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Bioinformatics, Volume 25
Volume 25, Number 1, January 2009
- Francesca Diella, Sophie Chabanis-Davidson, Katja Luck, Claudia Chica
, Chenna Ramu, Claus Nerlov, Toby J. Gibson
:
KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. 1-5
- Nawar Malhis
, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones
:
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection. 6-13 - Anna M. Ritz
, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael:
Discovery of phosphorylation motif mixtures in phosphoproteomics data. 14-21 - Anton V. Persikov, Robert Osada, Mona Singh
:
Predicting DNA recognition by Cys2His2 zinc finger proteins. 22-29 - Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, Xiao Sun:
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. 30-35
- Chikara Furusawa
, Naoaki Ono
, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo:
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. 36-41 - A. Marie Fitch, M. Beatrix Jones:
Shortest path analysis using partial correlations for classifying gene functions from gene expression data. 42-47 - Adam L. Asare
, Zhong Gao, Vincent J. Carey, Richard Wang, Vicki Seyfert-Margolis:
Power enhancement via multivariate outlier testing with gene expression arrays. 48-53
- James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Seven Goodison, Michael McClelland
, Dan Mercola
:
The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis. 54-60 - Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T. C. Wong:
Conditional random pattern algorithm for LOH inference and segmentation. 61-67 - Sharlee Climer
, Gerold Jäger, Alan R. Templeton
, Weixiong Zhang
:
How frugal is mother nature with haplotypes? 68-74
- Adi L. Tarca, Sorin Draghici
, Purvesh Khatri
, Sonia S. Hassan, Pooja Mittal, Jung-Sun Kim, Chong Jai Kim, Juan Pedro Kusanovic
, Roberto Romero:
A novel signaling pathway impact analysis. 75-82 - Hao Zhang, Claus Lundegaard, Morten Nielsen
:
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. 83-89 - Ross P. Carlson:
Decomposition of complex microbial behaviors into resource-based stress responses. 90-97 - Xuebing Wu
, Qifang Liu, Rui Jiang
:
Align human interactome with phenome to identify causative genes and networks underlying disease families. 98-104 - Jingkai Yu, Russell L. Finley Jr.
:
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. 105-111
- Rachel Cavill, Hector C. Keun, Elaine Holmes
, John C. Lindon
, Jeremy K. Nicholson
, Timothy M. D. Ebbels
:
Genetic algorithms for simultaneous variable and sample selection in metabonomics. 112-118
- Tim J. Carver, Nick R. Thomson
, Alan J. Bleasby, Matthew Berriman
, Julian Parkhill
:
DNAPlotter: circular and linear interactive genome visualization. 119-120
- Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble:
RANKPROP: a web server for protein remote homology detection. 121-122 - Gang-Qing Hu
, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She:
Prediction of translation initiation site for microbial genomes with TriTISA. 123-125
- Iain Milne
, Dominik Lindner
, Micha Bayer
, Dirk Husmeier
, Gráinne McGuire, David F. Marshall
, Frank Wright:
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. 126-127
- G. Golfier, Sophie Lemoine, A. van Miltenberg, A. Bendjoudi, J. Rossier, Stéphane Le Crom
, Marie-Claude Potier
:
Selection of oligonucleotides for whole-genome microarrays with semi-automatic update. 128-129 - Charles Addo-Quaye
, Webb Miller, Michael J. Axtell:
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. 130-131
- Manuel A. R. Ferreira
, Shaun Purcell:
A multivariate test of association. 132-133 - Christine Herold, Tim Becker:
Genetic association analysis with FAMHAP: a major program update. 134-136
- Jing Gao, Alexander S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H. V. Jagadish, David J. States:
Integrating and annotating the interactome using the MiMI plugin for cytoscape. 137-138 - Rutger W. W. Brouwer
, Sacha A. F. T. van Hijum, Oscar P. Kuipers
:
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. 139-140
- Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, Hans-Werner Mewes
, Andreas Ruepp:
