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ORCIDBioinformatics, Volume 29
Volume 29, Number 1, January 2013
- Ryan M. Layer, Kevin Skadron
, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan:
Binary Interval Search: a scalable algorithm for counting interval intersections. 1-7
- Massimo Andreatta, Ole Lund, Morten Nielsen:
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. 8-14 - Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras:
STAR: ultrafast universal RNA-seq aligner. 15-21 - Russell Bonneville, Victor X. Jin:
A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes. 22-28 - Wenhui Wang, Xiaolin Yin, Yoon Soo Pyon, Matthew Hayes, Jing Li:
Rare variant discovery and calling by sequencing pooled samples with overlaps. 29-38 - Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén:
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. 39-46
- Alex W. Slater, Javier I. Castellanos, Manfred J. Sippl, Francisco Melo:
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments. 47-53 - Jamie R. Hill, Charlotte M. Deane:
MP-T: improving membrane protein alignment for structure prediction. 54-61 - Benjamin Merget, David Zilian, Tobias Müller, Christoph A. Sotriffer:
MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules. 62-68 - Thomas L. Vincent, Peter J. Green, Derek N. Woolfson:
LOGICOIL - multi-state prediction of coiled-coil oligomeric state. 69-76
- Florian Erhard, Lars Dölken, Ralf Zimmer:
RIP-chip enrichment analysis. 77-83
- Androniki Menelaou, Jonathan Marchini:
Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. 84-91
- Chia Hsin Liu, Ker-Chau Li, Shinsheng Yuan:
Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence. 92-98 - Xi Chen, Hemant Ishwaran:
Pathway hunting by random survival forests. 99-105 - Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen:
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. 106-113
- Shiyuyun Tang, Ivan Antonov, Mark Borodovsky:
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. 114-116 - Arturo Magana-Mora, Haitham Ashoor, Boris R. Jankovic, Allan Kamau, Karim Awara, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic:
Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. 117-118 - Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM: PacBio reads simulator - toward accurate genome assembly. 119-121
- Zhengwei Zhu, Beifang Niu, Jing Chen, Sitao Wu, Shulei Sun, Weizhong Li:
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. 122-123 - Lu Zhang, Jing Zhang, Jing Yang, Dingge Ying, Yu-Lung Lau, Wanling Yang:
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data. 124-125
- Dimitrios Vlachakis, Dimosthenis Tsagkrasoulis, Vasileios Megalooikonomou, Sophia Kossida:
Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit. 126-128
- Mario Fasold, Hans Binder:
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. 129-131 - Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez:
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. 132-134
- Hailiang Huang, Sandeep Tata, Robert J. Prill:
BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters. 135-136
- Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano:
XiP: a computational environment to create, extend and share workflows. 137-139 - Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash:
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. 140-142 - Michael Weitzel, Katharina Nöh, Tolga Dalman, Sebastian Niedenführ, Birgit Stute, Wolfgang Wiechert:
13CFLUX2 - high-performance software suite for 13C-metabolic flux analysis. 143-145
- Mark Woodbridge, Christopher D. Tomlinson, Sarah A. Butcher:
ADAM: automated data management for research datasets. 146-147
Volume 29, Number 2, January 2013
- Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju Manyam, Kim-Anh Do:
iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data. 149-159 - Yang I. Li, Richard R. Copley:
Scaffolding low quality genomes using orthologous protein sequences. 160-165
- Saad I. Sheikh, Tamer Kahveci, Sanjay Ranka, J. Gordon Burleigh:
Stability analysis of phylogenetic trees. 166-174
- Ivan K. Huang, Jimin Pei, Nick V. Grishin:
Defining and predicting structurally conserved regions in protein superfamilies. 175-181
- Mehmet Kocak, E. Olusegun George, Saumyadipta Pyne, Stanley Pounds:
An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data. 182-188 - Andrew E. Teschendorff, Francesco Marabita, Matthias Lechner, Thomas E. Bartlett, Jesper Tegnér, David Gomez-Cabrero, Stephan Beck:
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. 189-196
- Mark Silberstein, Omer Weissbrod, Lars Otten, Anna Tzemach, Andrei Anisenia, Oren Shtark, Dvir Tuberg, Eddie Galfrin, Irena Gannon, Adel Shalata, Zvi U. Borochowitz, Rina Dechter, Elizabeth Thompson, Dan Geiger:
A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees. 197-205 - Barbara Rakitsch, Christoph Lippert, Oliver Stegle, Karsten M. Borgwardt:
A Lasso multi-marker mixed model for association mapping with population structure correction. 206-214
- Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Ariston de Carvalho Azevedo, Tobias Wittkop, Jan Baumbach:
Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. 215-222 - Thomas Sütterlin, Christoph Kolb, Hartmut Dickhaus, Dirk Jäger, Niels Grabe:
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. 223-229 - Li C. Xia, Dongmei Ai, Jacob A. Cram, Jed A. Fuhrman, Fengzhu Sun:
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. 230-237 - Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng:
Drug-target interaction prediction by learning from local information and neighbors. 238-245 - Robert J. Flassig, Sandra Heise, Kai Sundmacher, Steffen Klamt:
An effective framework for reconstructing gene regulatory networks from genetical genomics data. 246-254
- Frida Belinky, Iris Bahir, Gil Stelzer, Shahar Zimmerman, Naomi Rosen, Noam Nativ, Irina Dalah, Tsippi Iny Stein, Noa Rappaport, Toutai Mituyama, Marilyn Safran, Doron Lancet:
Non-redundant compendium of human ncRNA genes in GeneCards. 255-261
- Jenna L. Butler, Marjorie Elizabeth Osborne Locke, Kathleen A. Hill, Mark Daley:
HD-CNV: hotspot detector for copy number variants. 262-263 - David R. Powell, Torsten Seemann:
VAGUE: a graphical user interface for the Velvet assembler. 264-265 - Yunxin Chen, Hui Yao, Erika J. Thompson, Nizar M. Tannir, John N. Weinstein, Xiaoping Su:
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. 266-267 - Davide Campagna, Andrea Telatin, Claudio Forcato, Nicola Vitulo, Giorgio Valle:
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. 268-270
- Michael Golden, Darren Martin:
DOOSS: a tool for visual analysis of data overlaid on secondary structures. 271-272
- Dmitri D. Pervouchine, David G. Knowles, Roderic Guigó:
Intron-centric estimation of alternative splicing from RNA-seq data. 273-274
- Zamin Iqbal, Isaac Turner, Gil McVean:
High-throughput microbial population genomics using the Cortex variation assembler. 275-276
- Gerd Zschaler, Thilo Gross:
Largenet2: an object-oriented programming library for simulating large adaptive networks. 277-278 - Guomin Ren, Zhihua Liu:
NetCAD: a network analysis tool for coronary artery disease-associated PPI network. 279-280 - Achuthanunni Chokkathukalam, Andris Jankevics, Darren J. Creek, Fiona Achcar, Michael P. Barrett, Rainer Breitling:
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. 281-283
- Alexandre P. Blanchard, Graeme S. V. McDowell, Nico Valenzuela, Hongbin Xu, Sarah Gelbard, Martin Bertrand, Gary W. Slater, Daniel Figeys, Stephen Fai, Steffany A. L. Bennett:
Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass. 284-285 - Ola Spjuth, Valentin Georgiev, Lars Carlsson, Jonathan Alvarsson, Arvid Berg, Egon L. Willighagen, Jarl E. S. Wikberg, Martin Eklund:
Bioclipse-R: integrating management and visualization of life science data with statistical analysis. 286-289
- Nozomu Sakurai, Takeshi Ara, Shigehiko Kanaya, Yukiko Nakamura, Yoko Iijima, Mitsuo Enomoto, Takeshi Motegi, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata:
An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values. 290-291 - Jiayu Gong, Xiaofeng Liu, Xianwen Cao, Yanyan Diao, Daqi Gao, Honglin Li, Xuhong Qian:
PTID: an integrated web resource and computational tool for agrochemical discovery. 292-294 - Yaping Fang, Hui-Xin Liu, Ning Zhang, Grace L. Guo, Yu-Jui Yvonne Wan, Jianwen Fang:
NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse. 295-297
- Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld:
ImgLib2 - generic image processing in Java. 298
Volume 29, Number 3, February 2013
- Shengping Yang, Stanley Pounds, Kun Zhang, Zhide Fang:
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays. 299-307 - Yongchao Liu, Jan Schröder, Bertil Schmidt:
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. 308-315 - Paul M. Gontarz, Jennifer Berger, Chung F. Wong:
SRmapper: a fast and sensitive genome-hashing alignment tool. 316-321
- Takako Takeda, Rosario I. Corona, Jun-tao Guo:
A knowledge-based orientation potential for transcription factor-DNA docking. 322-330 - Orly Noivirt-Brik, Gershon Hazan, Ron Unger, Yanay Ofran:
Non-local residue-residue contacts in proteins are more conserved than local ones. 331-337
- Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov:
Inference of gene regulatory networks from genome-wide knockout fitness data. 338-346 - Yuan Shi, Gregory Mellier, Sinong Huang, Jacob K. White, Shazib Pervaiz, Lisa Tucker-Kellogg:
Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP. 347-354
- Chengwei Lei, Jianhua Ruan:
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. 355-364 - Yoshihiko Matsuta, Masahiro Ito, Yukako Tohsato:
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine. 365-372
- Fernando Amat, Eugene W. Myers, Philipp J. Keller:
Fast and robust optical flow for time-lapse microscopy using super-voxels. 373-380
- Chase A. Miller, Jon S. Anthony, Michelle M. Meyer, Gabor T. Marth:
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. 381-383 - Theodore R. Pak, Frederick P. Roth:
ChromoZoom: a flexible, fluid, web-based genome browser. 384-386 - Connor McCoy, Aaron Gallagher, Noah G. Hoffman, Frederick A. Matsen IV:
