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ORCIDBioinformatics, Volume 26
Volume 26, Number 1, January 2010
- Andreas S. Richter
, Christian Schleberger, Rolf Backofen, Claudia Steglich:
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. 1-5
- Bart P. P. van Houte, Jaap Heringa:
Accurate confidence aware clustering of array CGH tumor profiles. 6-14 - Shuangge Ma, Yawei Zhang, Jian Huang, Xuesong Han, Theodore Holford, Qing Lan, Nathaniel Rothman, Peter Boyle, Tongzhang Zheng:
Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method. 15-21 - Youngik Yang, Donald Gilbert, Sun Kim:
Annotation confidence score for genome annotation: a genome comparison approach. 22-29 - Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L. S. Tang, Weichuan Yu:
Predictive rule inference for epistatic interaction detection in genome-wide association studies. 30-37
- Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, W. Evan Johnson:
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. 38-45
- Jian Yu, Yong Zhou, Isao Tanaka, Min Yao:
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. 46-52 - Guillaume Bouvier, Nathalie Evrard-Todeschi, Jean-Pierre Girault, Gildas Bertho:
Automatic clustering of docking poses in virtual screening process using self-organizing map. 53-60 - Robert A. Forties, Ralf Bundschuh:
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure. 61-67
- Mohammadmahdi R. Yousefi, Jianping Hua, Chao Sima, Edward R. Dougherty:
Reporting bias when using real data sets to analyze classification performance. 68-76 - Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, Judith A. J. Steen:
Computational protein profile similarity screening for quantitative mass spectrometry experiments. 77-83 - Axel Rasche, Ralf Herwig:
ARH: predicting splice variants from genome-wide data with modified entropy. 84-90
- Stefano Volinia, Rosa Visone, Marco Galasso, Elda Rossi, Carlo Maria Croce:
Identification of microRNA activity by Targets' Reverse EXpression. 91-97 - Brian Carrillo, Corey Yanofsky, Sylvie Laboissiere, Robert Nadon, Robert E. Kearney:
Methods for combining peptide intensities to estimate relative protein abundance. 98-103 - Tina Toni, Michael P. H. Stumpf:
Simulation-based model selection for dynamical systems in systems and population biology. 104-110
- Yun Niu, David Otasek, Igor Jurisica:
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D. 111-119
- Troy Zerr, Gregory M. Cooper, Evan E. Eichler, Deborah A. Nickerson:
Targeted interrogation of copy number variation using SCIMMkit. 120-122
- Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, Silke R. Sperling:
MicroRazerS: rapid alignment of small RNA reads. 123-124 - Erik Arner, Yoshihide Hayashizaki, Carsten O. Daub:
NGSView: an extensible open source editor for next-generation sequencing data. 125-126 - Ji Qi, Fangqing Zhao, Anne Buboltz, Stephan C. Schuster:
inGAP: an integrated next-generation genome analysis pipeline. 127-129
- Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Ancestors 1.0: a web server for ancestral sequence reconstruction. 130-131 - Andrew L. Hipp, Marcial Escudero:
MATICCE: mapping transitions in continuous character evolution. 132-133
- Joshua Buckner, Justin Wilson, Mark Seligman, Brian D. Athey, Stanley J. Watson, Fan Meng:
The gputools package enables GPU computing in R. 134-135 - Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang:
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. 136-138 - Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth:
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. 139-140
- Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka:
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks. 141-142 - Ben D. MacArthur, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan:
GATE: software for the analysis and visualization of high-dimensional time series expression data. 143-144
- Wei Yu, Melinda Clyne, Muin J. Khoury, Marta Gwinn:
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations. 145-146 - Martijn J. Schuemie, Ning Kang, Maarten L. Hekkelman, Jan A. Kors:
GeneE: Gene and protein query expansion with disambiguation. 147-148
Volume 26, Number 2, January 2010
- Thiago M. Venancio, L. Aravind:
CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes. 149-152
- Nancy R. Zhang, Yasin Senbabaoglu, Jun Z. Li:
Joint estimation of DNA copy number from multiple platforms. 153-160 - Raj K. Gaire, James Bailey, Jennifer Bearfoot, Ian G. Campbell, Peter J. Stuckey, Izhak Haviv:
MIRAGAA - a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. 161-167 - Robert T. Morris, Timothy R. O'Connor, John J. Wyrick:
Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. 168-174
- Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler:
Target prediction and a statistical sampling algorithm for RNA-RNA interaction. 175-181
- Liam J. McGuffin, Daniel B. Roche:
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. 182-188 - Narendra Kumar, Debasisa Mohanty:
Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials. 189-197 - Danzhi Huang, Ting Zhou, Karine Lafleur, Cristina Nevado, Amedeo Caflisch:
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. 198-204
- Ramon Xulvi-Brunet, Hongzhe Li:
Co-expression networks: graph properties and topological comparisons. 205-214 - Ai-Jun Yang, Xin-Yuan Song:
Bayesian variable selection for disease classification using gene expression data. 215-222 - William Ritchie, Stephane Flamant, John E. J. Rasko:
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. 223-227 - Bin Wang, Xiao-Feng Wang, Paul Howell, Xuemin Qian, Kun Huang, Adam I. Riker, Jingfang Ju, Yaguang Xi:
A personalized microRNA microarray normalization method using a logistic regression model. 228-234
- Runqing Yang, Xin Wang, Zeyuan Wu, Daniel R. Prows, Min Lin:
Bayesian model selection for characterizing genomic imprinting effects and patterns. 235-241 - Benilton S. Carvalho, Thomas A. Louis, Rafael A. Irizarry:
Quantifying uncertainty in genotype calls. 242-249
- Herbert Pang, Debayan Datta, Hongyu Zhao:
Pathway analysis using random forests with bivariate node-split for survival outcomes. 250-258
- Eric R. Gamazon, Wei Zhang, Anuar Konkashbaev, Shiwei Duan, Emily O. Kistner, Dan L. Nicolae, M. Eileen Dolan, Nancy J. Cox:
SCAN: SNP and copy number annotation. 259-262
- Jean Muller, Christopher J. Creevey, Julie Dawn Thompson, Detlev Arendt, Peer Bork:
AQUA: automated quality improvement for multiple sequence alignments. 263-265
- J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight:
PyNAST: a flexible tool for aligning sequences to a template alignment. 266-267
- Shihao Shen, Claude C. Warzecha, Russ P. Carstens, Yi Xing:
MADS+: discovery of differential splicing events from Affymetrix exon junction array data. 268-269
- Kanchana Narayanan, Jing Li:
MAVEN: a tool for visualization and functional analysis of genome-wide association results. 270-272 - Chris Duran, Zoran Boskovic, Michael Imelfort, Jacqueline Batley, Nicholas A. Hamilton, David Edwards:
CMap3D: a 3D visualization tool for comparative genetic maps. 273-274
- Fei Li, Peng Li, Wenjian Xu, Yuxing Peng, Xiaochen Bo, Shengqi Wang:
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. 275-277 - Tomás Levitner, Stepán Timr, Dalibor Stys:
Expertomica Cells: analysis of cell monolayer development. 278-279 - Nathaniel Beagley, Kelly G. Stratton, Bobbie-Jo M. Webb-Robertson:
VIBE 2.0: Visual Integration for Bayesian Evaluation. 280-282 - Aaron Ikin, Carlos Riveros, Pablo Moscato, Alexandre Mendes:
The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis. 283-284 - Jesse Paquette, Taku A. Tokuyasu:
EGAN: exploratory gene association networks. 285-286
- Zhi Xie, Shaohui Hu, Seth Blackshaw, Heng Zhu, Jiang Qian:
hPDI: a database of experimental human protein-DNA interactions. 287-289 - Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam-Son Phan Tran:
LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. 290-291
- Ronglai Shen, Adam B. Olshen, Marc Ladanyi:
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. 292-293
Volume 26, Number 3, February 2010
- Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
Estimating DNA coverage and abundance in metagenomes using a gamma approximation. 295-301
- Thanh Le, Tom Altman, Katheleen J. Gardiner:
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences. 302-309
- Daniel T. Lavelle, William R. Pearson:
Globally, unrelated protein sequences appear random. 310-318 - N. A. Temiz, Andrew C. Trapp, Oleg A. Prokopyev, Carlos J. Camacho:
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting. 319-325 - Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya:
FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. 326-332
- Shuya Lu, Jia Li, Chi Song, Kui Shen, George C. Tseng:
Biomarker detection in the integration of multiple multi-class genomic studies. 333-340 - Yijing Shen, Wei Sun, Ker-Chau Li:
Dynamically weighted clustering with noise set. 341-347 - Rui Hu, Xing Qiu, Galina V. Glazko:
A new gene selection procedure based on the covariance distance. 348-354 - Steven J. Kiddle, Oliver P. F. Windram, Stuart McHattie, Andrew Meade, Jim Beynon, Vicky Buchanan-Wollaston, Katherine J. Denby, Sach Mukherjee:
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. 355-362 - Thang V. Pham, Sander R. Piersma, Marc Warmoes, Connie R. Jimenez:
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. 363-369 - Theresa Scharl, Bettina Grün, Friedrich Leisch:
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects. 370-377
- Monica Chagoyen, Florencio Pazos:
Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data. 378-384 - Suk Hoon Jung, Bo-ra Hyun, Woo-Hyuk Jang, Hee-Young Hur, Dong-Soo Han:
Protein complex prediction based on simultaneous protein interaction network. 385-391
- Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, Yvan Saeys:
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. 392-398
- Kousuke Hanada, Kenji Akiyama, Tetsuya Sakurai, Tetsuro Toyoda, Kazuo Shinozaki, Shin-Han Shiu:
sORF finder: a program package to identify small open reading frames with high coding potential. 399-400
- Iain Milne, Micha Bayer, Linda Cardle, Paul D. Shaw, Gordon Stephen, Frank Wright, David F. Marshall:
Tablet - next generation sequence assembly visualization. 401-402 - Emese Meglécz, Caroline Costedoat, Vincent Dubut, André Gilles, Thibaut Malausa, Nicolas Pech, Jean-François Martin:
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. 403-404 - Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu, Hongwei Xie:
Tmod: toolbox of motif discovery. 405-407
- Chi Ho Lin, Hao Zhao, Sean Harry Lowcay, Atif Shahab, Guillaume Bourque:
webMGR: an online tool for the multiple genome rearrangement problem. 408-410
- Nathan S. Watson-Haigh, Haja N. Kadarmideen, Antonio Reverter:
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. 411-413 - Keyan Salari, Robert Tibshirani, Jonathan R. Pollack:
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. 414-416
- Valery Terletskiy, Valentina Tyshchenko, Ilargi Martinez-Ballesteros, Javier Garaizar, Joseba Bikandi:
Validation of double digest selective label database for sequenced prokaryotic genomes. 417-418 - Emmanuel Paradis:
pegas: an R package for population genetics with an integrated-modular approach. 419-420
- Falko Krause, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp, Wolfram Liebermeister:
Annotation and merging of SBML models with semanticSBML. 421-422 - Kendell Clement, Nathaniel Gustafson, Amanda Berbert, Hyrum Carroll, Christopher Merris, Ammon Olsen, Mark J. Clement, Quinn Snell, Jared Allen, Randall J. Roper:
PathGen: a transitive gene pathway generator. 423-425 - Emmet Caulfield, Andreas Hellander:
CellMC - a multiplatform model compiler for the Cell Broadband Engine and x86. 426-428 - Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander:
ChiBE: interactive visualization and manipulation of BioPAX pathway models. 429-431 - Bart S. Hendriks, Christopher W. Espelin:
DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets. 432-433
- Carson M. Andorf, Carolyn J. Lawrence, Lisa C. Harper, Mary L. Schaeffer, Darwin A. Campbell, Taner Z. Sen:
The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps. 434-436
- Anne-Laure Boulesteix:
Over-optimism in bioinformatics research. 437-439 - Pawel Smialowski, Dmitrij Frishman, Stefan Kramer:
Pitfalls of supervised feature selection. 440-443
Volume 26, Number 4, February 2010
- Jason H. Moore, Folkert W. Asselbergs, Scott M. Williams:
Bioinformatics challenges for genome-wide association studies. 445-455
- Maureen A. Sartor, Vasudeva Mahavisno, Venkateshwar G. Keshamouni, James D. Cavalcoli, Zach Wright, Alla Karnovsky, Rork Kuick, H. V. Jagadish, Barbara Mirel, Terry E. Weymouth, Brian D. Athey, Gilbert S. Omenn:
ConceptGen: a gene set enrichment and gene set relation mapping tool. 456-463 - Qunyuan Zhang, Li Ding, David E. Larson, Daniel C. Koboldt, Michael D. McLellan, Ken Chen, Xiaoqi Shi, Aldi T. Kraja, Elaine R. Mardis, Richard K. Wilson, Ingrid B. Borecki, Michael A. Province:
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. 464-469
- Tuping Zhou, Nanjiang Shu, Sven Hovmöller:
A novel method for accurate one-dimensional protein structure prediction based on fragment matching. 470-477 - Shang-Hong Zhang, Ya-Zhi Huang:
Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA. 478-485
- Mingoo Kim, Sung-Bum Cho, Ju Han Kim:
Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. 486-492 - Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey:
RNA-Seq gene expression estimation with read mapping uncertainty. 493-500 - Benhuai Xie, Wei Pan, Xiaotong Shen:
Penalized mixtures of factor analyzers with application to clustering high-dimensional microarray data. 501-508 - Ping-Shi Wu, Hans-Georg Müller:
Functional embedding for the classification of gene expression profiles. 509-517
- Ninad Dewal, Matthew L. Freedman, Thomas LaFramboise, Itsik Pe'er:
Power to detect selective allelic amplification in genome-wide scans of tumor data. 518-528
- Kelvin Xi Zhang, B. F. Francis Ouellette:
Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence. 529-535 - Naama Tepper, Tomer Shlomi:
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. 536-543
- Kristian Kvilekval, Dmitry V. Fedorov, Boguslaw Obara, Ambuj K. Singh, B. S. Manjunath:
Bisque: a platform for bioimage analysis and management. 544-552 - Victoria Martin-Requena, Javier Ríos, Maximiliano García, Sergio Ramírez, Oswaldo Trelles:
jORCA: easily integrating bioinformatics Web Services. 553-559 - Christine Fong, Dennis C. Ko, Michael Wasnick, Matthew Radey, Samuel I. Miller, Mitchell J. Brittnacher:
GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. 560-564
- Jared T. Simpson, Rebecca E. McIntyre, David J. Adams, Richard Durbin:
Copy number variant detection in inbred strains from short read sequence data. 565-567
- Matthew Horton, Natacha Bodenhausen, Joy Bergelson:
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences. 568-569 - Peter Husemann, Jens Stoye:
r2cat: synteny plots and comparative assembly. 570-571 - Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi:
BRAT: bisulfite-treated reads analysis tool. 572-573
- Karl Frank, Markus Gruber, Manfred J. Sippl:
COPS Benchmark: interactive analysis of database search methods. 574-575
- Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama:
emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. 576-577