CRONOS: the cross-reference navigation server. 141-143
- Clare Sansom:
ISMB 2008 conference report. 144-146
- Anne Kupczok
, Arndt von Haeseler:
Comment on 'A congruence index for testing topological similarity between trees'. 147-149 - Damien M. de Vienne, Tatiana Giraud, Olivier C. Martin
:
In response to comment on 'A congruence index for testing topological similarity between trees'. 150-151
- Luis F. de Figueiredo
, Stefan Schuster, Christoph Kaleta, David A. Fell
:
Can sugars be produced from fatty acids? A test case for pathway analysis tools. 152-158
Volume 25, Number 2, January 2009
- Alex Bateman
, Robert D. Finn
, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding
:
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. 159-162
- Richard S. P. Horler
, Andrew Butcher, Nikitas Papangelopoulos, Peter D. Ashton
, Gavin H. Thomas
:
EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. 163-166
- Xiaohui Xie, Paul Rigor, Pierre Baldi:
MotifMap: a human genome-wide map of candidate regulatory motif sites. 167-174
- William H. Majoros, Uwe Ohler:
Complexity reduction in context-dependent DNA substitution models. 175-182 - Shijie Zhang, Wei Su, Jiong Yang:
ARCS-Motif: discovering correlated motifs from unaligned biological sequences. 183-189
- Yufeng Wu:
A practical method for exact computation of subtree prune and regraft distance. 190-196 - Alex Webb
, John M. Hancock
, Christopher C. Holmes
:
Phylogenetic inference under recombination using Bayesian stochastic topology selection. 197-203
- Ganesan Pugalenthi
, E. Ke Tang, Ponnuthurai N. Suganthan
, Saikat Chakrabarti:
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. 204-210
- Maureen A. Sartor, George D. Leikauf
, Mario Medvedovic:
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. 211-217 - Sebastian Böcker
, Matthias C. Letzel, Zsuzsanna Lipták
, Anton Pervukhin:
SIRIUS: decomposing isotope patterns for metabolite identification. 218-224
- Filip Van Nieuwerburgh
, Els Goetghebeur, Mado Vandewoestyne, Dieter Deforce
:
Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE. 225-229 - Saliha Yilmaz, Philippe Jonveaux, Cedric Bicep, Laurent Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes
:
Gene-disease relationship discovery based on model-driven data integration and database view definition. 230-236 - Lina Chen
, Liangcai Zhang, Yan Zhao, Liangde Xu, Yukui Shang, Qian Wang, Wan Li
, Hong Wang, Xia Li:
Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. 237-242
- Kevin Y. Yip
, Mark Gerstein:
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. 243-250 - Donald A. Barkauskas, Hyun Joo An
, Scott R. Kronewitter, Maria Lorna de Leoz
, Helen K. Chew, Ralph W. de Vere White, Gary S. Leiserowitz, Suzanne Miyamoto, Carlito B. Lebrilla, David M. Rocke
:
Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. 251-257
- Gavin Brelstaff, Manuele Bicego, Nicola Culeddu, Matilde Chessa:
Bag of Peaks: interpretation of NMR spectrometry. 258-264 - Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
Sparse combinatorial inference with an application in cancer biology. 265-271
- Nobutaka Kitamura, Kouhei Akazawa, Akinori Miyashita, Ryozo Kuwano, Shin-ichi Toyabe, Junichiro Nakamura, Norihito Nakamura, Tatsuhiko Sato, M. Aminul Hoque:
Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs. 272-273
- Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie:
Human genomes as email attachments. 274-275
- Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang
, Chenggang Zhang
:
MFEprimer: multiple factor evaluation of the specificity of PCR primers. 276-278 - Tim F. Rayner
, Faisal Ibne Rezwan
, Margus Lukk
, Xiangqun Zheng Bradley
, Anna Farne, Ele Holloway, James Malone, Eleanor Williams
, Helen E. Parkinson
:
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. 279-280
- Oliver S. P. Davis
, Robert Plomin
, Leonard C. Schalkwyk
:
The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays. 281-283 - Wei Chen, Liming Liang, Gonçalo R. Abecasis
:
GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes. 284-285
- Bartek Wilczynski
, Norbert Dojer:
BNFinder: exact and efficient method for learning Bayesian networks. 286-287
- Seth Carbon, Amelia Ireland, Christopher J. Mungall
