Volume 9, issue 1, December 2008
559 articles in this issue
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TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Authors
- Mallika Veeramalai
- Yuzhen Ye
- Adam Godzik
- Content type: Research article
- Open Access
- Published: 31 August 2008
- Article: 358
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Impact of residue accessible surface area on the prediction of protein secondary structures
Authors (first, second and last of 4)
- Amir Momen-Roknabadi
- Mehdi Sadeghi
- Sayed-Amir Marashi
- Content type: Research article
- Open Access
- Published: 31 August 2008
- Article: 357
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FERN – a Java framework for stochastic simulation and evaluation of reaction networks
Authors
- Florian Erhard
- Caroline C Friedel
- Ralf Zimmer
- Content type: Software
- Open Access
- Published: 29 August 2008
- Article: 356
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NITPICK: peak identification for mass spectrometry data
Authors (first, second and last of 5)
- Bernhard Y Renard
- Marc Kirchner
- Fred A Hamprecht
- Content type: Methodology article
- Open Access
- Published: 28 August 2008
- Article: 355
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Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration
Authors
- Yulan Liang
- Arpad Kelemen
- Content type: Methodology article
- Open Access
- Published: 28 August 2008
- Article: 354
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Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
Authors (first, second and last of 7)
- Alinda Nagy
- Hédi Hegyi
- László Patthy
- Content type: Research article
- Open Access
- Published: 27 August 2008
- Article: 353
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Alignment of protein structures in the presence of domain motions
Authors
- Roberto Mosca
- Barbara Brannetti
- Thomas R Schneider
- Content type: Methodology article
- Open Access
- Published: 27 August 2008
- Article: 352
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SynBlast: Assisting the analysis of conserved synteny information
Authors
- Jörg Lehmann
- Peter F Stadler
- Sonja J Prohaska
- Content type: Methodology article
- Open Access
- Published: 24 August 2008
- Article: 351
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Integration of relational and hierarchical network information for protein function prediction
Authors (first, second and last of 5)
- Xiaoyu Jiang
- Naoki Nariai
- Eric D Kolaczyk
- Content type: Methodology article
- Open Access
- Published: 22 August 2008
- Article: 350
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Protein structure search and local structure characterization
Authors
- Shih-Yen Ku
- Yuh-Jyh Hu
- Content type: Methodology article
- Open Access
- Published: 22 August 2008
- Article: 349
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Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
Authors
- Stephen W Tanner
- Pankaj Agarwal
- Content type: Methodology article
- Open Access
- Published: 22 August 2008
- Article: 348
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A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time
Authors
- Hua Xu
- Lanhao Yang
- Michael A Freitas
- Content type: Research article
- Open Access
- Published: 19 August 2008
- Article: 347
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AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images
Authors
- János Roszik
- János Szöllősi
- György Vereb
- Content type: Software
- Open Access
- Published: 19 August 2008
- Article: 346
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VisualRepbase: an interface for the study of occurrences of transposable element families
Authors
- Sébastien Tempel
- Matthew Jurka
- Jerzy Jurka
- Content type: Software
- Open Access
- Published: 18 August 2008
- Article: 345
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An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories
Authors (first, second and last of 4)
- Hong Sun
- Hakan Ferhatosmanoglu
- Yusu Wang
- Content type: Methodology article
- Open Access
- Published: 18 August 2008
- Article: 344
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Parameter estimation for robust HMM analysis of ChIP-chip data
Authors
- Peter Humburg
- David Bulger
- Glenn Stone
- Content type: Methodology article
- Open Access
- Published: 18 August 2008
- Article: 343
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SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
Authors (first, second and last of 4)
- Zhike Zi
- Yanan Zheng
- Edda Klipp
- Content type: Software
- Open Access
- Published: 15 August 2008
- Article: 342
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SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis
Authors (first, second and last of 4)
- Martin Kostka
- Magdalena Uzlikova
- Jaroslav Flegr
- Content type: Software
- Open Access
- Published: 15 August 2008
- Article: 341
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RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
Authors (first, second and last of 4)
- Mirela Andronescu
- Vera Bereg
- Anne Condon
- Content type: Database
- Open Access
- Published: 13 August 2008
- Article: 340
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A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics
Authors (first, second and last of 7)
- Arnab Bhattacharya
- Sasha Levy
- Stuart C Feinstein
- Content type: Research article
- Open Access
- Published: 12 August 2008
- Article: 339
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New time-scale criteria for model simplification of bio-reaction systems
Authors (first, second and last of 4)
- Junwon Choi
- Kyung-won Yang
- Sang Yup Lee
- Content type: Methodology article
- Open Access
- Published: 12 August 2008
- Article: 338
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Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
Authors (first, second and last of 9)
- Wei Dai
- Jens M Teodoridis
- Jim Paul
- Content type: Methodology article
- Open Access
- Published: 08 August 2008
- Article: 337
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Determining significance of pairwise co-occurrences of events in bursty sequences
Authors
- Niina Haiminen
- Heikki Mannila
- Evimaria Terzi
- Content type: Research article
- Open Access
- Published: 08 August 2008
- Article: 336
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Combining transcriptional datasets using the generalized singular value decomposition
Authors (first, second and last of 4)
- Andreas W Schreiber
- Neil J Shirley
- Geoffrey B Fincher
- Content type: Methodology article
