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    Journal: Bioinformatics

    Volume 30, Issue 9

    1193 -- 1197Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. O'Neill, Ronald O'Keefe, Jameel Gheba, Ivan Erill. Characterization of the SOS meta-regulon in the human gut microbiome
    1198 -- 1204Moritz Gerstung, Elli Papaemmanuil, Peter J. Campbell. Subclonal variant calling with multiple samples and prior knowledge
    1205 -- 1213Hannes Planatscher, Frederik Weiß, David Eisen, B. H. J. van den Berg, Andreas Zell, Thomas Joos, Oliver Poetz. Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
    1214 -- 1219Chengxi Ye, Chiaowen Hsiao, Héctor Corrada Bravo. BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
    1220 -- 1227Gorka Prieto, Asier Fullaondo, Jose A. Rodriguez. Prediction of nuclear export signals using weighted regular expressions (Wregex)
    1228 -- 1235Jared T. Simpson. Exploring genome characteristics and sequence quality without a reference
    1236 -- 1240Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka, Sebastien Pesseat, Antony F. Quinn, Amaia Sangrador-Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo Lopez, Sarah Hunter. InterProScan 5: genome-scale protein function classification
    1241 -- 1249Linda Dib, Daniele Silvestro, Nicolas Salamin. Evolutionary footprint of coevolving positions in genes
    1250 -- 1258Ali Esmaili-Taheri, Mohammad Ganjtabesh, Morteza Mohammad Noori. Evolutionary solution for the RNA design problem
    1259 -- 1265Noël Malod-Dognin, Natasa Przulj. GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
    1266 -- 1272Richard Durbin. Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)
    1273 -- 1279Stefan Maetschke, Mark A. Ragan. Characterizing cancer subtypes as attractors of Hopfield networks
    1280 -- 1286Pierre Mahé, Maud Arsac, Sonia Chatellier, Valérie Monnin, Nadine Perrot, Sandrine Mailler, Victoria Girard, Mahendrasingh Ramjeet, Jérémy Surre, Bruno Lacroix, Alex van Belkum, Jean-Baptiste Veyrieras. Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
    1287 -- 1289Burcu Bakir-Gungor, Ece Egemen, Osman Ugur Sezerman. PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
    1290 -- 1291David Sims, Nicholas E. Ilott, Stephen N. Sansom, Ian M. Sudbery, Jethro S. Johnson, Katherine A. Fawcett, Antonio J. Berlanga-Taylor, Sebastian Luna-Valero, Chris P. Ponting, Andreas Heger. CGAT: computational genomics analysis toolkit
    1292 -- 1294Samuel A. Assefa, Mark D. Preston, Susana G. Campino, Harold Ocholla, Colin J. Sutherland, Taane G. Clark. estMOI: estimating multiplicity of infection using parasite deep sequencing data
    1295 -- 1296Xin Lu, Roman K. Thomas, Martin Peifer. CGARS: cancer genome analysis by rank sums
    1297 -- 1299Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao. PanGP: A tool for quickly analyzing bacterial pan-genome profile
    1300 -- 1301Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch. Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
    1302 -- 1304Michael T. McCarthy, Christopher A. O'Callaghan. PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
    1305 -- 1307Glen Stecher, Li Liu, Maxwell Sanderford, Daniel Peterson, Koichiro Tamura, Sudhir Kumar. MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
    1308 -- 1309Garry Jolley-Rogers, Temi Varghese, Paul Harvey, Nick dos Remedios, Joseph T. Miller. PhyloJIVE: Integrating biodiversity data with the Tree of Life
    1310 -- 1311Jose Manuel Santorum, Diego Darriba, Guillermo L. Taboada, David Posada. jmodeltest.org: selection of nucleotide substitution models on the cloud
    1312 -- 1313Alexandros Stamatakis. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    1314 -- 1315Alejandro Panjkovich, Xavier Daura. PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
    1316 -- 1318Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sánchez-Rodríguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen. MAGIC: access portal to a cross-platform gene expression compendium for maize
    1319 -- 1321Ivan Montiel, Charlotte Konikoff, Bremen Braun, Mary Packard, Sian L. Gramates, Qian Sun, Jieping Ye, Sudhir Kumar. Drosophila embryos
    1322 -- 1324Laurent Gatto, Lisa M. Breckels, Samuel Wieczorek, Thomas Burger, Kathryn S. Lilley. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
    1325 -- 1326Yupeng Cun, Holger Fröhlich. netClass: an R-package for network based, integrative biomarker signature discovery
    1327 -- 1328Paul A. Jensen, Jason A. Papin. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data
    1329 -- 1330Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger Hoos, Ryan R. Brinkman. Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data
    1331 -- 1332Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch. Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
    1333 -- 1335Jamey D. Young. INCA: a computational platform for isotopically non-stationary metabolic flux analysis
    1336 -- 1337Ricardo R. Silva, Fabien Jourdan, Diego M. Salvanha, Fabien Letisse, Emilien L. Jamin, Simone Guidetti-Gonzalez, Carlos A. Labate, Ricardo Z. N. Vêncio. R package for Bayesian probabilistic annotation of LC-MS-based metabolomics
    1338 -- 1339Simon Jupp, James Malone, Jerven Bolleman, Marco Brandizi, Mark Davies, Leyla J. Garcia, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson. The EBI RDF platform: linked open data for the life sciences
    1340 -- 1342Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He. Ontodog: a web-based ontology community view generation tool

    Volume 30, Issue 8

    1049 -- 1055Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting-Fung Chan, Terrence Chi Kong Lau, Siu-Ming Yiu, Kevin Y. Yip. Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data
    1056 -- 1063Lei Bao, Minya Pu, Karen Messer. AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data
    1064 -- 1072Jan Schröder, Arthur Hsu, Samantha E. Boyle, Geoff Macintyre, Marek Cmero, Richard W. Tothill, Ricky W. Johnstone, Mark Shackleton, Anthony T. Papenfuss. Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
    1073 -- 1080Wanding Zhou, Tenghui Chen, Hao Zhao, Agda Karina Eterovic, Funda Meric-Bernstam, Gordon B. Mills, Ken Chen. Bias from removing read duplication in ultra-deep sequencing experiments
    1081 -- 1086Kamil S. Jaron, Jirí C. Moravec, Natália Martínková. SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
    1087 -- 1094Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray. D-Tailor: automated analysis and design of DNA sequences
    1095 -- 1103Atsushi Kurotani, Alexander A. Tokmakov, Yutaka Kuroda, Yasuo Fukami, Kazuo Shinozaki, Tetsuya Sakurai. Correlations between predicted protein disorder and post-translational modifications in plants
    1104 -- 1111Josep Gregori, Miquel Salicru, Esteban Domingo, Alex Sánchez-Pla, Juan I. Esteban, Francisco Rodríguez-Frías, Josep Quer. Inference with viral quasispecies diversity indices: clonal and NGS approaches
    1112 -- 1119Ka Chun Wong, Zhaolei Zhang. SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
    1120 -- 1128Ha X. Dang, Christopher B. Lawrence. Allerdictor: fast allergen prediction using text classification techniques
    1129 -- 1137Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin. Optimization strategies for fast detection of positive selection on phylogenetic trees
    1138 -- 1145Derek J. Pitman, Christian D. Schenkelberg, Yao-ming Huang, Frank D. Teets, Daniel DiTursi, Christopher Bystroff. Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design
    1146 -- 1153Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro. Estimation of fluorescence-tagged RNA numbers from spot intensities
    1154 -- 1162Hans-Ulrich Klein, Martin Schäfer, Bo T. Porse, Marie S. Hasemann, Katja Ickstadt, Martin Dugas. Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models
    1163 -- 1171Ming Wu, Christina Chan. Prediction of therapeutic microRNA based on the human metabolic network
    1172 -- 1174Hamid Younesy, Torsten Möller, Alireza Heravi Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones. ALEA: a toolbox for allele-specific epigenomics analysis
    1175 -- 1176Jianchao Yao, Kelvin Xi Zhang, Melissa Kramer, Matteo Pellegrini, W. Richard McCombie. FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies
    1177 -- 1179L. Cebamanos, A. Gray, I. Stewart, A. Tenesa. Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures
    1180 -- 1182An Xiao, Zhenchao Cheng, Lei Kong, Zuoyan Zhu, Shuo Lin, Ge Gao, Bo Zhang. CasOT: a genome-wide Cas9/gRNA off-target searching tool
    1183 -- 1184Emmanuel Dimont, Oliver Hofmann, Shannan J. Ho Sui, Alistair R. R. Forrest, Hideya Kawaji, Winston Hide. CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments
    1185 -- 1186Peter J. van der Most, Ahmad Vaez, Bram P. Prins, M. Loretto Munoz, Harold Snieder, Behrooz Z. Alizadeh, Ilja M. Nolte. QCGWAS: A flexible R package for automated quality control of genome-wide association results
    1187 -- 1189Jean-Marie Cornuet, Pierre Pudlo, Julien Veyssier, Alexandre Dehne-Garcia, Mathieu Gautier, Raphael Leblois, Jean-Michel Marin, Arnaud Estoup. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
    1190 -- 1192Daogang Guan, Jiaofang Shao, Youping Deng, Panwen Wang, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan. CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data

    Volume 30, Issue 7

    899 -- 902Kenneth B. Schou, Jens S. Andersen, Lotte B. Pedersen. A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins
    903 -- 907Lucian P. Smith, Erik Butterworth, James B. Bassingthwaighte, Herbert M. Sauro. SBML and CellML translation in Antimony and JSim
    908 -- 914Nha Nguyen, An Vo, Kyoung-Jae Won. A wavelet-based method to exploit epigenomic language in the regulatory region
    915 -- 922Yu Qian, Brian L. Browning, Sharon R. Browning. Efficient clustering of identity-by-descent between multiple individuals
    923 -- 930Yang Liao, Gordon K. Smyth, Wei Shi. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
    931 -- 940Dan Ofer, Michal Linial. NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
    941 -- 948Ronak Y. Patel, Gary D. Stormo. Discriminative motif optimization based on perceptron training
    949 -- 955Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li. Fingerprinting protein structures effectively and efficiently
    956 -- 961Amit G. Deshwar, Quaid Morris. PLIDA: cross-platform gene expression normalization using perturbed topic models
    962 -- 970Krzysztof Polanski, Johanna Rhodes, Claire Hill, Peijun Zhang, Dafyd J. Jenkins, Steven J. Kiddle, Aleksey Jironkin, Jim Beynon, Vicky Buchanan-Wollaston, Sascha Ott, Katherine J. Denby. Wigwams: identifying gene modules co-regulated across multiple biological conditions
    971 -- 974Hadi Jorjani, Mihaela Zavolan. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data
    975 -- 980Jon Pey, Francisco J. Planes, John E. Beasley. Refining carbon flux paths using atomic trace data
    981 -- 987Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa. FastPros: screening of reaction knockout strategies for metabolic engineering
    988 -- 995Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye. BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry
    996 -- 1002Lin Yang, Xin Qi, Fuyong Xing, Tahsin M. Kurç, Joel H. Saltz, David J. Foran. Parallel content-based sub-image retrieval using hierarchical searching
    1003 -- 1005Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
    1006 -- 1007Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre Kocher, Liguo Wang. CrossMap: a versatile tool for coordinate conversion between genome assemblies
    1008 -- 1009Daniel R. Zerbino, Nathan Johnson, Thomas Juettemann, Steven P. Wilder, Paul Flicek. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
    1010 -- 1012Jaebum Kim, Jian Ma. PSAR-Align: improving multiple sequence alignment using probabilistic sampling
    1013 -- 1014Hue Vuong, Robert M. Stephens, Natalia Volfovsky. AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
    1015 -- 1016Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl, Li Ding. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
    1017 -- 1019Sebastián Duchêne, Martyna Molak, Simon Y. W. Ho. ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
    1020 -- 1021Nicolas Rodrigue, Nicolas Lartillot. Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package
    1022 -- 1024Silvia Caprari, Daniele Toti, Le Viet Hung, Maurizio Di Stefano, Fabio Polticelli. ASSIST: a fast versatile local structural comparison tool
    1025 -- 1026Eric Wu, Tracy Nance, Stephen B. Montgomery. SplicePlot: a utility for visualizing splicing quantitative trait loci
    1027 -- 1028Ida Moltke, Anders Albrechtsen. RelateAdmix: a software tool for estimating relatedness between admixed individuals
    1029 -- 1030Charles Winterhalter, Pawel Widera, Natalio Krasnogor. JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
    1031 -- 1033Xiaoquan Su, Xuetao Wang, Gongchao Jing, Kang Ning. GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU
    1034 -- 1035Jan Taubert, Keywan Hassani-Pak, Nathalie Castells-Brooke, Christopher J. Rawlings. Ondex Web: web-based visualization and exploration of heterogeneous biological networks
    1036 -- 1038John T. Sauls, Joerg M. Buescher. Assimilating genome-scale metabolic reconstructions with modelBorgifier
    1039 -- 1040Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia. CheNER: chemical named entity recognizer
    1041 -- 1042Rodrigo Aldecoa, Ignacio Marín. SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization
    1043 -- 1044Mengyuan Fan, Hong Sang Low, Hufeng Zhou, Markus Wenk, Limsoon Wong. LipidGO: database for lipid-related GO terms and applications
    1045 -- 1046Changqing Zhang, Guangping Li, Shinong Zhu, Shuo Zhang, Jinggui Fang. tasiRNAdb: a database of ta-siRNA regulatory pathways
    1047 -- 1048Nestoras Karathanasis, Ioannis Tsamardinos, Panayiota Poirazi. Don't use a cannon to kill the ... miRNA mosquito

