Bioinformatics, Volume 30

Volume 30, Number 1, January 2014

Hitseq Papers Genome Analysis

• 
  Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna:
  Using Genome Query Language to uncover genetic variation. 1-8

Sequence Analysis

• 
  Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard:
  Specificity control for read alignments using an artificial reference genome-guided false discovery rate. 9-16
• 
  Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente:
  Further Steps in TANGO: improved taxonomic assignment in metagenomics. 17-23
• 
  Lilian Janin, Giovanna Rosone, Anthony J. Cox:
  Adaptive reference-free compression of sequence quality scores. 24-30
• 
  Rayan Chikhi, Paul Medvedev:
  Informed and automated k-mer size selection for genome assembly. 31-37
• 
  Daniel H. Huson, Chao Xie:
  A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA. 38-39

Original Papers Genome Analysis

• 
  David Hernández, Ryan Tewhey, Jean-Baptiste Veyrieras, Laurent Farinelli, Magne Østerås, Patrice François, Jacques Schrenzel:
  De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. 40-49
• 
  Noemi Andor, Julie V. Harness, Sabine Müller, Hans-Werner Mewes, Claudia Petritsch:
  EXPANDS: expanding ploidy and allele frequency on nested subpopulations. 50-60

Structural Bioinformatics

• 
  Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne Birmelé, Michele Borassi, Christophe Junot, Alberto Marchetti-Spaccamela, Andrea Marino, Leen Stougie, Fabien Jourdan, Pierluigi Crescenzi, Vincent Lacroix, Marie-France Sagot:
  Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. 61-70
• 
  Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
  Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. 71-80

Systems Biology

• 
  Yijie Wang, Xiaoning Qian:
  Functional module identification in protein interaction networks by interaction patterns. 81-93
• 
  Yungang Xu, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu:
  Inferring the soybean (Glycine max) microRNA functional network based on target gene network. 94-103

Data and Text Mining

• 
  Songhua Xu, Hong-Jun Yoon, Georgia D. Tourassi:
  A user-oriented web crawler for selectively acquiring online content in e-health research. 104-114

Applications Notes Genome Analysis

• 
  Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel:
  snoStrip: a snoRNA annotation pipeline. 115-116

Sequence Analysis

• 
  Armando J. Pinho, Diogo Pratas:
  MFCompress: a compression tool for FASTA and multi-FASTA data. 117-118
• 
  André Schumacher, Luca Pireddu, Matti Niemenmaa, Aleksi Kallio, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko:
  SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. 119-120
• 
  Christoph Gille, Birgit Weyand, Andreas Gille:
  Sequence alignment visualization in HTML5 without Java. 121-122

Phylogenetics

• 
  Michael J. Landis, Trevor Bedford:
  Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. 123-124

Structural Bioinformatics

• 
  Shannon L. N. Mayne, Hugh-George Patterton:
  AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. 125-126

Gene Expression

• 
  Thomas Sandmann, Sarah K. Kummerfeld, Robert Gentleman, Richard Bourgon:
  gCMAP: user-friendly connectivity mapping with R. 127-128

Systems Biology

• 
  Maxwell Lewis Neal, Michal Galdzicki, J. T. Gallimore, Herbert M. Sauro:
  A C library for retrieving specific reactions from the BioModels database. 129-130
• 
  Matthias Bock, Till Scharp, Chaitanya Talnikar, Edda Klipp:
  BooleSim: an interactive Boolean network simulator. 131-132
• 
  Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina Kechris:
  MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. 133-134
• 
  Minji Jeon, Sunwon Lee, Kyubum Lee, Aik Choon Tan, Jaewoo Kang:
  BEReX: Biomedical Entity-Relationship eXplorer. 135-136
• 
  Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski:
  StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. 137-138

Databases and Ontologies

• 
  Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir:
  Pattern search in BioPAX models. 139-140
• 
  Jianfei Hu, Hee-Sool Rho, Robert H. Newman, Jin Zhang, Heng Zhu, Jiang Qian:
  PhosphoNetworks: a database for human phosphorylation networks. 141-142