nestly - a framework for running software with nested parameter choices and aggregating results. 387-388 - Thomas M. Keane, Kim Wong, David J. Adams:
RetroSeq: transposable element discovery from next-generation sequencing data. 389-390
- Raeece Naeem, Mamoon Rashid, Arnab Pain:
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. 391-392
- Lane Votapka, Rommie E. Amaro:
Multistructural hot spot characterization with FTProd. 393-394 - Anna Maria Gallina, Paola Bisignano, Maurizio Bergamino, Domenico Bordo:
PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. 395-397 - Mickaël Krzeminski, Joseph A. Marsh, Chris Neale, Wing-Yiu Choy, Julie D. Forman-Kay:
Characterization of disordered proteins with ENSEMBLE. 398-399
- Brad Reisfeld, Jaime H. Ivy, Michael A. Lyons, Jesse M. Wright, Justin L. Rogers, Arthur N. Mayeno:
DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction. 400-401 - David M. Reif, Myroslav Sypa, Eric F. Lock, Fred A. Wright, Ander Wilson, Tommy Cathey, Richard S. Judson, Ivan Rusyn:
ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence. 402-403 - Gang Liu, Apurv Puri, Sriram Neelamegham:
Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology. 404-406
- Davide Albanese, Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, Cesare Furlanello:
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. 407-408
- Xinyi Liu, Shuyuan Wang, Fanlin Meng, Jizhe Wang, Yan Zhang, Enyu Dai, Xuexin Yu, Xia Li, Wei Jiang:
SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression. 409-411
- Oliver Serang:
Concerning the accuracy of Fido and parameter choice. 412
Volume 29, Number 4, February 2013
- Alan Medlar, Dorota Glowacka, Horia Stanescu, Kevin Bryson, Robert Kleta:
SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU. 413-419 - Jia-Shing Chen, Wei-Shiang Hung, Hsiang-Han Chan, Shaw-Jenq Tsai, Hsiao-Fang Sunny Sun:
In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. 420-427 - Nilgun Donmez, Michael Brudno:
SCARPA: scaffolding reads with practical algorithms. 428-434 - Scott C. Clark, Rob Egan, Peter I. Frazier, Zhong Wang:
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. 435-443
- Parameswaran Ramachandran, Gareth A. Palidwor, Christopher J. Porter, Theodore J. Perkins:
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. 444-450
- Mengjie Chen, Valentina Svicher, Anna Artese, Giosuè Costa, Claudia Alteri, Francesco Ortuso, Lucia Parrotta, Yang Liu, Chang Liu, Carlo-Federico Perno, Stefano Alcaro, Jing Zhang:
Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. 451-460
- Andrew McDavid, Greg Finak, Pratip K. Chattopadhyay, Maria Dominguez, Laurie Lamoreaux, Steven S. Ma, Mario Roederer, Raphael Gottardo:
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. 461-467
- Rosario M. Piro, Ivan Molineris, Ferdinando Di Cunto, Roland Eils, Rainer König:
Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. 468-475
- Jesse A. Gillis, Paul Pavlidis:
Assessing identity, redundancy and confounds in Gene Ontology annotations over time. 476-482 - Wayne B. Hayes, Kai Sun, Natasa Przulj:
Graphlet-based measures are suitable for biological network comparison. 483-491
- Jianrong Wang, Victoria V. Lunyak, I. King Jordan:
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. 492-493 - Marcus R. Breese, Yunlong Liu:
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. 494-496
- Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S. Joshua Swamidass, Curt M. Breneman:
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. 497-498 - Timothy P. Levine, Rachel D. Daniels, Alberto T. Gatta, Louise H. Wong, Matthew J. Hayes:
The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. 499-503 - Castrense Savojardo, Piero Fariselli, Rita Casadio:
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. 504-505
- Clemens Wrzodek, Johannes Eichner, Finja Büchel, Andreas Zell:
InCroMAP: integrated analysis of cross-platform microarray and pathway data. 506-508
- Daniel Bottomly, Beth Wilmot, Jeffrey W. Tyner, Christopher A. Eide, Marc M. Loriaux, Brian J. Druker, Shannon K. McWeeney:
HitWalker: variant prioritization for personalized functional cancer genomics. 509-510
- Linnea Järvstråt, Mikael Johansson, Urban Gullberg, Björn Nilsson:
Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling. 511-512 - Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri:
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. 513-514
- Woonghee Lee, Arash Bahrami, John L. Markley:
ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. 515-517 - Arsen Arakelyan, Lilit Nersisyan:
KEGGParser: parsing and editing KEGG pathway maps in Matlab. 518-519
- Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann, Tim Beißbarth:
rBiopaxParser - an R package to parse, modify and visualize BioPAX data. 520-522 - Nikolas Fechner, George Papadatos, David A. Evans, John Richard Morphy, Suzanne Clare Brewerton, David A. Thorner, Michael J. Bodkin:
ChEMBLSpace - a graphical explorer of the chemogenomic space covered by the ChEMBL database. 523-524 - Eamonn Maguire, Alejandra N. González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra:
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets. 525-527