    Volume 30, Issue 6

    748 -- 752Gong-Hua Li, Jing-Fei Huang. Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer
    753 -- 760Chandler Zuo, Sündüz Keles. A statistical framework for power calculations in ChIP-seq experiments
    761 -- 767Jung-Hsien Chiang, Chan-Hsien Lin. NCS: incorporating positioning data to quantify nucleosome stability in yeast
    768 -- 774Carson Holt, Bojan Losic, Deepa Pai, Zhen Zhao, Quang Trinh, Sujata Syam, Niloofar Arshadi, Gun Ho Jang, Johar Ali, Tim Beck, John McPherson, Lakshmi B. Muthuswamy. WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing
    775 -- 783Zizhen Yao, Kyle L. MacQuarrie, Abraham P. Fong, Stephen J. Tapscott, Walter L. Ruzzo, Robert Gentleman. Discriminative motif analysis of high-throughput dataset
    784 -- 791Frédéric Guyon, Pierre Tufféry. Fast protein fragment similarity scoring using a Binet-Cauchy kernel
    792 -- 800Lydia Benkaidali, François André, Boubekeur Maouche, Pridi Siregar, Mohamed Benyettou, François Maurel, Michel Petitjean. Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models
    801 -- 807Yufei Xiao, Tzu-Hung Hsiao, Uthra Suresh, Hung-I Harry Chen, Xiaowu Wu, Steven E. Wolf, Yidong Chen. A novel significance score for gene selection and ranking
    808 -- 814Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J. Fazakerley, James G. Burchfield, Christopher Gribben, Matthew J. Prior, David E. James, Yee Hwa Yang. Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway
    815 -- 822Koichiro Doi, Taku Monjo, Pham H. Hoang, Jun Yoshimura, Hideaki Yurino, Jun Mitsui, Hiroyuki Ishiura, Yuji Takahashi, Yaeko Ichikawa, Jun Goto, Shoji Tsuji, Shinichi Morishita. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing
    823 -- 830Pengzhan Hu, Zhongchao Shen, Haibo Tu, Li Zhang, Tieliu Shi. Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach
    831 -- 837Tanya P. Garcia, Samuel Müller, Raymond J. Carroll, Rosemary L. Walzem. Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data
    838 -- 845José A. Seoane, Ian N. M. Day, Tom R. Gaunt, Colin Campbell. A pathway-based data integration framework for prediction of disease progression
    846 -- 851Ivan Dimitrov, Lyudmila Naneva, Irini A. Doytchinova, Ivan Bangov. AllergenFP: allergenicity prediction by descriptor fingerprints
    852 -- 859Xiangtian Yu, Guojun Li, Luonan Chen. Prediction and early diagnosis of complex diseases by edge-network
    860 -- 867Senol Isci, Haluk Dogan, Cengizhan Ozturk, Hasan H. Otu. Bayesian network prior: network analysis of biological data using external knowledge
    868 -- 875Sampo Pyysalo, Sophia Ananiadou. Anatomical entity mention recognition at literature scale
    876 -- 883Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann. The functional therapeutic chemical classification system
    884 -- 886Ulrich Omasits, Christian H. Ahrens, Sebastian Müller, Bernd Wollscheid. Protter: interactive protein feature visualization and integration with experimental proteomic data
    887 -- 888Sutharzan Sreeskandarajan, Michelle M. Flowers, John E. Karro, Chun Liang. A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences
    889 -- 890Anton A. Polyansky, Anton O. Chugunov, Pavel E. Volynsky, Nikolay A. Krylov, Dmitry E. Nolde, Roman G. Efremov. PREDDIMER: a web server for prediction of transmembrane helical dimers
    891 -- 892Xavier Rogé, Xuegong Zhang. RNAseqViewer: visualization tool for RNA-Seq data
    893 -- 895Joram M. Posma, Steven L. Robinette, Elaine Holmes, Jeremy K. Nicholson. MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG
    896 -- 898Daniel Jaeger, Johannes Barth, Anna Niehues, Christian Fufezan. pyGCluster, a novel hierarchical clustering approach

    Volume 30, Issue 5

    597 -- 600Balamurugan Palanisamy, Rajasekaran Ekambaram, Klaus Heese. Plasmodium falciparum 3D7
    601 -- 605Douglas D. Baumann, Rebecca W. Doerge. Robust adjustment of sequence tag abundance
    606 -- 613Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard. GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads
    614 -- 620Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis. PEAR: a fast and accurate Illumina Paired-End reAd mergeR
    621 -- 628Yue Li, Anna Goldenberg, Ka Chun Wong, Zhaolei Zhang. A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information
    629 -- 635Luis M. Rodriguez-R, Konstantinos T. Konstantinidis. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
    636 -- 643Matthew Levinson, Qing Zhou. A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes
    644 -- 651Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin Collins, Evan E. Eichler, Süleyman Cenk Sahinalp. ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
    652 -- 659Hongseok Tae, Dong-Yun Kim, John McCormick, Robert E. Settlage, Harold R. Garner. Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs
    660 -- 667Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik. FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking
    668 -- 674Giuseppe Maccari, Giulia L. B. Spampinato, Valentina Tozzini. SecStAnT: secondary structure analysis tool for data selection, statistics and models building
    675 -- 681Ben-teng, Ting Huang, Zengyou He. Decoy-free protein-level false discovery rate estimation
    682 -- 689David A. Liebner, Kun Huang, Jeffrey D. Parvin. MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples
    690 -- 697Marina Evangelou, Frank Dudbridge, Lorenz Wernisch. Two novel pathway analysis methods based on a hierarchical model
    698 -- 705Emily Rose Holzinger, Scott M. Dudek, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie. ATHENA: the analysis tool for heritable and environmental network associations
    706 -- 711Tomomi Ichimiya, Shoko Nishihara, Sayaka Takase-Yoden, Hiroshi Kida, Kiyoko F. Aoki-Kinoshita. Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection
    712 -- 718Joseph Geraci, Moyez Dharsee, Paulo A. S. Nuin, Alexandria Haslehurst, Madhuri Koti, Harriet E. Feilotter, Ken Evans. Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems
    719 -- 725Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier. Mouse model phenotypes provide information about human drug targets
    726 -- 733Johannes Stegmaier, Maryam Shahid, Masanari Takamiya, Lixin Yang, Sepand Rastegar, Markus Reischl, Uwe Strähle, Ralf Mikut. Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish
    734 -- 736Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov. orthAgogue: an agile tool for the rapid prediction of orthology relations
    737 -- 739Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu. iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis
    740 -- 742Sébastien Harispe, Sylvie Ranwez, Stefan Janaqi, Jacky Montmain. The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies
    743 -- 745Eric C. Anderson, Thomas C. Ng. Comment on 'Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching'

    Volume 30, Issue 4

    449 -- 456Olga Tanaseichuk, James Borneman, Tao Jiang. Phylogeny-based classification of microbial communities
    457 -- 463Ruslan A. Soldatov, Svetlana V. Vinogradova, Andrey A. Mironov. RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments
    464 -- 471Francisco Fernandes, Ana T. Freitas. slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array
    472 -- 479Bin Liu 0014, 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
    480 -- 487Song Yan, Yun Li. BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing
    488 -- 496Nicolas Lartillot. A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data
    497 -- 505Hua Zhang, Lukasz A. Kurgan. Sequence-based Gaussian network model for protein dynamics
    506 -- 513Chen Suo, Stefano Calza, Agus Salim, Yudi Pawitan. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data
    514 -- 522Hongjie Zhu, Man Luo. Chemical structure informing statistical hypothesis testing in metabolomics
    523 -- 530Andreas Krämer, Jeff Green, Jack Pollard Jr., Stuart Tugendreich. Causal analysis approaches in Ingenuity Pathway Analysis
    531 -- 539Ferhat Alkan, Cesim Erten. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
    540 -- 548Jialu Hu, Birte Kehr, Knut Reinert. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks
    549 -- 558Cong 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
    559 -- 565Tomaz Hocevar, Janez Demsar. A combinatorial approach to graphlet counting
    566 -- 568Richard M. Leggett, Bernardo J. Clavijo, Leah Clissold, Matthew D. Clark, Mario Caccamo. NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
    569 -- 570José Colmenares, Jesús Ortiz, Walter Rocchia. GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi
    571 -- 573Nicolas 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
    574 -- 575Raghavendra Hosur, Suzanne Szak, Alice Thai, Norm Allaire, Jadwiga Bienkowska. ProbeSelect: selecting differentially expressed probes in transcriptional profile data
    576 -- 577Darren Kessner, John Novembre. forqs: forward-in-time simulation of recombination, quantitative traits and selection
    578 -- 580Michel Petitjean, Anne Vanet. VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations
    581 -- 583Jiarui Zhou, Ralf J. M. Weber, James William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He 0001, Mark R. Viant. in silico mass spectral fragmentation libraries
    584 -- 585Longfei Mao, Wynand S. Verwoerd. ORCA: a COBRA toolbox extension for model-driven discovery and analysis
    586 -- 587Cheng 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
    588 -- 589Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha. HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data
    590 -- 592Muhammad A. Shah, Emily Denton, Lihua Liu, Matthieu Schapira. ChromoHub V2: cancer genomics
    593 -- 595Dennis Bromley, Steven J. Rysavy, Robert Su, Rudesh D. Toofanny, Tom Schmidlin, Valerie Daggett. DIVE: a data intensive visualization engine
    596 -- 0Sarah Sheppard, Nathan D. Lawson, Lihua Julie Zhu. Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier

    Volume 30, Issue 3

    301 -- 304Yuwen Liu, Jie Zhou, Kevin P. White. RNA-seq differential expression studies: more sequence or more replication?
    305 -- 309Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-Yu Zhang. Identification of transcription factors for drug-associated gene modules and biomedical implications
    310 -- 316Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi. Spatial regulation dominates gene function in the ganglia chain
    317 -- 325Kazunori Yamada, Kentaro Tomii. Revisiting amino acid substitution matrices for identifying distantly related proteins
    326 -- 334Ali 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
    335 -- 342Douglas E. V. Pires, David B. Ascher, Tom L. Blundell. mCSM: predicting the effects of mutations in proteins using graph-based signatures
    343 -- 352Luke 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
    353 -- 359Hamidreza Khataee, Alan Wee-Chung Liew. A mathematical model describing the mechanical kinetics of kinesin stepping
    360 -- 368Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko. Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
    369 -- 376Chuan 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
    377 -- 383Hari 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
    384 -- 391Barbara 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
    392 -- 397Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen. Protein-driven inference of miRNA-disease associations
    398 -- 405Jianlong 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
    406 -- 413Matan Bodaker, Eran Meshorer, Eduardo Mitrani, Yoram Louzoun. Genes related to differentiation are correlated with the gene regulatory network structure
    414 -- 419Sebastian 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
    420 -- 427Violeta N. Kovacheva, Adnan Mujahid Khan, Michael Khan, David Bernard Alper Epstein, Nasir M. Rajpoot. DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data
    428 -- 430Tiffany J. Morris, Lee M. Butcher, Andrew Feber, Andrew E. Teschendorff, Ankur R. Chakravarthy, Tomasz K. Wojdacz, Stephan Beck. ChAMP: 450k Chip Analysis Methylation Pipeline
    431 -- 433Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Wang, Guoqiang Yu. AISAIC: a software suite for accurate identification of significant aberrations in cancers
    434 -- 436Guan-Zheng Luo, Wei Yang, Ying-Ke Ma, Xiu-Jie Wang. ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data
    437 -- 438Esteban López-Camacho, María Jesús García-Godoy, Antonio J. Nebro, José Francisco Aldana Montes. jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework
    439 -- 441Mohammad 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
    442 -- 444Biao Li, Gao Wang, Suzanne M. Leal. PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants
    445 -- 447Zeliha Görmez, Burcu Bakir-Gungor, Mahmut Samil Sagiroglu. HomSI: a homozygous stretch identifier from next-generation sequencing data