, Shengqiang Shu
, Brad Marshall, Suzanna Lewis
:
AmiGO: online access to ontology and annotation data. 288-289
Volume 25, Number 3, February 2009
- Bogumil Kaczkowski
, Elfar Torarinsson, Kristin Reiche
, Jakob Hull Havgaard, Peter F. Stadler
, Jan Gorodkin
:
Structural profiles of human miRNA families from pairwise clustering. 291-294
- Benedict Paten, Javier Herrero
, Kathryn Beal, Ewan Birney
:
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. 295-301 - Denise Y. F. Mak, Gary Benson:
All hits all the time: parameter-free calculation of spaced seed sensitivity. 302-308
- Jumamurat R. Bayjanov, Michiel Wels, Marjo Starrenburg, Johan E. T. van Hylckama Vlieg, Roland J. Siezen, Douwe Molenaar
:
PanCGH: a genotype-calling algorithm for pangenome CGH data. 309-314
- Stan Pounds
, Cheng Cheng, Charles Mullighan
, Susana C. Raimondi, Sheila Shurtleff, James R. Downing:
Reference alignment of SNP microarray signals for copy number analysis of tumors. 315-321 - Krzysztof Wabnik
, Torgeir R. Hvidsten
, Anna M. Kedzierska, Jelle Van Leene
, Geert De Jaeger
, Gerrit T. S. Beemster
, Henryk Jan Komorowski
, Martin T. R. Kuiper
:
Gene expression trends and protein features effectively complement each other in gene function prediction. 322-330 - KunHong Liu, Chun-Gui Xu:
A genetic programming-based approach to the classification of multiclass microarray datasets. 331-337
- Junghyun Namkung, Kyunga Kim, Sung-Gon Yi, Wonil Chung, Min-Seok Kwon, Taesung Park:
New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis. 338-345
- Ekaterina M. Myasnikova, Svetlana Surkova
, Lena Panok, Maria Samsonova, John Reinitz:
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. 346-352 - Mahesh Yaragatti, Ted Sandler, Lyle H. Ungar:
A predictive model for identifying mini-regulatory modules in the mouse genome. 353-357 - Hu Li, Choong Yong Ung, Xiao Hua Ma, Bao Wen Li
, Boon Chuan Low
, Zhi Wei Cao, Yu Zong Chen
:
Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1. 358-364 - David Goldberg
, Marshall W. Bern, Simon J. North, Stuart M. Haslam, Anne Dell
:
Glycan family analysis for deducing N-glycan topology from single MS. 365-371 - Hailiang Huang
, Joel S. Bader
:
Precision and recall estimates for two-hybrid screens. 372-378
- Anthony Y. C. Kuk, Han Zhang
, Yaning Yang:
Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium. 379-386 - Je-Gun Joung, Zhangjun Fei:
Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. 387-393 - Yusuke Miyao, Kenji Sagae, Rune Sætre, Takuya Matsuzaki, Jun'ichi Tsujii:
Evaluating contributions of natural language parsers to protein-protein interaction extraction. 394-400 - Age K. Smilde
, Henk A. L. Kiers, S. Bijlsma, C. M. Rubingh, M. J. van Erk:
Matrix correlations for high-dimensional data: the modified RV-coefficient. 401-405
- Davide Bolchini
, Anthony Finkelstein, Vito Perrone, Sylvia Nagl:
Better bioinformatics through usability analysis. 406-412
- Christopher Reynolds
, David Damerell, Susan Jones:
ProtorP: a protein-protein interaction analysis server. 413-414
- Audrey Kauffmann, Robert Gentleman, Wolfgang Huber
:
arrayQualityMetrics - a bioconductor package for quality assessment of microarray data. 415-416
- Julien Chiquet
, Alexander Smith
, Gilles Grasseau, Catherine Matias, Christophe Ambroise:
SIMoNe: Statistical Inference for MOdular NEtworks. 417-418 - Martino Barenco, E. Papouli, Sonia H. Shah
, Daniel Brewer
, Crispin J. Miller
, Michael Hubank
:
rHVDM: an R package to predict the activity and targets of a transcription factor. 419-420
Volume 25, Number 4, February 2009
- Robert P. Guralnick, Andrew W. Hill:
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes. 421-428
- Alex Bateman
, John Quackenbush
:
Editorial. 429
- Fuxiao Xin, Meng Li, Curtis Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, Kenneth P. Nephew:
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. 430-434
- Helge G. Roider, Thomas Manke
, Sean O'Keeffe, Martin Vingron, Stefan A. Haas
:
PASTAA: identifying transcription factors associated with sets of co-regulated genes. 435-442
- Norman E. Davey
, Denis C. Shields, Richard J. Edwards
:
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. 443-450 - Tala Bakheet, Andrew J. Doig