Message from the ISCB Databases and Ontologies

• 
  Burkhard Rost:
  ISCB: past-present perspective for the International Society for Computational Biology. 143-145
• 
  Andreas W. M. Dress, Michal Linial, Olga G. Troyanskaya, Martin Vingron:
  ISCB/SPRINGER series in computational biology. 146-147
• 
  Jim Cavalcoli, Lonnie R. Welch, Bruce J. Aronow, Sorin Draghici, Daisuke Kihara:
  The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. 148-149

Volume 30, Number 2, January 2014

Genome Analysis

• 
  Laurence O. W. Wilson, Andrew Spriggs, Jennifer M. Taylor, Aude M. Fahrer:
  A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. 151-156
• 
  Dandi Qiao, Michael H. Cho, Heide Loehlein Fier, Per S. Bakke, Amund Gulsvik, Edwin K. Silverman, Christoph Lange:
  On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. 157-164
• 
  Sebastian M. Waszak, Helena Kilpinen, Andreas R. Gschwind, Andrea Orioli, Sunil K. Raghav, Robert M. Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez, Alexandre Reymond, Emmanouil T. Dermitzakis, Bart Deplancke:
  Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. 165-171
• 
  Longjie Cheng, Yu Zhu:
  A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data. 172-179

Gene Expression

• 
  Ernest Turro, William J. Astle, Simon Tavaré:
  Flexible analysis of RNA-seq data using mixed effects models. 180-188
• 
  Kevin Lim, Limsoon Wong:
  Finding consistent disease subnetworks using PFSNet. 189-196
• 
  Yaqing Si, Peng Liu, Pinghua Li, Thomas P. Brutnell:
  Model-based clustering for RNA-seq data. 197-205

Genetics and Population Analysis

• 
  Buhm Han, Eun Yong Kang, Soumya Raychaudhuri, Paul I. W. de Bakker, Eleazar Eskin:
  Fast pairwise IBD association testing in genome-wide association studies. 206-213

Systems Biology

• 
  Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore, Joshua N. Sampson:
  Testing multiple biological mediators simultaneously. 214-220
• 
  Mikael Sunnåker, Elías Zamora-Sillero, Adrián López García de Lomana, Florian Rudroff, Uwe Sauer, Jörg Stelling, Andreas Wagner:
  Topological augmentation to infer hidden processes in biological systems. 221-227
• 
  Marianna De Santis, Francesco Rinaldi, Emmanuela Falcone, Stefano Lucidi, Giulia Piaggio, Aymone Gurtner, Lorenzo Farina:
  Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes. 228-233

Data and Text Mining

• 
  Attila Kertész-Farkas, Beáta Reiz, Roberto Vera, Michael P. Myers, Sándor Pongor:
  PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 234-241
• 
  Mohammad Shahrokh Esfahani, Edward R. Dougherty:
  Effect of separate sampling on classification accuracy. 242-250

Databases and Ontologies

• 
  Mandy L. Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud:
  Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. 251-257
• 
  Álvaro Sebastián, Bruno Contreras-Moreira:
  footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. 258-265

Bioimage Informatics

• 
  Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye:
  Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. 266-273

Sequence Analysis

• 
  Nicolas Terrapon, January 3rd Weiner, Sonja Grath, Andrew D. Moore, Erich Bornberg-Bauer:
  Rapid similarity search of proteins using alignments of domain arrangements. 274-281

Applications Notes - Sequence Analysis

• 
  Andrew D. Moore, Andreas Held, Nicolas Terrapon, January 3rd Weiner, Erich Bornberg-Bauer:
  DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. 282-283
• 
  Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chavez:
  MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. 284-286
• 
  João F. Matias Rodrigues, Christian von Mering:
  HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. 287-288

Gene Expression

• 
  Toma Tebaldi, Erik Dassi, Galena Kostoska, Gabriella Viero, Alessandro Quattrone:
  tRanslatome: an R/Bioconductor package to portray translational control. 289-291

Systems Biology

• 
  Michael L. Blinov, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru, Leslie M. Loew:
  Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. 292-294

Databases and Ontologies

• 
  Luke E. Ulrich, Igor B. Zhulin:
  SeqDepot: streamlined database of biological sequences and precomputed features. 295-297
• 
  Rodrigo Ochoa, Mark Davies, George Papadatos, Francis Atkinson, John P. Overington:
  myChEMBL: a virtual machine implementation of open data and cheminformatics tools. 298-300