    Volume 30, Issue 24

    3443 -- 3450Valentina Boeva, Tatiana Popova, Maxime Lienard, Sebastien Toffoli, Maud Kamal, Christophe Le Tourneau, David Gentien, Nicolas Servant, Pierre Gestraud, Thomas Rio Frio, Philippe Hupé, Emmanuel Barillot, Jean-François Laes. Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
    3451 -- 3457Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre. MindTheGap: integrated detection and assembly of short and long insertions
    3458 -- 3466Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael. Characterization of structural variants with single molecule and hybrid sequencing approaches
    3467 -- 3475Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa. Detecting differential peaks in ChIP-seq signals with ODIN
    3476 -- 3483Shoshana Marcus, Hayan Lee, Michael C. Schatz. SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
    3484 -- 3490Kathrin Trappe, Anne-Katrin Emde, Hans-Christian Ehrlich, Knut Reinert. Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone
    3491 -- 3498Ajay Ummat, Ali Bashir. Resolving complex tandem repeats with long reads
    3499 -- 3505René Rahn, David Weese, Knut Reinert. Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop
    3506 -- 3514Leena Salmela, Eric Rivals. LoRDEC: accurate and efficient long read error correction
    3515 -- 3523Ilan Ben-Bassat, Benny Chor. String graph construction using incremental hashing
    3524 -- 3531James Holt, Leonard McMillan. Merging of multi-string BWTs with applications
    3532 -- 3540Layla Oesper, Gryte Satas, Benjamin J. Raphael. Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
    3541 -- 3547Páll Melsted, Bjarni V. Halldórsson. k-mer abundance estimation
    3548 -- 3555Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy Warnow. TIPP: taxonomic identification and phylogenetic profiling
    3556 -- 3557Marco Beccuti, Matteo Carrara, Francesca Cordero, Fulvio Lazzarato, Susanna Donatelli, Francesca Nadalin, Alberto Policriti, Raffaele Calogero. Chimera: a Bioconductor package for secondary analysis of fusion products
    3558 -- 3560Michael Keane, Thomas Craig, Jessica Alföldi, Aaron M. Berlin, Jeremy Johnson, Andrei Seluanov, Vera Gorbunova, Federica Di Palma, Kerstin Lindblad-Toh, George M. Church, João Pedro de Magalhães. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
    3561 -- 3566Gang Hu, Kui Wang, Jody Groenendyk, Khaled Barakat, Marcin J. Mizianty, Jishou Ruan, Marek Michalak, Lukasz A. Kurgan. Human structural proteome-wide characterization of Cyclosporine A targets
    3567 -- 3574David E. Frankhouser, Mark Murphy, James S. Blachly, Jincheol Park, Mike W. Zoller, Javkhlan-Ochir Ganbat, John Curfman, John C. Byrd, Shili Lin, Guido Marcucci, Pearlly Yan, Ralf Bundschuh. PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data
    3575 -- 3582Sergey L. Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge. Frameshift alignment: statistics and post-genomic applications
    3583 -- 3589K. Yugandhar, M. Michael Gromiha. Protein-protein binding affinity prediction from amino acid sequence
    3590 -- 3597Jérôme Ambroise, Yann Deccache, Leonid Irenge, Encho Savov, Annie Robert, Jean-Luc Gala. Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping
    3598 -- 3600Daniel Lobo, Erica B. Feldman, Michelle Shah, Taylor J. Malone, Michael Levin. Limbform: a functional ontology-based database of limb regeneration experiments

    Volume 30, Issue 23

    3293 -- 3301Ngan Nguyen, Glenn Hickey, Brian J. Raney, Joel Armstrong, Hiram Clawson, Ann S. Zweig, Donna Karolchik, William James Kent, David Haussler, Benedict Paten. Comparative assembly hubs: Web-accessible browsers for comparative genomics
    3302 -- 3309Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto. HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations
    3310 -- 3316András Szolek, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, Oliver Kohlbacher. OptiType: precision HLA typing from next-generation sequencing data
    3317 -- 3324Julia Chifman, Laura Salter Kubatko. Quartet Inference from SNP Data Under the Coalescent Model
    3325 -- 3333Fan Zhu, Lihong Shi, Hongdong Li, Ridvan Eksi, James Douglas Engel, Yuanfang Guan. ex vivo human erythroid differentiation
    3334 -- 3341Wei Xie, Murat Kantarcioglu, William S. Bush, Dana C. Crawford, Joshua C. Denny, Raymond Heatherly, Bradley A. Malin. SecureMA: protecting participant privacy in genetic association meta-analysis
    3342 -- 3348Oliver S. Burren, Hui Guo, Chris Wallace. ESRRA as key transcription factors in type 1 diabetes
    3349 -- 3355Ulisses Braga-Neto, Amin Zollanvari, Edward R. Dougherty. Cross-validation under separate sampling: strong bias and how to correct it
    3356 -- 3364Cornelia M. Hooper, Sandra K. Tanz, Ian R. Castleden, Michael A. Vacher, Ian D. Small, A. Harvey Millar. Arabidopsis proteome
    3365 -- 3371Quoc-Chinh Bui, Peter M. A. Sloot, Erik M. van Mulligen, Jan A. Kors. A novel feature-based approach to extract drug-drug interactions from biomedical text
    3372 -- 3378Kristen Feher, Jenny Kirsch, Andreas Radbruch, Hyun-Dong Chang, Toralf Kaiser. Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm
    3379 -- 3386Ming Ni, Fuqiang Ye, Juanjuan Zhu, Zongwei Li, Shuai Yang, Bite Yang, Lu Han, Yongge Wu, Ying Chen, Fei Li, Shengqi Wang, Xiaochen Bo. ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO
    3387 -- 3389Ian M. Campbell, Regis A. James, Edward S. Chen, Chad A. Shaw. NetComm: a network analysis tool based on communicability
    3390 -- 3393Aaron M. Newman, Scott V. Bratman, Henning Stehr, Luke J. Lee, Chih Long Liu, Maximilian Diehn, Ash A. Alizadeh. FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution
    3394 -- 3395Lukas R. Cara, Medina Baitemirova, Franklin Duong, Maia Larios-Sanz, Albert Ribes-Zamora. Finder, a Web-based tool for the identification of putative novel ATM and ATR targets
    3396 -- 3398Joaquín Tárraga, Vicente Arnau, Héctor Martínez, Raul Moreno, Diego Cazorla, José Salavert Torres, Ignacio Blanquer Espert, Joaquín Dopazo, Ignacio Medina. Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
    3399 -- 3401Nicholas J. Loman, Aaron R. Quinlan. Poretools: a toolkit for analyzing nanopore sequence data
    3402 -- 3404Justin Chu, Sara Sadeghi, Anthony Raymond, Shaun D. Jackman, Ka Ming Nip, Richard Mar, Hamid Mohamadi, Yaron S. N. Butterfield, A. Gordon Robertson, Inanç Birol. BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
    3405 -- 3407Melissa Gymrek. PyBamView: a browser-based application for viewing short read alignments
    3408 -- 3409Kiran Mukhyala, Alexandre Masselot. Visualization of protein sequence features using JavaScript and SVG with pViz.js
    3410 -- 3411Christopher Weidner, Cornelius Fischer, Sascha Sauer. PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins
    3412 -- 3413Carsten Kuenne, Jens Preussner, Mario Herzog, Thomas Braun, Mario Looso. MIRPIPE: quantification of microRNAs in niche model organisms
    3414 -- 3416Chen Wang, Jaime I. Davila, Saurabh Baheti, Aditya Bhagwate, Xue Wang, Jean-Pierre Kocher, Susan L. Slager, Andrew L. Feldman, Anne J. Novak, James R. Cerhan, E. Aubrey Thompson, Yan W. Asmann. RVboost: RNA-seq variants prioritization using a boosting method
    3417 -- 3418Sanjay Agravat, Joel H. Saltz, Richard D. Cummings, David F. Smith. GlycoPattern: a web platform for glycan array mining
    3419 -- 3420C. Winterhalter, Rémy Nicolle, A. Louis, Cuong To, François Radvanyi, Mohamed Elati. Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks
    3421 -- 3423Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma. READemption - a tool for the computational analysis of deep-sequencing-based transcriptome data
    3424 -- 3426David G. Robinson, John D. Storey. subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling
    3427 -- 3429Ilya Shlyakhter, Pardis C. Sabeti, Stephen F. Schaffner. Cosi2: an efficient simulator of exact and approximate coalescent with selection
    3430 -- 3431Paula Tataru, Jasmine A. Nirody, Yun S. Song. diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals
    3432 -- 3434Benjamin Voight. MR_predictor: a simulation engine for Mendelian Randomization studies
    3435 -- 3437Maarten van Iterson, Elmar W. Tobi, Roderick C. Slieker, Wouter den Hollander, René Luijk, P. Eline Slagboom, Bastiaan T. Heijmans. MethylAid: visual and interactive quality control of large Illumina 450k datasets
    3438 -- 3439Sean S. Ephraim, Nikhil Anand, Adam P. DeLuca, Kyle R. Taylor, Diana L. Kolbe, Allen C. Simpson, Hela Azaiez, Christina M. Sloan, A. Eliot Shearer, Andrea R. Hallier, Thomas L. Casavant, Todd E. Scheetz, Richard J. H. Smith, Terry A. Braun. Cordova: Web-based management of genetic variation data
    3440 -- 3442Imtiaz A. Khan, Adam Fraser, Mark-Anthony Bray, Paul J. Smith, Nick S. White, Anne E. Carpenter, Rachel J. Errington. ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments

    Volume 30, Issue 22

    3143 -- 3151Eduardo G. Gusmão, Christoph Dieterich, Martin Zenke, Ivan G. Costa. Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications
    3152 -- 3158Ying Ding, Shaowu Tang, Serena G. Liao, Jia Jia, Steffi Oesterreich, Yan Lin, George C. Tseng. Bias correction for selecting the minimal-error classifier from many machine learning models
    3159 -- 3165Timothy Daley, Andrew D. Smith. Modeling genome coverage in single-cell sequencing
    3166 -- 3173Joshua Loving, Yozen Hernandez, Gary Benson. BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm
    3174 -- 3180Yeting Zhang, Yazhou Sun. de novo nucleic acid diagnostic target discovery
    3181 -- 3188Niclas Thomas, Katharine Best, Mattia Cinelli, Shlomit Reich-Zeliger, Hilah Gal, Eric Shifrut, Asaf Madi, Nir Friedman, John Shawe-Taylor, Benny Chain. Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
    3189 -- 3196Daniel Taylor, Gavin C. Cawley, Steven Hayward. Quantitative method for the assignment of hinge and shear mechanism in protein domain movements
    3197 -- 3205Sungkyoung Choi, Sungyoung Lee, Sven Cichon, Markus M. Nöthen, Christoph Lange 0003, Taesung Park, Sungho Won. FARVAT: a family-based rare variant association test
    3206 -- 3214Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Myers Kadie, David Heckerman, Jennifer Listgarten. Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
    3215 -- 3222Damian Smedley, Sebastian Köhler, Johanna Christina Czeschik, Joanna S. Amberger, Carol A. Bocchini, Ada Hamosh, Julian Veldboer, Tomasz Zemojtel, Peter N. Robinson. Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases
    3223 -- 3231Dapeng Hao, Chuanxing Li, Shaojun Zhang, Jianping Lu, Yongshuai Jiang, Shiyuan Wang, Meng Zhou. Network-based analysis of genotype-phenotype correlations between different inheritance modes
    3232 -- 3239Siu Hung Joshua Chan, Christian Solem, Peter Ruhdal Jensen, Ping Ji. Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property
    3240 -- 3248Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur. Retro: concept-based clustering of biomedical topical sets
    3249 -- 3256Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider 0002, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos. +: a knowledge integration platform for literature mining and concept discovery
    3257 -- 3263Verena Starke, Andrew Steele. Thresher: an improved algorithm for peak height thresholding of microbial community profiles
    3264 -- 3265Eun-Cheon Lim, Jonas Müller, Jörg Hagmann, Stefan R. Henz, Sang-Tae Kim, Detlef Weigel. Trowel: a fast and accurate error correction module for Illumina sequencing reads
    3266 -- 3267David M. Curran, John S. Gilleard, James Wasmuth. Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes
    3268 -- 3269Carolin Walter, Daniel Schuetzmann, Frank Rosenbauer, Martin Dugas. Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
    3270 -- 3271Phi-Vu Nguyen, Chandra Shekhar Verma, Samuel Ken-En Gan. DNAApp: a mobile application for sequencing data analysis
    3272 -- 3273Michael Olejnik, Michel Steuwer, Sergei Gorlatch, Dominik Heider. gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing
    3274 -- 3275Heng Li. Fast construction of FM-index for long sequence reads
    3276 -- 3278Anders Larsson. AliView: a fast and lightweight alignment viewer and editor for large datasets
    3279 -- 3280Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Mar Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley. Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
    3281 -- 3283Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers
    3284 -- 3286Seon-Kyu Kim, Jong-Hwan Kim, Seok-Joong Yun, Wun-Jae Kim, Seon-Young Kim. APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer
    3287 -- 3288Michael Nodzenski, Michael J. Muehlbauer, James R. Bain, Anna C. Reisetter, William L. Lowe Jr., Denise M. Scholtens. Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data
    3289 -- 3290Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan. Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets
    3291 -- 3292David Breuer, Zoran Nikoloski. img2net: automated network-based analysis of imaged phenotypes

