformatics

• 
  Krishna Choudhary,Nathan P. Shih,Fei Deng,Mirko Ledda,Bo Li,Sharon Aviran:
  Metrics for rapid quality control in RNA structure probing experiments.3575-3583
• 
  Jing Lu,Heather A. Carlson:
  ChemTreeMap: an interactive map of biochemical similarity in molecular datasets.3584-3592

Gene expression

• 
  Ei-Wen Yang,Tao Jiang:
  SDEAP: a splice graph based differential transcript expression analysis tool for population data.3593-3602

Genetics and Population Analysis

• 
  Xiang Zhan,Santhosh Girirajan,Ni Zhao,Michael C. Wu,Debashis Ghosh:
  A novel copy number variants kernel association test with application to autism spectrum disorders studies.3603-3610

Data and Text Mining

• 
  Steven B. Cogill,Liangjiang Wang:
  Support vector machine model of developmental brain gene expression data for prioritization of Autism risk gene candidates.3611-3618
• 
  Dong Xu,Meizhuo Zhang,Yanping Xie,Fan Wang,Ming Chen,Kenny Q. Zhu,Jia Wei:
  DTMiner: identification of potential disease targets through biomedical literature mining.3619-3626
• 
  Gianluca Corrado,Toma Tebaldi,Fabrizio Costa,Paolo Frasconi,Andrea Passerini:
  RNAcommender: genome-wide recommendation of RNA-protein interactions.3627-3634
• 
  Serguei V. S. Pakhomov,Gregory P. Finley,Reed McEwan,Yan Wang,Genevieve B. Melton:
  Corpus domain effects on distributional semantic modeling of medical terms.3635-3644
• 
  Vedrana Vidulin,Tomislav Smuc,Fran Supek:
  Extensive complementarity between gene function prediction methods.3645-3653

Databases and Ontologies

• 
  Shicai Wang,Mihaela A. Mares,Yike Guo:
  CGDM: collaborative genomic data model for molecular profiling data using NoSQL.3654-3660

Applications Notes
Genome Analysis

• 
  Louis-Philippe Lemieux Perreault,Marc-André Legault,Géraldine Asselin,Marie-Pierre Dubé:
  genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.3661-3663
• 
  Rickard Hammarén,Chandan Pal,Johan Bengtsson-Palme:
  FARAO: the flexible all-round annotation organizer.3664-3666
• 
  Zongli Xu,Jack A. Taylor,Yuet-Kin Leung,Shuk-Mei Ho,Liang Niu:
  oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.3667-3669

Sequence Analysis

• 
  Jamie Waese,Asher Pasha,Tingting Wang,Anna van Weringh,David S. Guttman,Nicholas J. Provart:
  Gene Slider: sequence logo interactive data-visualization for education and research.3670-3672

Structural Bioinformatics

• 
  Erwin Holzhauser,Ping Ge,Shaojie Zhang:
  WebSTAR3D: a web server for RNA 3D structural alignment.3673-3675
• 
  Li C. Xue,João P. G. L. M. Rodrigues,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Anna Vangone:
  PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.3676-3678

Gene expression

• 
  Jasmine Dumas,Michael A. Gargano,Garrett M. Dancik:
  shinyGEO: a web-based application for analyzing gene expression omnibus datasets.3679-3681
• 
  Thomas Eder,Florian Grebien,Thomas Rattei:
  NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.3682-3684

Systems Biology

• 
  Zhou Lan,Yize Zhao,Jian Kang,Tianwei Yu:
  Bayesian network feature finder (BANFF): an R package for gene network feature selection.3685-3687

Data and Text Mining

• 
  Stephen G. Gaffney,Jeffrey P. Townsend:
  PathScore: a web tool for identifying altered pathways in cancer data.3688-3690

Bioimage Informatics

• 
  Jan R. Detrez,Jean-Marie Vanderwinden,Michaël Barbier,Marlies Verschuuren,Rony Nuydens,Xavier Langlois,Jean-Pierre Timmermans,Winnok De Vos:
  BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes.3691-3693

Corrigendum
Bioimage Informatics

• 
  X. Hu,Q. Dong,J. Yang,Y. Zhang:
  Recognizing metal and acid radical ion-binding sites by integratingab initio modeling with template-based transferals.3694

Volume 32, Number 24, December 2016

Original Papers
Genome Analysis

• 
  Hua-Jun Wu,Franziska Michor:
  A computational strategy to adjust for copy number in tumor Hi-C data.3695-3701
• 
  Rolf Hilker,Kai Bernd Stadermann,Oliver Schwengers,Evgeny Anisiforov,Sebastian Jaenicke,Bernd Weisshaar,Tobias Zimmermann,Alexander Goesmann:
  ReadXplorer 2 - detailed read mapping analysis and visualization from one single source.3702-3708
• 
  Rodrigo Cánovas,Alistair Moffat,Andrew Turpin:
  CSAM: Compressed SAM format.3709-3716
• 
  Jack P. Hou,Amin Emad,Gregory J. Puleo,Jian Ma,Olgica Milenkovic:
  A new correlation clustering method for cancer mutation analysis.3717-3728

Sequence Analysis

• 
  Lisle E. Mose,Sara R. Selitsky,Lisa M. Bixby,David L. Marron,Michael D. Iglesia,Jonathan S. Serody,Charles M. Perou,Benjamin Vincent,Joel S. Parker:
  Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.3729-3734
• 
  Minzhu Xie,Qiong Wu,Jianxin Wang,Tao Jiang:
  H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids.3735-3744
• 
  Weizhong Lin,Dong Xu:
  Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types.3745-3752

Phylogenetics

• 
  Cristina Frías-López,José F. Sánchez-Herrero,Sara Guirao-Rico,Elisa Mora,Miquel A. Arnedo,Alejandro Sánchez-Gracia,Julio Rozas:
  DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.3753-3759

Structural Bioinformatics

• 
  Jinchao Yu,Raphaël Guérois:
  PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets.3760-3767
• 
  Jianzhao Gao,Yuedong Yang,Yaoqi Zhou:
  Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks.3768-3773
• 
  Qiwei Li,David B. Dahl,Marina Vannucci,Hyun Joo,Jerry W. Tsai:
  KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure.3774-3781

Systems Biology

• 
  Yiyi Liu,Hongyu Zhao:
  Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes.3782-3789
• 
  Eoin C. Whelan,Alexander C. Nwala,Christopher Osgood,Stephan Olariu:
  Selective mutation accumulation: a computational model of the paternal age effect.3790-3797
• 
  Andy L. Olivares,Miguel Ángel González Ballester,Jérôme Noailly:
  Virtual exploration of early stage atherosclerosis.3798-3806
• 
  Pedro A. Saa,Lars Keld Nielsen:
  Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models.3807-3814

Data and Text Mining

• 
  Sara Hillenmeyer,Lea K. Davis,Eric R. Gamazon,Edwin H. Cook Jr.,Nancy J. Cox,Russ B. Altman:
  STAMS: STRING-assisted module search for genome wide association studies and application to autism.3815-3822

Applications Notes
Sequence Analysis

• 
  Rachid Ounit,Stefano Lonardi:
  Higher classification sensitivity of short metagenomic reads with CLARK-S.3823-3825
• 
  Jorge González-Domínguez,Yongchao Liu,Juan Touriño,Bertil Schmidt:
  MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.3826-3828
• 
  Bayo Lau,Marghoob Mohiyuddin,John C. Mu,Li Tai Fang,Narges Bani Asadi,Carolina Dallett,Hugo Y. K. Lam:
  LongISLND:in silico sequencing of lengthy and noisy datatypes.3829-3832

Structural Bioinformatics

• 
  Andreas Prlic,Tara Kalro,Roshni Bhattacharya,Cole H. Christie,Stephen K. Burley,Peter W. Rose:
  Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.3833-3835

Gene expression

• 
  Solaiappan Manimaran,Heather Marie Selby,Kwame Okrah,Claire Ruberman,Jeffrey T. Leek,John Quackenbush,Benjamin Haibe-Kains,Héctor Corrada Bravo,W. Evan Johnson:
  BatchQC: interactive software for evaluating sample and batch effects in genomic data.3836-3838

Genetics and Population Analysis

• 
  Andrew D. Kern,Daniel R. Schrider:
  Discoal: flexible coalescent simulations with selection.3839-3841

Systems Biology

• 
  Amit Frishberg,Avital Brodt,Yael Steuerman,Irit Gat-Viks:
  ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data.3842-3843
• 
  Aristidis G. Vrahatis,Panos Balomenos,Athanasios K. Tsakalidis,Anastasios Bezerianos:
  DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.3844-3846
• 
  Jamie Soul,Sara L. Dunn,Tim E. Hardingham,Ray P. Boot-Handford,Jean-Marc Schwartz:
  PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations.3847-3849

Databases and Ontologies

• 
  Joseph Ward,Christian Cole,Melanie Febrer,Geoffrey J. Barton:
  AlmostSignificant: simplifying quality control of high-throughput sequencing data.3850-3851

Bioimage Informatics

• 
  Eisuke Hayakawa,Yoshinori Fujimura,Daisuke Miura:
  MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data.3852-3854

Corrigendum
Bioimage Informatics

• 
  Arnon Mazza,Konrad Klockmeier,Erich E. Wanker,Roded Sharan:
  An integer programming framework for inferring disease complexes from network data.3855