:
Properties and identification of human protein drug targets. 451-457 - René L. Warren, Brad H. Nelson
, Robert A. Holt
:
Profiling model T-cell metagenomes with short reads. 458-464 - Michiaki Hamada
, Hisanori Kiryu, Kengo Sato
, Toutai Mituyama
, Kiyoshi Asai:
Prediction of RNA secondary structure using generalized centroid estimators. 465-473
- Dirk Stratmann, Carine van Heijenoort
, Eric Guittet
:
NOEnet-Use of NOE networks for NMR resonance assignment of proteins with known 3D structure. 474-481
- Daniel M. Gatti, Andrey A. Shabalin
, Tieu-Chong Lam, Fred A. Wright, Ivan Rusyn
, Andrew B. Nobel:
FastMap: Fast eQTL mapping in homozygous populations. 482-489 - Anagha Joshi, Riet De Smet, Kathleen Marchal
, Yves Van de Peer
, Tom Michoel
:
Module networks revisited: computational assessment and prioritization of model predictions. 490-496
- Mingyao Li, Kai Wang
, Struan F. A. Grant
, Hakon Hakonarson, Chun Li
:
ATOM: a powerful gene-based association test by combining optimally weighted markers. 497-503 - Can Yang, Zengyou He
, Xiang Wan, Qiang Yang, Hong Xue
, Weichuan Yu
:
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. 504-511
- Simon Rogers
, Richard A. Scheltema
, Mark A. Girolami
, Rainer Breitling
:
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. 512-518 - Oliver Kotte, Matthias Heinemann
:
A divide-and-conquer approach to analyze underdetermined biochemical models. 519-525
- Bai Zhang, Huai Li, Rebecca B. Riggins
, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman
, Robert Clarke
, Yue Joseph Wang:
Differential dependency network analysis to identify condition-specific topological changes in biological networks. 526-532
- Sascha Steinbiss
, Gordon Gremme, Christin Schärfer
, Malte Mader
, Stefan Kurtz:
AnnotationSketch: a genome annotation drawing library. 533-534 - Michael S. Barker, Katrina M. Dlugosch
, A. Chaitanya C. Reddy, Sarah N. Amyotte, Loren H. Rieseberg
:
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses. 535-536
- Jeremy M. Brown
, Robert ElDabaje:
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. 537-538
- Benjamin M. Bulheller, Jonathan D. Hirst
:
DichroCalc - circular and linear dichroism online. 539-540
- Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn
, Fred A. Wright, William T. Barry:
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. 541-542 - Ryosuke R. Ishiwata
, Masaki S. Morioka, Soichi Ogishima, Hiroshi Tanaka:
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. 543-544 - Qihao Qi, Yingdong Zhao, Ming-Chung Li, Richard M. Simon:
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. 545-547 - Edward Ryder
, H. Spriggs, E. Drummond, Daniel St Johnston
, Steven Russell
:
The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster. 548-549 - Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers
, Sacha A. F. T. van Hijum:
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. 550-551
- Gilles Guillot
, Matthieu Foll
:
Correcting for ascertainment bias in the inference of population structure. 552-554
- Uma Mudunuri, Anney Che, Ming Yi
, Robert M. Stephens:
bioDBnet: the biological database network. 555-556 - Jeff Heard, William Kaufmann, Xiaojun Guan:
A novel method for large tree visualization. 557-558
Volume 25, Number 5, March 2009
- Shahar Alon, Eli Eisenberg
, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine
, Reiko Toyama, Steven L. Coon, David C. Klein
, Yoav Gothilf
:
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland. 559-562
- Shamim Ahmed, Ayumu Saito, Miho Suzuki, Naoto Nemoto, Koichi Nishigaki:
Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity. 563-570 - Xu Ling, Xin He, Dong Xin:
Detecting gene clusters under evolutionary constraint in a large number of genomes. 571-577 - Leila Taher
, Ivan Ovcharenko:
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. 578-584
- Xue-wen Chen, Jong Cheol Jeong:
Sequence-based prediction of protein interaction sites with an integrative method. 585-591
- Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta
, Joseph G. Ibrahim, Todd J. Vision
:
A hierarchical model for incomplete alignments in phylogenetic inference. 592-598