    Volume 30, Issue 21

    2993 -- 2998Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, et al.. Big data and other challenges in the quest for orthologs
    2999 -- 3003Irene Papatheodorou, Rudolfs Petrovs, Janet M. Thornton. Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing
    3004 -- 3011Thomas Hackl, Rainer Hedrich, Jörg Schultz, Frank Förster. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus
    3012 -- 3019Jessen T. Havill, Chinmoy Bhatiya, Steven M. Johnson, Joseph D. Sheets, Jeffrey S. Thompson. A new approach for detecting riboswitches in DNA sequences
    3020 -- 3028Benjamin Horvilleur, Nicolas Lartillot. Monte Carlo algorithms for Brownian phylogenetic models
    3029 -- 3035Christopher W. Wood, Marc Bruning, Amaurys Ávila Ibarra, Gail J. Bartlett, Andrew R. Thomson, Richard B. Sessions, R. Leo Brady, Derek N. Woolfson. CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
    3036 -- 3043Aliccia Bollig-Fischer, Luca Marchetti, Cristina Mitrea, Jiusheng Wu, Adéle Kruger, Vincenzo Manca, Sorin Draghici. Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion
    3044 -- 3053Megan Orr, Peng Liu, Dan Nettleton. An improved method for computing q-values when the distribution of effect sizes is asymmetric
    3054 -- 3061Chun-Pei Cheng, I-Ying Kuo, Hakan Alakus, Kelly A. Frazer, Olivier Harismendy, Yi-Ching Wang, Vincent S. Tseng. Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression
    3062 -- 3069Sihai Dave Zhao, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron. Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis
    3070 -- 3077Junpeng Zhang, Thuc Duy Le, Lin Liu 0001, Bing Liu 0002, Jianfeng He 0001, Gregory J. Goodall, Jiuyong Li. Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data
    3078 -- 3085Francesco Sambo, Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli. Compression and fast retrieval of SNP data
    3086 -- 3092Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock. ASP-G: an ASP-based method for finding attractors in genetic regulatory networks
    3093 -- 3100Ingo Vogt, Jeanette Prinz, Karolina Worf, Mónica Campillos. Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations
    3101 -- 3108Seunghwa Kang, Simon Kahan, Jason McDermott, Nicholas S. Flann, Ilya Shmulevich. Biocellion: accelerating computer simulation of multicellular biological system models
    3109 -- 3114Eduard Porta-Pardo, Adam Godzik. e-Driver: a novel method to identify protein regions driving cancer
    3115 -- 3117Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
    3118 -- 3119Ezequiel L. Nicolazzi, Daniela Iamartino, John L. Williams. AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
    3120 -- 3122Yoli Shavit, Fiona Kathryn Hamey, Pietro Liò. FisHiCal: an R package for iterative FISH-based calibration of Hi-C data
    3123 -- 3124Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko. STAMP: statistical analysis of taxonomic and functional profiles
    3125 -- 3127Jonathan Crabtree, Sonia Agrawal, Anup Mahurkar, Garry S. A. Myers, David A. Rasko, Owen White. Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
    3128 -- 3130Stefan Seemayer, Markus Gruber, Johannes Söding. CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations
    3131 -- 3133Lou Gotz, Jodie L. Abrahams, Julien Mariethoz, Pauline M. Rudd, Niclas G. Karlsson, Nicolle H. Packer, Matthew P. Campbell, Frédérique Lisacek. GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
    3134 -- 3135Gabriel E. Hoffman, Jason G. Mezey, Eric E. Schadt. lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R
    3136 -- 3138Bo Wen, Shaohang Xu, Gloria M. Sheynkman, Qiang Feng, Liang Lin, Quanhui Wang, Xun Xu, Jun Wang, Siqi Liu. sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments
    3139 -- 3141Ahmed Mohamed, Timothy Hancock, Canh Hao Nguyen, Hiroshi Mamitsuka. NetPathMiner: R/Bioconductor package for network path mining through gene expression
    3142 -- 0Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng. FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model

    Volume 30, Issue 20

    2843 -- 2851Heng Li. Toward better understanding of artifacts in variant calling from high-coverage samples
    2852 -- 2859Alberto Magi, Lorenzo Tattini, Flavia Palombo, Matteo Benelli, Alessandro Gialluisi, Betti Giusti, Rosanna Abbate, Marco Seri, Gian Franco Gensini, Giovanni Romeo, Tommaso Pippucci. 2: detection of runs of homozygosity from whole-exome sequencing data
    2860 -- 2867Qi Zhang, Sündüz Keles. CNV-guided multi-read allocation for ChIP-seq
    2868 -- 2874Jianling Zhong, Todd Wasson, Alexander J. Hartemink. Learning protein-DNA interaction landscapes by integrating experimental data through computational models
    2875 -- 2882Javier Arnedo, Rocío Romero-Záliz, Igor Zwir, Coral del Val. A multiobjective method for robust identification of bacterial small non-coding RNAs
    2883 -- 2890Philip Heller, H. James Tripp, Kendra Turk-Kubo, Jonathan P. Zehr. nifH sequences from GenBank
    2891 -- 2898Javier Vargas, Ana-Lucia Álvarez-Cabrera, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano. Efficient initial volume determination from electron microscopy images of single particles
    2899 -- 2905Francesc Fernández-Albert, Rafael Llorach, Mar Garcia-Aloy, Andrey Ziyatdinov, Cristina Andres-Lacueva, Alexandre Perera-Lluna. Intensity drift removal in LC/MS metabolomics by common variance compensation
    2906 -- 2914Bogdan Pasaniuc, Noah Zaitlen, Huwenbo Shi, Gaurav Bhatia, Alexander Gusev, Joseph Pickrell, Joel Hirschhorn, David P. Strachan, Nick Patterson, Alkes L. Price. Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
    2915 -- 2922John Michael Rañola, John Novembre, Kenneth Lange. Fast spatial ancestry via flexible allele frequency surfaces
    2923 -- 2930Wenhui Wang, Sen Yang, Xiang Zhang, Jing Li. Drug repositioning by integrating target information through a heterogeneous network model
    2931 -- 2940Vikram Saraph, Tijana Milenkovic. MAGNA: Maximizing Accuracy in Global Network Alignment
    2941 -- 2948Tianwei Yu, Dean P. Jones. Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach
    2949 -- 2955Ehsan Behnam, Andrew D. Smith. The Amordad database engine for metagenomics
    2956 -- 2958Erik Gafni, Lovelace J. Luquette, Alex Lancaster, Jared B. Hawkins, Jae-Yoon Jung, Yassine Souilmi, Dennis P. Wall, Peter J. Tonellato. COSMOS: Python library for massively parallel workflows
    2959 -- 2961Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier. GATB: Genome Assembly & Analysis Tool Box
    2962 -- 2964Anna-Sapfo Malaspinas, Ole Tange, José Víctor Moreno-Mayar, Morten Rasmussen, Michael DeGiorgio, Yong Wang, Cristina E. Valdiosera, Gustavo Politis, Eske Willerslev, Rasmus Nielsen. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
    2965 -- 2967Kitty K. Lo, Christopher Boustred, Lyn S. Chitty, Vincent Plagnol. RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy
    2968 -- 2970Marc Güell, Luhan Yang, George M. Church. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
    2971 -- 2972Ruth Heller, Shay Yaacoby, Daniel Yekutieli. repfdr: a tool for replicability analysis for genome-wide association studies
    2973 -- 2974Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio. TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs
    2975 -- 2977Federico Agostini, Davide Cirillo, Carmen Maria Livi, Riccardo Delli Ponti, Gian Gaetano Tartaglia. Escherichia coli
    2978 -- 2980Hitesh Patel, Björn A. Grüning, Stefan Günther, Irmgard Merfort. PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
    2981 -- 2982Elmar Krieger, Gert Vriend. YASARA View - molecular graphics for all devices - from smartphones to workstations
    2983 -- 2985Christopher Pooley, David Ruau, Patrick Lombard, Berthold Göttgens, Anagha Joshi. TRES predicts transcription control in embryonic stem cells
    2986 -- 2988Gilles Vieira, Marc Carnicer, Jean-Charles Portais, Stéphanie Heux. in silico design of synthetic metabolic pathways
    2989 -- 2990Jae-Seong Yang, Eduard Sabidó, Luis Serrano, Christina Kiel. TAPAS: tools to assist the targeted protein quantification of human alternative splice variants
    2991 -- 2992Andrei Kramer, Vassilios Stathopoulos, Mark A. Girolami, Nicole Radde. mcmc_clib-an advanced MCMC sampling package for ode models

    Volume 30, Issue 2

    151 -- 156Laurence O. W. Wilson, Andrew Spriggs, Jennifer M. Taylor, Aude M. Fahrer. A novel splicing outcome reveals more than 2000 new mammalian protein isoforms
    157 -- 164Dandi Qiao, Michael H. Cho, Heide 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
    165 -- 171Sebastian 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
    172 -- 179Longjie Cheng, Yu Zhu. A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data
    180 -- 188Ernest Turro, William J. Astle, Simon Tavaré. Flexible analysis of RNA-seq data using mixed effects models
    189 -- 196Kevin Lim, Limsoon Wong. Finding consistent disease subnetworks using PFSNet
    197 -- 205Yaqing Si, Peng Liu, Pinghua Li, Thomas P. Brutnell. Model-based clustering for RNA-seq data
    206 -- 213Buhm Han, Eun Yong Kang, Soumya Raychaudhuri, Paul I. W. de Bakker, Eleazar Eskin. Fast pairwise IBD association testing in genome-wide association studies
    214 -- 220Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore, Joshua N. Sampson. Testing multiple biological mediators simultaneously
    221 -- 227Mikael 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
    228 -- 233Marianna 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
    234 -- 241Attila 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
    242 -- 250Mohammad Shahrokh Esfahani, Edward R. Dougherty. Effect of separate sampling on classification accuracy
    251 -- 257Mandy L. Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud. Chlamydomonas reinhardtii expression vectors
    258 -- 265Álvaro Sebastián, Bruno Contreras-Moreira. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces
    266 -- 273Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye. Drosophila embryos in images containing spatial patterns of expression
    274 -- 281Nicolas Terrapon, January Weiner, Sonja Grath, Andrew D. Moore, Erich Bornberg-Bauer. Rapid similarity search of proteins using alignments of domain arrangements
    282 -- 283Andrew D. Moore, Andreas Held, Nicolas Terrapon, January Weiner, 3rd, Erich Bornberg-Bauer. DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins
    284 -- 286Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chavez. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
    287 -- 288João F. Matias Rodrigues, Christian von Mering. HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences
    289 -- 291Toma Tebaldi, Erik Dassi, Galena Kostoska, Gabriella Viero, Alessandro Quattrone. tRanslatome: an R/Bioconductor package to portray translational control
    292 -- 294Michael 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
    295 -- 297Luke E. Ulrich, Igor B. Zhulin. SeqDepot: streamlined database of biological sequences and precomputed features
    298 -- 300Rodrigo Ochoa, Mark Davies, George Papadatos, Francis Atkinson, John P. Overington. myChEMBL: a virtual machine implementation of open data and cheminformatics tools