Volume 30, Number 3, February 2014

Discovery Notes - Gene Expression

• 
  Yuwen Liu, Jie Zhou, Kevin P. White:
  RNA-seq differential expression studies: more sequence or more replication? 301-304

Systems Biology

• 
  Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-yu Zhang:
  Identification of transcription factors for drug-associated gene modules and biomedical implications. 305-309

Original Papers Genome Analysis

• 
  Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi:
  Spatial regulation dominates gene function in the ganglia chain. 310-316

Sequence Analysis

• 
  Kazunori D. Yamada, Kentaro Tomii:
  Revisiting amino acid substitution matrices for identifying distantly related proteins. 317-325

Structural Bioinformatics

• 
  Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
  Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. 326-334
• 
  Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
  mCSM: predicting the effects of mutations in proteins using graph-based signatures. 335-342
• 
  Luke Day, Ouala Abdelhadi Ep Souki, Andreas Alexander Albrecht, Kathleen Steinhöfel:
  Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs. 343-352
• 
  Hamidreza Khataee, Alan Wee-Chung Liew:
  A mathematical model describing the mechanical kinetics of kinesin stepping. 353-359

Gene Expression

• 
  Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko:
  Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. 360-368
• 
  Chuan Gao, Nicole L. Tignor, Jacqueline Salit, Yael Strulovici-Barel, Neil R. Hackett, Ronald G. Crystal, Jason G. Mezey:
  HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. 369-376
• 
  Hari Krishna Yalamanchili, Bin Yan, Mulin Jun Li, Jing Qin, Zhongying Zhao, Francis Y. L. Chin, Junwen Wang:
  DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. 377-383

Genetics and Population Analysis

• 
  Barbara Di Camillo, Francesco Sambo, Gianna Toffolo, Claudio Cobelli:
  ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. 384-391

Systems Biology

• 
  Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen:
  Protein-driven inference of miRNA-disease associations. 392-397
• 
  Jianlong Peng, Jing Lu, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
  In silico site of metabolism prediction for human UGT-catalyzed reactions. 398-405
• 
  Matan Bodaker, Eran Meshorer, Eduardo Mitrani, Yoram Louzoun:
  Genes related to differentiation are correlated with the gene regulatory network structure. 406-413
• 
  Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch:
  Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. 414-419

Bioimage Informatics

• 
  Violeta N. Kovacheva, Adnan Mujahid Khan, Michael Khan, David B. A. Epstein, Nasir M. Rajpoot:
  DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data. 420-427

Applications Notes - Genome Analysis

• 
  Tiffany J. Morris, Lee M. Butcher, Andrew Feber, Andrew E. Teschendorff, Ankur R. Chakravarthy, Tomasz K. Wojdacz, Stephan Beck:
  ChAMP: 450k Chip Analysis Methylation Pipeline. 428-430
• 
  Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Joseph Wang, Guoqiang Yu:
  AISAIC: a software suite for accurate identification of significant aberrations in cancers. 431-433

Sequence Analysis

• 
  Guan-Zheng Luo, Wei Yang, Ying-Ke Ma, Xiu-Jie Wang:
  ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. 434-436

Structural Bioinformatics

• 
  Esteban López-Camacho, María Jesús García-Godoy, Antonio J. Nebro, José Francisco Aldana Montes:
  jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework. 437-438
• 
  Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel:
  MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. 439-441

Genetics and Population Analysis

• 
  Biao Li, Gao T. Wang, Suzanne M. Leal:
  PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants. 442-444

Data and Text Mining

• 
  Zeliha Görmez, Burcu Bakir-Gungor, Mahmut Samil Sagiroglu:
  HomSI: a homozygous stretch identifier from next-generation sequencing data. 445-447

Volume 30, Number 4, February 2014

Sequence Analysis

• 
  Olga Tanaseichuk, James Borneman, Tao Jiang:
  Phylogeny-based classification of microbial communities. 449-456
• 
  Ruslan A. Soldatov, Svetlana V. Vinogradova, Andrey A. Mironov:
  RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. 457-463
• 
  Francisco Fernandes, Ana T. Freitas:
  slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array. 464-471
• 
  Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou:
  Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. 472-479
• 
  Song Yan, Yun Li:
  BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. 480-487