- Open Access
- Published: 08 August 2008
- Article: 335
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Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data
Authors (first, second and last of 12)
- Peter Li
- Juan I Castrillo
- Douglas B Kell
- Content type: Software
- Open Access
- Published: 07 August 2008
- Article: 334
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The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
Authors (first, second and last of 5)
- Hamilton Ganesan
- Anna S Rakitianskaia
- Oleg N Reva
- Content type: Software
- Open Access
- Published: 07 August 2008
- Article: 333
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Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores
Authors
- Olivier Bastien
- Eric Maréchal
- Content type: Research article
- Open Access
- Published: 07 August 2008
- Article: 332
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HAPSIMU: a genetic simulation platform for population-based association studies
Authors (first, second and last of 4)
- Feng Zhang
- Jianfeng Liu
- Hong-Wen Deng
- Content type: Software
- Open Access
- Published: 05 August 2008
- Article: 331
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NullHap – a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles
Authors
- Robert M Nowak
- Rafał Płoski
- Content type: Software
- Open Access
- Published: 05 August 2008
- Article: 330
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Evaluation of genomic island predictors using a comparative genomics approach
Authors
- Morgan GI Langille
- William WL Hsiao
- Fiona SL Brinkman
- Content type: Research article
- Open Access
- Published: 05 August 2008
- Article: 329
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A Java-based tool for the design of classification microarrays
Authors
- Da Meng
- Shira L Broschat
- Douglas R Call
- Content type: Software
- Open Access
- Published: 04 August 2008
- Article: 328
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Gene Ontology term overlap as a measure of gene functional similarity
Authors
- Meeta Mistry
- Paul Pavlidis
- Content type: Research article
- Open Access
- Published: 04 August 2008
- Article: 327
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A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition
Authors (first, second and last of 5)
- Michele Guescini
- Davide Sisti
- Vilberto Stocchi
- Content type: Methodology article
- Open Access
- Published: 30 July 2008
- Article: 326
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A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
Authors
- Cong Zhou
- Lucas D Bowler
- Jianfeng Feng
- Content type: Research article
- Open Access
- Published: 30 July 2008
- Article: 325
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Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis
Authors
- Yuanxin Xi
- David M Rocke
- Content type: Methodology article
- Open Access
- Published: 29 July 2008
- Article: 324
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LOSITAN: A workbench to detect molecular adaptation based on a F st -outlier method
Authors (first, second and last of 5)
- Tiago Antao
- Ana Lopes
- Gordon Luikart
- Content type: Software
- Open Access
- Published: 28 July 2008
- Article: 323
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PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
Authors
- Cuong Than
- Derek Ruths
- Luay Nakhleh
- Content type: Software
- Open Access
- Published: 28 July 2008
- Article: 322
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GBParsy: A GenBank flatfile parser library with high speed
Authors
- Tae-Ho Lee
- Yeon-Ki Kim
- Baek Hie Nahm
- Content type: Software
- Open Access
- Published: 25 July 2008
- Article: 321
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Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements
Authors
- Qingwu Yang
- Sing-Hoi Sze
- Content type: Research article
- Open Access
- Published: 23 July 2008
- Article: 320
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A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification
Authors
- Alexander Statnikov
- Lily Wang
- Constantin F Aliferis
- Content type: Research article
- Open Access
- Published: 22 July 2008
- Article: 319
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Directed acyclic graph kernels for structural RNA analysis
Authors (first, second and last of 4)
- Kengo Sato
- Toutai Mituyama
- Yasubumi Sakakibara
- Content type: Methodology article
- Open Access
- Published: 22 July 2008
- Article: 318
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Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis
Authors (first, second and last of 7)
- Angela P Presson
- Eric M Sobel
- Jeanette C Papp
- Content type: Software
- Open Access
- Published: 21 July 2008
- Article: 317
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PatternLab for proteomics: a tool for differential shotgun proteomics
Authors (first, second and last of 5)
- Paulo C Carvalho
- Juliana SG Fischer
- Valmir C Barbosa
- Content type: Software
- Open Access
- Published: 21 July 2008
- Article: 316
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Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies
Authors (first, second and last of 5)
- Li Ma
- H Birali Runesha
- Yang Da
- Content type: Software
- Open Access
- Published: 21 July 2008
- Article: 315
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Assessing probe-specific dye and slide biases in two-color microarray data
Authors (first, second and last of 12)
- Ruixiao Lu
- Geun-Cheol Lee
- David M Rocke
- Content type: Research article
- Open Access
- Published: 19 July 2008
- Article: 314
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SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
Authors (first, second and last of 7)
- Michael C Ryan
- Barry R Zeeberg
- John N Weinstein
- Content type: Database
- Open Access
- Published: 18 July 2008
- Article: 313
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MSDmotif: exploring protein sites and motifs
Authors
- Adel Golovin
- Kim Henrick
- Content type: Software
- Open Access
- Published: 17 July 2008
- Article: 312
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Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Authors
- Don L Armstrong
- Chaim O Jacob
- Raphael Zidovetzki
- Content type: Software
- Open Access
- Published: 17 July 2008
- Article: 311
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Computational identification of ubiquitylation sites from protein sequences
Authors
- Chun-Wei Tung
- Shinn-Ying Ho
- Content type: Research article
- Open Access
- Published: 15 July 2008
- Article: 310