    Volume 30, Issue 19

    2693 -- 2701Zi Wang, Edward Curry, Giovanni Montana. Network-guided regression for detecting associations between DNA methylation and gene expression
    2702 -- 2708Javier Pérez-Rodríguez, Alexis G. Arroyo-Peña, Nicolás García-Pedrajas. Improving translation initiation site and stop codon recognition by using more than two classes
    2709 -- 2716Sagar M. Utturkar, Dawn M. Klingeman, Miriam L. Land, Christopher W. Schadt, Mitchel J. Doktycz, Dale A. Pelletier, Steven D. Brown. de novo and hybrid assembly techniques to derive high-quality genome sequences
    2717 -- 2722Bahlul Haider, Tae-Hyuk Ahn, Brian Bushnell, Juanjuan Chai, Alex Copeland, Chongle Pan. de novo Assembler for Metagenomics
    2723 -- 2732Paul Greenfield, Konsta Duesing, Alexie Papanicolaou, Denis C. Bauer. Blue: correcting sequencing errors using consensus and context
    2733 -- 2740Mario Abdel Messih, Rosalba Lepore, Paolo Marcatili, Anna Tramontano. Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies
    2741 -- 2746So Young Ryu, Wei-Jun Qian, David G. Camp II, Richard D. Smith, Ronald G. Tompkins, Ronald W. Davis, Wenzhong Xiao. Detecting differential protein expression in large-scale population proteomics
    2747 -- 2756Pashupati Mishra, Petri Törönen, Yrjö Leino, Liisa Holm. Gene set analysis: limitations in popular existing methods and proposed improvements
    2757 -- 2763Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig. Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
    2764 -- 2771Rónán Daly, Simon Rogers, Joe Wandy, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling. MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach
    2772 -- 2778Fan Zhu, Yuanfang Guan. Predicting dynamic signaling network response under unseen perturbations
    2779 -- 2786Ying Wang, Christopher A. Penfold, David A. Hodgson, Miriam L. Gifford, Nigel J. Burroughs. Correcting for link loss in causal network inference caused by regulator interference
    2787 -- 2795Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Christopher Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael I. Jordan, David A. Patterson. SMaSH: a benchmarking toolkit for human genome variant calling
    2796 -- 2801Lilian Janin, Ole Schulz-Trieglaff, Anthony J. Cox. BEETL-fastq: a searchable compressed archive for DNA reads
    2802 -- 2807Yinan Zheng, Zhe Fei, Wei Zhang, Justin B. Starren, Lei Liu, Andrea A. Baccarelli, Yi Li, Lifang Hou. PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures
    2808 -- 2810Douglas H. Phanstiel, Alan P. Boyle, Carlos L. Araya, Michael P. Snyder. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
    2811 -- 2812Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors. circlize implements and enhances circular visualization in R
    2813 -- 2815Lisle E. Mose, Matthew D. Wilkerson, D. Neil Hayes, Charles M. Perou, Joel S. Parker. ABRA: improved coding indel detection via assembly-based realignment
    2816 -- 2817Simone Leo, Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Nicola Soranzo, Enis Afgan, Gianluigi Zanetti. BioBlend.objects: metacomputing with Galaxy
    2818 -- 2819James K. Bonfield. The Scramble conversion tool
    2820 -- 2821Yongkyu Kim, Werner Liesack. DAFGA: diversity analysis of functional gene amplicons
    2822 -- 2825Dariusz Mrozek, Bozena Malysiak-Mrozek, Artur Klapcinski. Cloud4Psi: cloud computing for 3D protein structure similarity searching
    2826 -- 2827Jihoon Kim, Eric Levy, Alex Ferbrache, Petra Stepanowsky, Claudiu Farcas, Shuang Wang, Stefan Brunner, Tyler Bath, Yuan Wu, Lucila Ohno-Machado. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
    2828 -- 2829Shuang Feng, Dajiang Liu, Xiaowei Zhan, Mary Kate Wing, Gonçalo R. Abecasis. RAREMETAL: fast and powerful meta-analysis for rare variants
    2830 -- 2831Max Flöttmann, Jannis Uhlendorf, Till Scharp, Edda Klipp, Thomas W. Spiesser. SensA: web-based sensitivity analysis of SBML models
    2832 -- 2833Gerard Wong, Jeffrey Chan, Bronwyn A. Kingwell, Christopher Leckie, Peter J. Meikle. LICRE: unsupervised feature correlation reduction for lipidomics
    2834 -- 2836Shailesh Tripathi, Matthias Dehmer, Frank Emmert-Streib. NetBioV: an R package for visualizing large network data in biology and medicine
    2837 -- 2839Jikai Lei, Yanni Sun. miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data
    2840 -- 2842Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman. Literome: PubMed-scale genomic knowledge base in the cloud

    Volume 30, Issue 18

    2543 -- 2550Huy Hoang Do, Wing-Kin Sung. CWig: compressed representation of Wiggle/BedGraph format
    2551 -- 2558Israel T. Silva, Rafael Rosales, Adriano J. Holanda, Michel C. Nussenzweig, Mila Jankovic. Identification of chromosomal translocation hotspots via scan statistics
    2559 -- 2567Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada. Reference-free prediction of rearrangement breakpoint reads
    2568 -- 2575Yan-Xiao Zhang, Yu-Hsuan Lin, Timothy D. Johnson, Laura S. Rozek, Maureen A. Sartor. PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
    2576 -- 2583Zhenhua Yu, Yuanning Liu, Yi Shen, Minghui Wang, Ao Li. CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data
    2584 -- 2591Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger. Memory-efficient RNA energy landscape exploration
    2592 -- 2597Christophe N. Magnan, Pierre Baldi. SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity
    2598 -- 2602María José Nueda, Sonia Tarazona, Ana Conesa. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
    2603 -- 2610Andrew Quinn, Punita Juneja, Francis M. Jiggins. Drosophila with a single genome sequence and RNA-seq data
    2611 -- 2618Meng Wang, Shili Lin. FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads
    2619 -- 2626Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey Jr.. DualAligner: a dual alignment-based strategy to align protein interaction networks
    2627 -- 2635Yue Li, Cheng Liang, Ka Chun Wong, Jiawei Luo, Zhaolei Zhang. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion
    2636 -- 2643Christopher J. Conley, Robert Smith, Ralf J. O. Torgrip, Ryan M. Taylor, Ralf Tautenhahn, John T. Prince. Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection
    2644 -- 2651Sotiris Dimopoulos, Christian E. Mayer, Fabian Rudolf, Jörg Stelling. Accurate cell segmentation in microscopy images using membrane patterns
    2652 -- 2653Marek S. Wiewiórka, Antonio Messina, Alicja Pacholewska, Sergio Maffioletti, Piotr Gawrysiak, Michal J. Okoniewski. SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision
    2654 -- 2655Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak. GenomeVISTA - an integrated software package for whole-genome alignment and visualization
    2656 -- 2658Matthias Zytnicki, Eduard Akhunov, Hadi Quesneville. de novo assembler
    2659 -- 2661Erika Sallet, Jérôme Gouzy, Thomas Schiex. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes
    2662 -- 2664Marco Falda, Paolo Fontana, Luisa Barzon, Stefano Toppo, Enrico Lavezzo. keeSeek: searching distant non-existing words in genomes for PCR-based applications
    2665 -- 2667Peng Jiang, Susanne Meyer, Zhonggang Hou, Nicholas E. Propson, H. Tom Soh, James A. Thomson, Ron M. Stewart. MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers
    2668 -- 2669Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen. MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions
    2670 -- 2672Evan A. Boyle, Brian J. O'Roak, Beth K. Martin, Akash Kumar, Jay Shendure. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing
    2673 -- 2675Aidan O'Brien, Timothy L. Bailey. GT-Scan: identifying unique genomic targets
    2676 -- 2677Niko Popitsch. CODOC: efficient access, analysis and compression of depth of coverage signals
    2678 -- 2680Chen Wang, Jared Evans, Aditya Bhagwate, Naresh Prodduturi, Vivekananda Sarangi, Mridu Middha, Hugues Sicotte, Peter T. Vedell, Steven N. Hart, Gavin R. Oliver, Jean-Pierre Kocher, Matthew J. Maurer, Anne J. Novak, Susan L. Slager, James R. Cerhan, Yan W. Asmann. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data
    2681 -- 2683Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar. ProDy for bridging protein sequence evolution and structural dynamics
    2684 -- 2685Barbora Kozlíková, Eva Sebestova, Vilém Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonin Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry, Artur Góra, Jirí Damborský, Jiri Sochor. CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
    2686 -- 2688John M. Hickey, Gregor Gorjanc, Sarah Hearne, Bevan Emma Huang. AlphaMPSim: flexible simulation of multi-parent crosses
    2689 -- 2690Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer. MaxLink: network-based prioritization of genes tightly linked to a disease seed set
    2691 -- 2692Stephen Taylor, Roger Noble. HTML5 PivotViewer: high-throughput visualization and querying of image data on the web

    Volume 30, Issue 17

    345 -- 348Marie-Dominique Devignes, Yves Moreau. th European Conference on Computational Biology
    349 -- 355Hannes Hauswedell, Jochen Singer, Knut Reinert. Lambda: the local aligner for massive biological data
    356 -- 363Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard. Fiona: a parallel and automatic strategy for read error correction
    364 -- 370Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli, Fariza Tahi. Towards a piRNA prediction using multiple kernel fusion and support vector machine
    371 -- 378Sepideh Mazrouee, Wei Wang. FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs
    379 -- 385Volodymyr Kuleshov. Probabilistic single-individual haplotyping
    386 -- 392Céline Lévy-Leduc, Maud Delattre, Tristan Mary-Huard, Stéphane Robin. Two-dimensional segmentation for analyzing Hi-C data
    393 -- 400Raymond G. Cavalcante, Chee Lee, Ryan P. Welch, Snehal Patil, Terry E. Weymouth, Laura J. Scott, Maureen A. Sartor. Broad-Enrich: functional interpretation of large sets of broad genomic regions
    401 -- 407Theresa Schacht, Marcus Oswald, Roland Eils, Stefan B. Eichmüller, Rainer König. Estimating the activity of transcription factors by the effect on their target genes
    408 -- 414John A. Capra, Dennis Kostka. Modeling DNA methylation dynamics with approaches from phylogenetics
    415 -- 421Thorsten Will, Volkhard Helms. Identifying transcription factor complexes and their roles
    422 -- 429Taejin Ahn, Eunjin Lee, Nam Huh, Taesung Park. Personalized identification of altered pathways in cancer using accumulated normal tissue data
    430 -- 437Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane. Alignment-free protein interaction network comparison
    438 -- 444Somaye Hashemifar, Jinbo Xu. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks
    445 -- 452Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan. Experimental design schemes for learning Boolean network models
    453 -- 460YongSoo Kim, Jin-Hyeok Jang, Seungjin Choi, Daehee Hwang. TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information
    461 -- 467Tommi Suvitaival, Simon Rogers, Samuel Kaski. Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations
    468 -- 474Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee. Causal network inference using biochemical kinetics
    475 -- 481Peter Kreyssig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich. Effects of small particle numbers on long-term behaviour in discrete biochemical systems
    482 -- 488Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson. PconsFold: improved contact predictions improve protein models
    489 -- 496Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
    497 -- 504Suleiman A. Khan, Seppo Virtanen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski. Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis
    505 -- 511Gabriel Studer, Marco Biasini, Torsten Schwede. Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)
    512 -- 518James H. Collier, Lloyd Allison, Arthur M. Lesk, Maria Garcia de la Banda, Arun Siddharth Konagurthu. A new statistical framework to assess structural alignment quality using information compression
    519 -- 526Manuel Lafond, Cedric Chauve, Riccardo Dondi, Nadia El-Mabrouk. Polytomy refinement for the correction of dubious duplications in gene trees
    527 -- 533Christina Kratsch, Alice Carolyn McHardy. RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
    534 -- 540Philipp Benner, Miroslav Bacák, Pierre-Yves Bourguignon. Point estimates in phylogenetic reconstructions
    541 -- 548Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy Warnow. ASTRAL: genome-scale coalescent-based species tree estimation
    549 -- 555Michael P. Schroeder, Carlota Rubio-Perez, David Tamborero, Abel Gonzalez-Perez, Núria López-Bigas. OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action
    556 -- 563Mehmet Gönen, Adam A. Margolin. Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning
    564 -- 571Jingwen Yan, Lei Du, Sungeun Kim, Shannon L. Risacher, Heng Huang, Jason H. Moore, Andrew J. Saykin, Li Shen. Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm
    572 -- 578Rui Tian, Malay Kumar Basu, Emidio Capriotti. ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples
    579 -- 586Xueping Liu, Mónica Campillos. Unveiling new biological relationships using shared hits of chemical screening assay pairs
    587 -- 593Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone, Giulio Iannello. Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images
    594 -- 600Vladimir Gligorijevic, Vuk Janjic, Natasa Przulj. Integration of molecular network data reconstructs Gene Ontology
    601 -- 608Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, Robert Stevens. Extracting patterns of database and software usage from the bioinformatics literature
    609 -- 616Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective
    617 -- 623Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez. Fast randomization of large genomic datasets while preserving alteration counts
    624 -- 630Nadav Rappoport, Amos Stern, Nathan Linial, Michal Linial. Entropy-driven partitioning of the hierarchical protein space
    631 -- 638Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer. Microarray R-based analysis of complex lysate experiments with MIRACLE
    639 -- 645Evangelos Bellos, Lachlan J. M. Coin. cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data
    2393 -- 2398Jihye Kim, Vihas T. Vasu, Rangnath Mishra, Katherine R. Singleton, Minjae Yoo, Sonia M. Leach, Eveline Farias-Hesson, Robert J. Mason, Jaewoo Kang, Preveen Ramamoorthy, Jeffrey A. Kern, Lynn E. Heasley, James H. Finigan, Aik Choon Tan. Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy
    2399 -- 2405Rotem Ben-Hamo, Moriah Gidoni, Sol Efroni. PhenoNet: identification of key networks associated with disease phenotype
    2406 -- 2413Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher. Probabilistic partitioning methods to find significant patterns in ChIP-Seq data
    2414 -- 2422Yongseok Park, Maria E. Figueroa, Laura S. Rozek, Maureen A. Sartor. MethylSig: a whole genome DNA methylation analysis pipeline
    2423 -- 2431Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander. k-mer-based estimation of bacterial community composition
    2432 -- 2439Walyd Khenoussi, Renaud Vanhoutrève, Olivier Poch, Julie D. Thompson. SIBIS: a Bayesian model for inconsistent protein sequence estimation
    2440 -- 2446Lizong Deng, Aiping Wu, Wentao Dai, Tingrui Song, Ya Cui, Taijiao Jiang. Exploring protein domain organization by recognition of secondary structure packing interfaces
    2447 -- 2455Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert. Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
    2456 -- 2463Navodit Misra, Ewa Szczurek, Martin Vingron. Inferring the paths of somatic evolution in cancer
    2464 -- 2470Mehrab Ghanat Bari, Xuepo Ma, Jianqiu Zhang. PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM
    2471 -- 2479Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela. Exploration and retrieval of whole-metagenome sequencing samples
    2480 -- 2485Charny Park, Namhee Yu, Ikjung Choi, Wan Kyu Kim, Sanghyuk Lee. lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
    2486 -- 2493Florian Gomez, Ralph Lukas Stoop, Ruedi Stoop. Universal dynamical properties preclude standard clustering in a large class of biochemical data
    2494 -- 2495Jan De Neve, Joris Meys, Jean-Pierre Ottoy, Lieven Clement, Olivier Thas. unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R
    2496 -- 2497Kamil Slowikowski, Xinli Hu, Soumya Raychaudhuri. SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci
    2498 -- 2500Weixin Wang, Panwen Wang, Feng Xu, Ruibang Luo, Maria P. Wong, Tak Wah Lam, Junwen Wang. FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data
    2501 -- 2502Alex Lancaster, Andrew Nutter-Upham, Susan Lindquist, Oliver D. King. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition
    2503 -- 2505Gregory G. Faust, Ira M. Hall. SAMBLASTER: fast duplicate marking and structural variant read extraction
    2506 -- 2507Michael J. Sanderson. Ceiba: scalable visualization of phylogenies and 2D/3D image collections
    2508 -- 2510Guillermo Rodrigo, Alfonso Jaramillo. RiboMaker: computational design of conformation-based riboregulation
    2511 -- 2513George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
    2514 -- 2516Francesco Russo, Claudia Angelini. RNASeqGUI: a GUI for analysing RNA-Seq data
    2517 -- 2518Charlotte Soneson. compcodeR - an R package for benchmarking differential expression methods for RNA-seq data
    2519 -- 2520Thomas Nussbaumer, Karl G. Kugler, Kai Christian Bader, Sapna Sharma, Michael Seidel, Klaus F. X. Mayer. RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data
    2521 -- 2523Daniel Broudy, Trevor Killeen, Meena Choi, Nicholas Shulman, Deepak R. Mani, Susan E. Abbatiello, Deepak Mani, Rushdy Ahmad, Alexandria K. Sahu, Birgit Schilling, Kaipo Tamura, Yuval Boss, Vagisha Sharma, Bradford W. Gibson, Steven A. Carr, Olga Vitek, Michael J. MacCoss, Brendan MacLean. A framework for installable external tools in Skyline
    2524 -- 2526Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
    2527 -- 2528Ken-Chi Yang, Chia-Lang Hsu, Chen-Ching Lin, Hsueh-Fen Juan, Hsuan-Cheng Huang. Mirin: identifying microRNA regulatory modules in protein-protein interaction networks
    2529 -- 2531Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming. fastGapFill: efficient gap filling in metabolic networks
    2532 -- 2533Paul Müller, Petra Schwille, Thomas Weidemann. PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy
    2534 -- 2536Jia-Hong Wang, Ling-Feng Zhao, Pei Lin, Xiao-Rong Su, Shi-Jun Chen, Li-Qiang Huang, Hua-Feng Wang, Hai Zhang, Zhen-Fu Hu, Kai-Tai Yao, Zhong-Xi Huang. GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
    2537 -- 2539Jordan Plieskatt, Gabriel Rinaldi, Paul J. Brindley, Xinying Jia, Jeremy Potriquet, Jeffrey Bethony, Jason P. Mulvenna. Bioclojure: a functional library for the manipulation of biological sequences
    2540 -- 2542Daeun Ryu, SeongBeom Cho, Hun Kim, Sanghyuk Lee, Wan Kyu Kim. GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype

    Volume 30, Issue 16

    2243 -- 2246Laurent F. Thomas, Pål Sætrom. Circular RNAs are depleted of polymorphisms at microRNA binding sites
    2247 -- 2254Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann. ReadXplorer - visualization and analysis of mapped sequences
    2255 -- 2262Andreas Futschik, Thomas Hotz, Axel Munk, Hannes Sieling. Multiscale DNA partitioning: statistical evidence for segments
    2263 -- 2271Maria Cha, Qing Zhou. Detecting clustering and ordering binding patterns among transcription factors via point process models
    2272 -- 2279Timothy G. Vaughan, Denise Kühnert, Alex Popinga, David Welch, Alexei J. Drummond. Efficient Bayesian inference under the structured coalescent
    2280 -- 2287Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida. kdetrees: non-parametric estimation of phylogenetic tree distributions
    2288 -- 2294Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane. Improving B-cell epitope prediction and its application to global antibody-antigen docking
    2295 -- 2301Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, Chen Keasar. Redundancy-weighting for better inference of protein structural features
    2302 -- 2309Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding. Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
    2310 -- 2316Matthew N. McCall, Helene R. McMurray, Hartmut Land, Anthony Almudevar. On non-detects in qPCR data
    2317 -- 2323Hokeun Sun, Shuang Wang. A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data
    2324 -- 2333Trisevgeni Rapakoulia, Konstantinos A. Theofilatos, Dimitris Kleftogiannis, Spiridon Likothanasis, Athanasios K. Tsakalidis, Seferina Mavroudi. EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms
    2334 -- 2342Shibin Mathew, Sankaramanivel Sundararaj, Hikaru Mamiya, Ipsita Banerjee. Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway
    2343 -- 2350Xiaoke Ma, Long Gao, Kai Tan. Modeling disease progression using dynamics of pathway connectivity
    2351 -- 2359Connor Clark, Jugal Kalita. A comparison of algorithms for the pairwise alignment of biological networks
    2360 -- 2366Yinming Jiao, Martin Widschwendter, Andrew E. Teschendorff. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
    2367 -- 2374James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier. The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
    2375 -- 2376Robert J. Carroll, Lisa Bastarache, Joshua C. Denny. R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment
    2377 -- 2378Gao T. Wang, Biao Li, Regie P. Lyn Santos-Cortez, Bo Peng, Suzanne M. Leal. Power analysis and sample size estimation for sequence-based association studies
    2379 -- 2380Hiroshi Tsugawa, Mitsuhiro Kanazawa, Atsushi Ogiwara, Masanori Arita. MRMPROBS suite for metabolomics using large-scale MRM assays
    2381 -- 2383Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis. in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
    2384 -- 2385Matthew Horridge, Tania Tudorache, Csongor Nyulas, Jennifer Vendetti, Natalya Fridman Noy, Mark A. Musen. WebProtégé: a collaborative Web-based platform for editing biomedical ontologies
    2386 -- 2388Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen. S-glutathionylation
    2389 -- 2390Martin Ovesný, Pavel Krízek, Josef Borkovec, Zdenek Svindrych, Guy M. Hagen. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

    Volume 30, Issue 15

    2093 -- 2097Darius Kazlauskas, Ceslovas Venclovas. Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase
    2098 -- 2104Rong W. Zablocki, Andrew J. Schork, Richard A. Levine, Ole A. Andreassen, Anders M. Dale, Wesley K. Thompson. Covariate-modulated local false discovery rate for genome-wide association studies
    2105 -- 2113Hervé Marie-Nelly, Martial Marbouty, Axel Cournac, Gianni Liti, Gilles Fischer, Christophe Zimmer, Romain Koszul. Filling annotation gaps in yeast genomes using genome-wide contact maps
    2114 -- 2120Anthony M. Bolger, Marc Lohse, Björn Usadel. Trimmomatic: a flexible trimmer for Illumina sequence data
    2121 -- 2129Yi Li, Xiaohui Xie. Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
    2130 -- 2136Rodrigo Cánovas, Alistair Moffat, Andrew Turpin. Lossy compression of quality scores in genomic data
    2137 -- 2141Amir Toporik, Itamar Borukhov, Avihay Apatoff, Doron Gerber, Yossef Kliger. Computational identification of natural peptides based on analysis of molecular evolution
    2142 -- 2149Zeyneb Kurt, Nizamettin Aydin, Gökmen Altay. A comprehensive comparison of association estimators for gene network inference algorithms
    2150 -- 2154Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik. CABS-flex predictions of protein flexibility compared with NMR ensembles
    2155 -- 2161Alexandra Jauhiainen, Basetti Madhu, Masako Narita, Masashi Narita, John Griffiths, Simon Tavaré. Normalization of metabolomics data with applications to correlation maps
    2162 -- 2170Wei Wang, Zhi Wei, Hongzhe Li. A change-point model for identifying 3′UTR switching by next-generation RNA sequencing
    2171 -- 2178Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor, Kai Yu. A fast and powerful tree-based association test for detecting complex joint effects in case-control studies
    2179 -- 2188Andriy Derkach, Theodore Chiang, Jiafen Gong, Laura Addis, Sara Dobbins, Ian Tomlinson, Richard Houlston, Deb K. Pal, Lisa J. Strug. Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic
    2189 -- 2196Alexandre Bureau, Samuel G. Younkin, Margaret M. Parker, Joan E. Bailey-Wilson, Mary L. Marazita, Jeffrey C. Murray, Elisabeth Mangold, Hasan Albacha-Hejazi, Terri H. Beaty, Ingo Ruczinski. Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives
    2197 -- 2203Jon Pey, Francisco J. Planes. Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks
    2204 -- 2205Sylvain Mareschal, Sydney Dubois, Thierry Lecroq, Fabrice Jardin. Rgb: a scriptable genome browser for R
    2206 -- 2207Xin Zhou, Daofeng Li, Rebecca F. Lowdon, Joseph F. Costello, Ting Wang. methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser
    2208 -- 2209Sung Kyu Robin Park, Aaron Aslanian, Daniel B. McClatchy, Xuemei Han, Harshil Shah, Meha Singh, Navin Rauniyar, James J. Moresco, Antonio F. M. Pinto, Jolene K. Diedrich, Claire Delahunty, John R. Yates III. Census 2: isobaric labeling data analysis
    2210 -- 2212Ju Xin Chin, Bevan Kai-Sheng Chung, Dong-Yup Lee. Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
    2213 -- 2215Lukasz Roguski, Sebastian Deorowicz. DSRC 2 - Industry-oriented compression of FASTQ files
    2216 -- 2218Matthew W. Pennell, Jonathan M. Eastman, Graham J. Slater, Joseph W. Brown, Josef C. Uyeda, Richard G. FitzJohn, Michael E. Alfaro, Luke J. Harmon. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
    2219 -- 2220Sébastien Morin, Troels E. Linnet, Mathilde Lescanne, Paul Schanda, Gary S. Thompson, Martin Tollinger, Kaare Teilum, Stéphane Gagné, Dominique Marion, Christian Griesinger, Martin Blackledge, Edward J. d'Auvergne. relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data
    2221 -- 2223Björn Wallner. ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
    2224 -- 2226Wandaliz Torres-García, SiYuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak. PRADA: pipeline for RNA sequencing data analysis
    2227 -- 2229Raeece Naeem, Lailatul Hidayah, Mark D. Preston, Taane G. Clark, Arnab Pain. SVAMP: sequence variation analysis, maps and phylogeny
    2230 -- 2232Alvin Leung, Gary D. Bader, Jüri Reimand. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
    2233 -- 2234Frédéric Fournier, Charles Joly Beauparlant, René Paradis, Arnaud Droit. rTANDEM, an R/Bioconductor package for MS/MS protein identification
    2235 -- 2236Horacio Caniza, Alfonso E. Romero, Samuel Heron, Haixuan Yang, Alessandra Devoto, Marco Frasca, Marco Mesiti, Giorgio Valentini, Alberto Paccanaro. GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology
    2237 -- 2238Dongfang Wang, Jin Gu, Ting Wang, Zijian Ding. OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs
    2239 -- 2241William Duren, Terry E. Weymouth, Tim Hull, Gilbert S. Omenn, Brian D. Athey, Charles F. Burant, Alla Karnovsky. MetDisease - connecting metabolites to diseases via literature
    2242 -- 0Jinghua Gu, Jianhua Xuan, Rebecca B. Riggins, Li Chen, Yue Wang, Robert Clarke. Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic

    Volume 30, Issue 14

    1943 -- 1949Xiaowei Zhou, Jiming Liu, Xiang Wan, Weichuan Yu. Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
    1950 -- 1957Rajat Shuvro Roy, Debashish Bhattacharya, Alexander Schliep. k-mers with cache-efficient algorithms
    1958 -- 1964William H. Majoros, Niel Lebeck, Uwe Ohler, Song Li. Improved transcript isoform discovery using ORF graphs
    1965 -- 1973Emi Tanaka, Timothy L. Bailey, Uri Keich. Improving MEME via a two-tiered significance analysis
    1974 -- 1982Christophe Charpilloz, Anne-Lise Veuthey, Bastien Chopard, Jean-Luc Falcone. Motifs tree: a new method for predicting post-translational modifications
    1983 -- 1990A. Mary Thangakani, Sandeep Kumar, R. Nagarajan, Devadasan Velmurugan, M. Michael Gromiha. GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies
    1991 -- 1999Chris-Andre Leimeister, Marcus Boden, Sebastian Horwege, Sebastian Lindner, Burkhard Morgenstern. Fast alignment-free sequence comparison using spaced-word frequencies
    2000 -- 2008Chris-Andre Leimeister, Burkhard Morgenstern. k-mismatch average common substring approach to alignment-free sequence comparison
    2009 -- 2017Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin. Basin Hopping Graph: a computational framework to characterize RNA folding landscapes
    2018 -- 2025Yuan-De Tan, Hongyan Xu. A general method for accurate estimation of false discovery rates in identification of differentially expressed genes
    2026 -- 2034Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J. Kangas, Pasi Soininen, Paul O'Reilly, Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T. Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, Samuel Kaski. Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression
    2035 -- 2042Amir R. Kermany, Laure Segurel, Tiffany R. Oliver, Molly Przeworski. TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception
    2043 -- 2050Mario Latendresse, Markus Krummenacker, Peter D. Karp. Optimal metabolic route search based on atom mappings
    2051 -- 2059Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles
    2060 -- 2065Davide Rambaldi, Salvatore Pece, Pier Paolo Di Fiore. flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies
    2066 -- 2067Uciel Chorostecki, Javier F. Palatnik. comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants
    2068 -- 2069Torsten Seemann. Prokka: rapid prokaryotic genome annotation
    2070 -- 2072Peter Audano, Fredrik Vannberg. KAnalyze: a fast versatile pipelined K-mer toolkit
    2073 -- 2075Zhenpeng Li, Yang Huang, Yabo Ouyang, Yang Jiao, Hui Xing, Lingjie Liao, Shibo Jiang, Yiming Shao, Liying Ma. CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure
    2076 -- 2078Valerie Obenchain, Michael F. Lawrence, Vincent J. Carey, Stephanie M. Gogarten, Paul Shannon, Martin Morgan. VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants
    2079 -- 2080Andreas Sand, Morten Kragelund Holt, Jens Johansen, Gerth Stølting Brodal, Thomas Mailund, Christian N. S. Pedersen. tqDist: a library for computing the quartet and triplet distances between binary or general trees
    2081 -- 2083Dario Ghersi, Mona Singh. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments
    2084 -- 2085Sam Buckberry, Stephen J. Bent, Tina Bianco-Miotto, Claire T. Roberts. massiR: a method for predicting the sex of samples in gene expression microarray datasets
    2086 -- 2088Dale R. Nyholt. SECA: SNP effect concordance analysis using genome-wide association summary results
    2089 -- 2090So Young Ryu, Samuel H. Payne, Christoph Schaab, Wenzhong Xiao. Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013
    2091 -- 2092Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg. The automated function prediction SIG looks back at 2013 and prepares for 2014

    Volume 30, Issue 13

    1793 -- 1799Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer. Challenges in RNA virus bioinformatics
    1800 -- 1804Max T. B. Clabbers, René C. L. Olsthoorn, Alexander P. Gultyaev. Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region
    1805 -- 1813Ambarish Biswas, Peter C. Fineran, Chris M. Brown. Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs
    1814 -- 1822Peter A. Stockwell, Aniruddha Chatterjee, Euan J. Rodger, Ian M. Morison. DMAP: differential methylation analysis package for RRBS and WGBS data
    1823 -- 1829Arief Gusnanto, Charles C. Taylor, Ibrahim Nafisah, Henry M. Wood, Pamela Rabbitts, Stefano Berri. Estimating optimal window size for analysis of low-coverage next-generation sequence data
    1830 -- 1836Yongzhuang Liu, Bingshan Li, Renjie Tan, Xiaolin Zhu, Yadong Wang. de novo mutations in parent-offspring trios
    1837 -- 1843Christian Otto, Peter F. Stadler, Steve Hoffmann. Lacking alignments? The next-generation sequencing mapper segemehl revisited
    1844 -- 1849Deren A. R. Eaton. de novo RADseq loci for phylogenetic analyses
    1850 -- 1857Pooya Zakeri, Ben Jeuris, Raf Vandebril, Yves Moreau. Protein fold recognition using geometric kernel data fusion
    1858 -- 1866Md. Jamiul Jahid, Tim Hui-Ming Huang, Jianhua Ruan. A personalized committee classification approach to improving prediction of breast cancer metastasis
    1867 -- 1875Florian Buettner, Victoria Moignard, Berthold Göttgens, Fabian J. Theis. Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
    1876 -- 1883Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng. FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model
    1884 -- 1891Francesco Pappalardo, Marzio Pennisi, Alessia Ricupito, Francesco Topputo, Matteo Bellone. Induction of T-cell memory by a dendritic cell vaccine: a computational model
    1892 -- 1898Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf. Derivative processes for modelling metabolic fluxes
    1899 -- 1907Huiming Peng, Tao Peng, Jianguo Wen, David A. Engler, Risë K. Matsunami, Jing Su, Le Zhang, Chung-Che Jeff Chang, Xiaobo Zhou. Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach
    1908 -- 1916Suh-Yuen Liang, Sz-Wei Wu, Tsung-Hsien Pu, Fang-Yu Chang, Kay-Hooi Khoo. An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry
    1917 -- 1919Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko. Wrangling Galaxy's reference data
    1920 -- 1922Jean-Pierre Kocher, Daniel J. Quest, Patrick H. Duffy, Michael A. Meiners, Raymond M. Moore, David N. Rider, Asif Hossain, Steven N. Hart, Valentin Dinu. The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
    1923 -- 1925Chih Lee, Chun-Hsi Huang. LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser
    1926 -- 1927Florent E. Angly, Christopher J. Fields, Gene W. Tyson. The Bio-Community Perl toolkit for microbial ecology
    1928 -- 1929Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia. Orione, a web-based framework for NGS analysis in microbiology
    1930 -- 1932Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
    1933 -- 1934Kemal Akman, Thomas Haaf, Silvia Gravina, Jan Vijg, Achim Tresch. Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
    1935 -- 1936Jaume Bonet, Joan Segura, Joan Planas-Iglesias, Baldomero Oliva, Narcis Fernandez-Fuentes. de novo structure-based protein design
    1937 -- 1939Francesc Fernández-Albert, Rafael Llorach, Cristina Andres-Lacueva, Alexandre Perera. An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)
    1940 -- 1941Steven Gazal, Mourad Sahbatou, Marie-Claude Babron, Emmanuelle Génin, Anne-Louise Leutenegger. FSuite: exploiting inbreeding in dense SNP chip and exome data
    1942 -- 0Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

    Volume 30, Issue 12

    1 -- 2Serafim Batzoglou, Russell Schwartz. Editorial
    9 -- 18Cristina G. Ghiurcuta, Bernard M. E. Moret. Evaluating synteny for improved comparative studies
    19 -- 25Ya'ara Arkin, Elior Rahmani, Marcus E. Kleber, Reijo Laaksonen, Winfried März, Eran Halperin. EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits
    26 -- 33Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert. A statistical approach for inferring the 3D structure of the genome
    34 -- 42Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker. Inferring gene ontologies from pairwise similarity data
    43 -- 51Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida. Automated detection and tracking of many cells by using 4D live-cell imaging data
    52 -- 59Anika Oellrich, Julius Jacobsen, Irene Papatheodorou, Damian Smedley. Using association rule mining to determine promising secondary phenotyping hypotheses
    60 -- 68Nagarajan Natarajan, Inderjit S. Dhillon. Inductive matrix completion for predicting gene-disease associations
    69 -- 77Kourosh Zarringhalam, Ahmed Enayetallah, Padmalatha Reddy, Daniel Ziemek. Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks
    78 -- 86Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
    87 -- 95Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation
    96 -- 104Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci. Large scale analysis of signal reachability
    105 -- 112Christoph Bernau, Markus Riester, Anne-Laure Boulesteix, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron, Lorenzo Trippa. Cross-study validation for the assessment of prediction algorithms
    113 -- 120Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
    121 -- 129Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey. Deep learning of the tissue-regulated splicing code
    130 -- 138Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer. Functional association networks as priors for gene regulatory network inference
    139 -- 148Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang. Graph-regularized dual Lasso for robust eQTL mapping
    149 -- 156Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard. Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics
    157 -- 164Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu. Metabolite identification through multiple kernel learning on fragmentation trees
    165 -- 174Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach
    175 -- 184A. Ercument Cicek, Kathryn Roeder, Gultekin Özsoyoglu. MIRA: mutual information-based reporter algorithm for metabolic networks
    185 -- 194Richard Leslie, Christopher J. O'Donnell, Andrew D. Johnson. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database
    195 -- 203Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael. Detecting independent and recurrent copy number aberrations using interval graphs
    204 -- 211Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Feng Guan, Rafail Ostrovsky, Amit Sahai, Eleazar Eskin. Privacy preserving protocol for detecting genetic relatives using rare variants
    212 -- 218Ladislav Rampásek, Aryan Arbabi, Michael Brudno. Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing
    219 -- 227Mengfei Cao, Christopher M. Pietras, Xian Feng, Kathryn J. Doroschak, Thomas Schaffner, Jisoo Park, Hao Zhang, Lenore J. Cowen, Benjamin J. Hescott. New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
    228 -- 236Lei Huang, Fuhai Li, Jianting Sheng, Xiaofeng Xia, Jinwen Ma, Ming Zhan, Stephen T. C. Wong. DrugComboRanker: drug combination discovery based on target network analysis
    237 -- 245Marc Hulsman, Christos Dimitrakopoulos, Jeroen de Ridder. Scale-space measures for graph topology link protein network architecture to function
    246 -- 254Marinka Zitnik, Blaz Zupan. Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
    255 -- 263Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng. An efficient parallel algorithm for accelerating computational protein design
    264 -- 273Jing Ren, Qian Liu, John Ellis, Jinyan Li. Tertiary structure-based prediction of conformational B-cell epitopes through B factors
    274 -- 282Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen. BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
    283 -- 292Zhaojun Zhang, Wei Wang. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
    293 -- 301Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey A. Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son K. Pham, Anton Korobeynikov, Alla Lapidus, Pavel A. Pevzner. ExSPAnder: a universal repeat resolver for DNA fragment assembly
    302 -- 309Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham. Ragout - a reference-assisted assembly tool for bacterial genomes
    310 -- 318Alastair M. Kilpatrick, Bruce Ward, Stuart Aitken. Stochastic EM-based TFBS motif discovery with MITSU
    319 -- 328Ergude Bao, Tao Jiang, Thomas Girke. de novo genome assembly guided by closely related references
    329 -- 337Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin. Accurate viral population assembly from ultra-deep sequencing data
    1643 -- 1650Guofeng Meng, Martin Vingron. Condition-specific target prediction from motifs and expression
    1651 -- 1659Seyed Yahya Anvar, Kristiaan J. van der Gaag, Jaap W. F. van der Heijden, Marcel H. A. M. Veltrop, Rolf H. A. M. Vossen, Rick H. de Leeuw, Cor Breukel, Henk P. J. Buermans, J. Sjef Verbeek, Peter de Knijff, Johan T. den Dunnen, Jeroen F. J. Laros. TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
    1660 -- 1666Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li, Xin Zhou, Tak Wah Lam, Yingrui Li, Xun Xu, Gane Ka-Shu Wong, Jun Wang. de novo transcriptome assembly with short RNA-Seq reads
    1667 -- 1673Daniel Quang, Xiaohui Xie. EXTREME: an online EM algorithm for motif discovery
    1674 -- 1680Yang Cao, Lei Li. Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model
    1681 -- 1689Ken Nagata, Arlo Randall, Pierre Baldi. Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures
    1690 -- 1697Kevin H. Eng, Bret M. Hanlon. Discrete mixture modeling to address genetic heterogeneity in time-to-event regression
    1698 -- 1706H. Robert Frost, Jason H. Moore. Optimization of gene set annotations via entropy minimization over variable clusters (EMVC)
    1707 -- 1713Anthony Youzhi Cheng, Yik-Ying Teo, Rick Twee-Hee Ong. Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
    1714 -- 1720Jin Zhou, Erwin Tantoso, Lai-Ping Wong, Rick Twee-Hee Ong, Jin-Xin Bei, Yi Li, Jianjun Liu, Chiea-Chuen Khor, Yik-Ying Teo. iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
    1721 -- 1729Fazle E. Faisal, Tijana Milenkovic. Dynamic networks reveal key players in aging
    1730 -- 1738Nikhil Prakash Damle, Debasisa Mohanty. Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network
    1739 -- 1746Hsiu-Sen Chiang, Dong-Her Shih, Binshan Lin, Ming-Hung Shih. An APN model for Arrhythmic beat classification
    1747 -- 1754Eduard Hermann, Stephanie Bleicken, Yamunadevi Subburaj, Ana J. García-Sáez. Automated analysis of giant unilamellar vesicles using circular Hough transformation
    1755 -- 1756Yeonok Lee, Debashis Ghosh, Ross C. Hardison, Yu Zhang. MRHMMs: Multivariate Regression Hidden Markov Models and the variantS
    1757 -- 1758Jordi Deu-Pons, Michael P. Schroeder, Nuria Lopez-Bigas. jHeatmap: an interactive heatmap viewer for the web
    1759 -- 1761Ramon Diaz-Uriarte. ADaCGH2: parallelized analysis of (big) CNA data
    1762 -- 1764Adrian Lärkeryd, Kerstin Myrtennäs, Edvin Karlsson, Chinmay Kumar Dwibedi, Mats Forsman, Pär Larsson, Anders Johansson, Andreas Sjödin. CanSNPer: a hierarchical genotype classifier of clonal pathogens
    1765 -- 1766Maxim I. Pyatkov, Anton N. Pankratov. SBARS: fast creation of dotplots for DNA sequences on different scales using GA-, GC-content
    1767 -- 1768Francisco J. López-Domingo, Javier P. Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo Lopez. ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing
    1769 -- 1770Tim Seifert, Andreas Lund, Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann, Andreas Hildebrandt. SKINK: a web server for string kernel based kink prediction in α-helices
    1771 -- 1773Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
    1774 -- 1776Ling-Hong Hung, Ram Samudrala. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
    1777 -- 1779Xi Wang, Murray J. Cairns. SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
    1780 -- 1781Mario Huerta, Marc Munyi, David Expósito, Enric Querol, Juan Cedano. MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes
    1782 -- 1784Matias D. Butti, Hernan Chanfreau, Diego Martinez, Diego García, Ezequiel Lacunza, Martin C. Abba. BioPlat: a software for human cancer biomarker discovery
    1785 -- 1786Rodrigo Santamaría, Roberto Therón, Luis Quintales. BicOverlapper 2.0: visual analysis for gene expression
    1787 -- 1788Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo. Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis
    1789 -- 1790Emre Guney, Javier Garcia-Garcia, Baldo Oliva. GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
    1791 -- 1792Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver, Valerie Wood. Canto: an online tool for community literature curation

    Volume 30, Issue 11

    1493 -- 1500Charles C. Berry, Karen E. Ocwieja, Nirav Malani, Frederic D. Bushman. Comparing DNA integration site clusters with scan statistics
    1501 -- 1507Jun Hu, Jung-Ying Tzeng. Integrative gene set analysis of multi-platform data with sample heterogeneity
    1508 -- 1513Megan J. Puckelwartz, Lorenzo L. Pesce, Viswateja Nelakuditi, Lisa Dellefave-Castillo, Jessica R. Golbus, Sharlene M. Day, Thomas P. Cappola, Gerald W. Dorn II, Ian T. Foster, Elizabeth M. McNally. Supercomputing for the parallelization of whole genome analysis
    1514 -- 1521Eitan Halper-Stromberg, Jared Steranka, Kathleen H. Burns, Sarven Sabunciyan, Rafael A. Irizarry. Visualization and probability-based scoring of structural variants within repetitive sequences
    1522 -- 1529Shou-Hui Guo, En-Ze Deng, Li-Qin Xu, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    1530 -- 1538Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt. Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
    1539 -- 1546Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis Bach, Jean-Philippe Vert. SegAnnDB: interactive Web-based genomic segmentation
    1547 -- 1554Peng Yu, Chad A. Shaw. An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function
    1555 -- 1561Daniah Trabzuni, Peter C. Thomson. Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain
    1562 -- 1568David C. Kessler, Jack A. Taylor, David B. Dunson. Learning phenotype densities conditional on many interacting predictors
    1569 -- 1578Kristopher A. Hunt, James P. Folsom, Reed L. Taffs, Ross P. Carlson. Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition
    1579 -- 1586Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen. Identifying critical transitions of complex diseases based on a single sample
    1587 -- 1594Deyu Zhou, Dayou Zhong, Yulan He. Event trigger identification for biomedical events extraction using domain knowledge
    1595 -- 1600Clinton J. Mielke, Lawrence J. Mandarino, Valentin Dinu. AMASS: a database for investigating protein structures
    1601 -- 1608Petr Klus, Benedetta Bolognesi, Federico Agostini, Domenica Marchese, Andreas Zanzoni, Gian Gaetano Tartaglia. The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
    1609 -- 1617Martin Maska, Vladimír Ulman, David Svoboda, Pavel Matula, Petr Matula, Cristina Ederra, Ainhoa Urbiola, Tomás España, Subramanian Venkatesan, Deepak M. W. Balak, Pavel Karas, Tereza Bolcková, Markéta Streitová, Craig Carthel, Stefano Coraluppi, Nathalie Harder, Karl Rohr, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Pavel Krízek, Guy M. Hagen, David Pastor-Escuredo, Daniel Jimenez-Carretero, María J. Ledesma-Carbayo, Arrate Muñoz-Barrutia, Erik Meijering, Michal Kozubek, Carlos Ortiz-de-Solorzano. A benchmark for comparison of cell tracking algorithms
    1618 -- 1619Andy Pohl, Miguel Beato. bwtool: a tool for bigWig files
    1620 -- 1622Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
    1623 -- 1624Jeffrey B. Endelman, Christophe Plomion. LPmerge: an R package for merging genetic maps by linear programming
    1625 -- 1626Paul C. Lott, Ian Korf. StochHMM: a flexible hidden Markov model tool and C++ library
    1627 -- 1629Travis M. Drucker, Sarah H. Johnson, Stephen J. Murphy, Kendall W. Cradic, Terry M. Therneau, George Vasmatzis. BIMA V3: an aligner customized for mate pair library sequencing
    1630 -- 1632Raul Aguirre-Gamboa, Victor Trevino. SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis
    1633 -- 1634Pete Donnell, Murad Banaji, Anca Marginean, Casian Pantea. CoNtRol: an open source framework for the analysis of chemical reaction networks
    1635 -- 1636Natalia Novoselova, Cristina Della Beffa, Junxi Wang, Jialiang Li, Frank Pessler, Frank Klawonn. HUM calculator and HUM package for R: easy-to-use software tools for multicategory receiver operating characteristic analysis
    1637 -- 1639Mark Maienschein-Cline, Zhengdeng Lei, Vincent Gardeux, Taimur Abbasi, Roberto F. Machado, Victor Gordeuk, Ankit A. Desai, Santosh Saraf, Neil Bahroos, Yves A. Lussier. ARTS: automated randomization of multiple traits for study design
    1640 -- 1642Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, Yixue Li. The 3DGD: a database of genome 3D structure

    Volume 30, Issue 10

    1343 -- 1352Clara Pizzuti, Simona E. Rombo. Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
    1353 -- 0Robert F. Murphy. A new era in bioimage informatics
    1354 -- 1362Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu. BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
    1363 -- 1369Martin J. Aryee, Andrew E. Jaffe, Héctor Corrada Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
    1370 -- 1376Priyadip Ray, Lingling Zheng, Joseph E. Lucas, Lawrence Carin. Bayesian joint analysis of heterogeneous genomics data
    1377 -- 1383Xiaowei Wang. Composition of seed sequence is a major determinant of microRNA targeting patterns
    1384 -- 1391Kaiyong Zhao, Xiaowen Chu. G-BLASTN: accelerating nucleotide alignment by graphics processors
    1392 -- 1399Marta 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
    1400 -- 1408Iwona Pawlikowska, Gang Wu, Michael Edmonson, Zhifa Liu, Tanja Gruber, Jinghui Zhang, Stan Pounds. The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression
    1409 -- 1416Bogdan Mirauta, Pierre Nicolas, Hugues Richard. Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
    1417 -- 1423Martin Vincent, Katharina Perell, Finn Cilius Nielsen, Gedske Daugaard, Niels Richard Hansen. Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases
    1424 -- 1430Klaus Jung, Hassan Dihazi, Asima Bibi, Gry H. Dihazi, Tim Beißbarth. Adaption of the global test idea to proteomics data with missing values
    1431 -- 1439E. Andres Houseman, John Molitor, Carmen J. Marsit. Reference-free cell mixture adjustments in analysis of DNA methylation data
    1440 -- 1448Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer. Comparison of approaches for parameter identifiability analysis of biological systems
    1449 -- 1455Dana Silverbush, Roded Sharan. Network orientation via shortest paths
    1456 -- 1463Kaifang Pang, Ying-Wooi Wan, William T. Choi, Lawrence A. Donehower, Jingchun Sun, Dhruv Pant, Zhandong Liu. Combinatorial therapy discovery using mixed integer linear programming
    1464 -- 1466Paul Theodor Pyl, Julian Gehring, Bernd Fischer 0003, Wolfgang Huber. h5vc: scalable nucleotide tallies with HDF5
    1467 -- 1468Alex Chun-Hong Fok, Sunny Siu-Nam Mok, Sau Dan Lee, Kevin Y. Yip. ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications
    1469 -- 1470Andrey Tovchigrechko, Pratap Venepally, Samuel H. Payne. PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
    1471 -- 1472Fabian A. Buske, Hugh J. French, Martin A. Smith, Susan J. Clark, Denis C. Bauer. NGSANE: a lightweight production informatics framework for high-throughput data analysis
    1473 -- 1475Sangsu Bae, Jeongbin Park, Jin-Soo Kim. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
    1476 -- 1477Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis. PUmPER: phylogenies updated perpetually
    1478 -- 1480Ramon Guixà-González, Ismael Rodriguez-Espigares, Juan Manuel Ramírez-Anguita, Pau Carrió-Gaspar, Hector Martinez-Seara, Toni Giorgino, Jana Selent. MEMBPLUGIN: studying membrane complexity in VMD
    1481 -- 1483Jamel Meslamani, Steven G. Smith, Roberto Sanchez, Ming-Ming Zhou. ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains
    1484 -- 1485Sander Bollen, Mathias Leddin, Miguel A. Andrade-Navarro, Nancy Mah. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
    1486 -- 1487Matteo Fumagalli, Filipe G. Vieira, Tyler Linderoth, Rasmus Nielsen. ngsTools: methods for population genetics analyses from next-generation sequencing data
    1488 -- 1490James T. Monacell, Ignazio Carbone. Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
    1491 -- 1492Michael Pedersen, Nicolas Oury, Colin Gravill, Andrew Phillips. Bio Simulators: a web UI for biological simulation

    Volume 30, Issue 1

    1 -- 8Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna. Using Genome Query Language to uncover genetic variation
    9 -- 16Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard. Specificity control for read alignments using an artificial reference genome-guided false discovery rate
    17 -- 23Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente. Further Steps in TANGO: improved taxonomic assignment in metagenomics
    24 -- 30Lilian Janin, Giovanna Rosone, Anthony J. Cox. Adaptive reference-free compression of sequence quality scores
    31 -- 37Rayan Chikhi, Paul Medvedev. k-mer size selection for genome assembly
    38 -- 39Daniel H. Huson, Chao Xie. A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA
    40 -- 49David Hernández, Ryan Tewhey, Jean-Baptiste Veyrieras, Laurent Farinelli, Magne Østerås, Patrice François, Jacques Schrenzel. Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
    50 -- 60Noemi Andor, Julie V. Harness, Sabine Müller, Hans-Werner Mewes, Claudia Petritsch. EXPANDS: expanding ploidy and allele frequency on nested subpopulations
    61 -- 70Paulo 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
    71 -- 80Mingjun 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
    81 -- 93Yijie Wang, Xiaoning Qian. Functional module identification in protein interaction networks by interaction patterns
    94 -- 103Yungang Xu, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu. Glycine max) microRNA functional network based on target gene network
    104 -- 114Songhua Xu, Hong-Jun Yoon, Georgia D. Tourassi. A user-oriented web crawler for selectively acquiring online content in e-health research
    115 -- 116Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel. snoStrip: a snoRNA annotation pipeline
    117 -- 118Armando J. Pinho, Diogo Pratas. MFCompress: a compression tool for FASTA and multi-FASTA data
    119 -- 120André 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
    121 -- 122Christoph Gille, Weyand Birgit, Andreas Gille. Sequence alignment visualization in HTML5 without Java
    123 -- 124Michael J. Landis, Trevor Bedford. Phylowood: interactive web-based animations of biogeographic and phylogeographic histories
    125 -- 126Shannon L. N. Mayne, Hugh-George Patterton. AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes
    127 -- 128Thomas Sandmann, Sarah K. Kummerfeld, Robert Gentleman, Richard Bourgon. gCMAP: user-friendly connectivity mapping with R
    129 -- 130Maxwell Lewis Neal, Michal Galdzicki, J. T. Gallimore, H. M. Sauro. A C library for retrieving specific reactions from the BioModels database
    131 -- 132Matthias Bock, Till Scharp, Chaitanya Talnikar, Edda Klipp. BooleSim: an interactive Boolean network simulator
    133 -- 134Grant 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
    135 -- 136Minji Jeon, Sunwon Lee, Kyubum Lee, Aik Choon Tan, Jaewoo Kang. BEReX: Biomedical Entity-Relationship eXplorer
    137 -- 138Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski. StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems
    139 -- 140Özgün Babur, Bülent Arman Aksoy, Igor Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir. Pattern search in BioPAX models
    141 -- 142Jianfei Hu, Hee-Sool Rho, Robert H. Newman, Jin Zhang, Heng Zhu, Jiang Qian. PhosphoNetworks: a database for human phosphorylation networks
    143 -- 145Burkhard Rost. ISCB: past-present perspective for the International Society for Computational Biology
    146 -- 147Series editors. Andreas Dress, Michal Linial, Olga Troyanskaya, Martin Vingron: ISCB/SPRINGER series in computational biology
    148 -- 149Jim Cavalcoli, Lonnie 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
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