Phylogenetics

• 
  Nicolas Lartillot:
  A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. 488-496

Structural Bioinformatics

• 
  Hua Zhang, Lukasz A. Kurgan:
  Sequence-based Gaussian network model for protein dynamics. 497-505

Gene Expression

• 
  Chen Suo, Stefano Calza, Agus Salim, Yudi Pawitan:
  Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. 506-513
• 
  Hongjie Zhu, Man Luo:
  Chemical structure informing statistical hypothesis testing in metabolomics. 514-522

Systems Biology

• 
  Andreas Krämer, Jeff Green, Jack Pollard Jr., Stuart Tugendreich:
  Causal analysis approaches in Ingenuity Pathway Analysis. 523-530
• 
  Ferhat Alkan, Cesim Erten:
  BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. 531-539
• 
  Jialu Hu, Birte Kehr, Knut Reinert:
  NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. 540-548
• 
  Cong Zhou, Michael J. Walker, Andrew J. K. Williamson, Andrew Pierce, Carlo Berzuini, Caroline Dive, Anthony D. Whetton:
  A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data. 549-558

Data and Text Mining

• 
  Tomaz Hocevar, Janez Demsar:
  A combinatorial approach to graphlet counting. 559-565

Applications Notes - Sequence Analysis

• 
  Richard M. Leggett, Bernardo J. Clavijo, Leah Clissold, Matthew D. Clark, Mario Cáccamo:
  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. 566-568

Structural Bioinformatics

• 
  José Colmenares, Jesús Ortiz, Walter Rocchia:
  GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. 569-570

Gene Expression

• 
  Nicolas Jung, Frédéric Bertrand, Seiamak Bahram, Laurent Vallat, Myriam Maumy-Bertrand:
  Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network. 571-573
• 
  Raghavendra Hosur, Suzanne Szak, Alice Thai, Norm Allaire, Jadwiga R. Bienkowska:
  ProbeSelect: selecting differentially expressed probes in transcriptional profile data. 574-575

Genetics and Population Analysis

• 
  Darren Kessner, John Novembre:
  forqs: forward-in-time simulation of recombination, quantitative traits and selection. 576-577
• 
  Michel Petitjean, Anne Vanet:
  VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. 578-580

Systems Biology

• 
  Jiarui Zhou, Ralf J. M. Weber, James William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He, Mark R. Viant:
  HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries. 581-583
• 
  Longfei Mao, Wynand S. Verwoerd:
  ORCA: a COBRA toolbox extension for model-driven discovery and analysis. 584-585
• 
  Cheng Chang, Jiyang Zhang, Mingfei Han, Jie Ma, Wei Zhang, Songfeng Wu, Kehui Liu, Hongwei Xie, Fuchu He, Yunping Zhu:
  SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. 586-587

Data and Text Mining

• 
  Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha:
  HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. 588-589

Databases and Ontologies

• 
  Muhammad A. Shah, Emily Denton, Lihua Liu, Matthieu Schapira:
  ChromoHub V2: cancer genomics. 590-592
• 
  Dennis Bromley, Steven J. Rysavy, Robert Su, Rudesh D. Toofanny, Tom Schmidlin, Valerie Daggett:
  DIVE: a data intensive visualization engine. 593-595

Erratum - Sequence Analysis

• 
  Sarah Sheppard, Nathan D. Lawson, Lihua Julie Zhu:
  Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier. 596

Volume 30, Number 5, March 2014

Discovery note - Genome Analysis

• 
  Balamurugan Palanisamy, Rajasekaran Ekambaram, Klaus Heese:
  Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7. 597-600

Original Papers - Genome Analysis

• 
  Douglas D. Baumann, Rebecca W. Doerge:
  Robust adjustment of sequence tag abundance. 601-605
• 
  Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard:
  GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. 606-613
• 
  Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis:
  PEAR: a fast and accurate Illumina Paired-End reAd mergeR. 614-620
• 
  Yue Li, Anna Goldenberg, Ka-Chun Wong, Zhaolei Zhang:
  A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. 621-628

Sequence Analysis

• 
  Luis Miguel Rodriguez-Rojas, Konstantinos T. Konstantinidis:
  Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. 629-635
• 
  Matthew Levinson, Qing Zhou:
  A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes. 636-643
• 
  Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins,