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Bioinformatics, 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