Volume 10, issue 1, December 2009
455 articles in this issue
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Identifying differentially methylated genes using mixed effect and generalized least square models
Authors (first, second and last of 4)
- Shuying Sun
- Pearlly S Yan
- Shili Lin
- Content type: Research article
- Open Access
- Published: 09 December 2009
- Article: 404
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Investigating heterogeneous protein annotations toward cross-corpora utilization
Authors (first, second and last of 5)
- Yue Wang
- Jin-Dong Kim
- Jun'ichi Tsujii
- Content type: Research article
- Open Access
- Published: 09 December 2009
- Article: 403
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A close examination of double filtering with fold change and t test in microarray analysis
Authors
- Song Zhang
- Jing Cao
- Content type: Research article
- Open Access
- Published: 08 December 2009
- Article: 402
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Erratum to: Granger causality vs. dynamic Bayesian network inference: a comparative study
Authors
- Cunlu Zou
- Katherine J Denby
- Jianfeng Feng
- Content type: Erratum
- Open Access
- Published: 07 December 2009
- Article: 401
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Uncovering transcriptional interactions via an adaptive fuzzy logic approach
Authors (first, second and last of 4)
- Cheng-Long Chuang
- Kenneth Hung
- Grace S Shieh
- Content type: Research article
- Open Access
- Published: 06 December 2009
- Article: 400
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Considering scores between unrelated proteins in the search database improves profile comparison
Authors
- Ruslan I Sadreyev
- Yong Wang
- Nick V Grishin
- Content type: Research article
- Open Access
- Published: 04 December 2009
- Article: 399
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Sorting by reversals and block-interchanges with various weight assignments
Authors
- Ying Chih Lin
- Chun-Yuan Lin
- Chunhung Richard Lin
- Content type: Research article
- Open Access
- Published: 04 December 2009
- Article: 398
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Bioclipse 2: A scriptable integration platform for the life sciences
Authors (first, second and last of 11)
- Ola Spjuth
- Jonathan Alvarsson
- Jarl ES Wikberg
- Content type: Software
- Open Access
- Published: 03 December 2009
- Article: 397
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Optimizing substitution matrix choice and gap parameters for sequence alignment
Authors
- Robert C Edgar
- Content type: Research article
- Open Access
- Published: 02 December 2009
- Article: 396
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Inferring protein function by domain context similarities in protein-protein interaction networks
Authors (first, second and last of 4)
- Song Zhang
- Hu Chen
- Zhirong Sun
- Content type: Research article
- Open Access
- Published: 02 December 2009
- Article: 395
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Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
Authors (first, second and last of 5)
- Yohan Kim
- John Sidney
- Bjoern Peters
- Content type: Research article
- Open Access
- Published: 30 November 2009
- Article: 394
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Phylogeny-guided interaction mapping in seven eukaryotes
Authors
- Janusz Dutkowski
- Jerzy Tiuryn
- Content type: Research article
- Open Access
- Published: 30 November 2009
- Article: 393
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siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
Authors (first, second and last of 4)
- Yuki Naito
- Jun Yoshimura
- Kumiko Ui-Tei
- Content type: Software
- Open Access
- Published: 30 November 2009
- Article: 392
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JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Authors (first, second and last of 7)
- Chunguang Liang
- Alexander Schmid
- Thomas Dandekar
- Content type: Software
- Open Access
- Published: 29 November 2009
- Article: 391
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iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis
Authors (first, second and last of 8)
- Gernot Stocker
- Maria Fischer
- Zlatko Trajanoski
- Content type: Software
- Open Access
- Published: 26 November 2009
- Article: 390
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A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
Authors (first, second and last of 5)
- Herman MJ Sontrop
- Perry D Moerland
- Wim FJ Verhaegh
- Content type: Research article
- Open Access
- Published: 26 November 2009
- Article: 389
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DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices
Authors
- Isabelle da Piedade
- Man-Hung Eric Tang
- Olivier Elemento
- Content type: Methodology article
- Open Access
- Published: 26 November 2009
- Article: 388
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Modeling lymphocyte homing and encounters in lymph nodes
Authors (first, second and last of 4)
- Valentina Baldazzi
- Paola Paci
- Filippo Castiglione
- Content type: Methodology article
- Open Access
- Published: 25 November 2009
- Article: 387
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Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses
Authors
- Gonzalo Guillén-Gosálbez
- Albert Sorribas
- Content type: Research article
- Open Access
- Published: 24 November 2009
- Article: 386
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Automated vocabulary discovery for geo-parsing online epidemic intelligence
Authors
- Mikaela Keller
- Clark C Freifeld
- John S Brownstein
- Content type: Research article
- Open Access
- Published: 24 November 2009
- Article: 385
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Regularized estimation of large-scale gene association networks using graphical Gaussian models
Authors
- Nicole Krämer
- Juliane Schäfer
- Anne-Laure Boulesteix
- Content type: Research article
- Open Access
- Published: 24 November 2009
- Article: 384
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Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Authors
- ValentÃn Ruano-Rubio
- Olivier Poch
- Julie D Thompson
- Content type: Research article
- Open Access
- Published: 24 November 2009
- Article: 383
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Iterative pruning PCA improves resolution of highly structured populations
Authors (first, second and last of 8)
- Apichart Intarapanich
- Philip J Shaw
- Sissades Tongsima
- Content type: Methodology article
- Open Access
- Published: 23 November 2009
- Article: 382
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Prediction of protein binding sites in protein structures using hidden Markov support vector machine
Authors (first, second and last of 6)
- Bin Liu
- Xiaolong Wang
- Xuan Wang
- Content type: Research article
- Open Access
- Published: 20 November 2009
- Article: 381
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An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH
Authors (first, second and last of 6)
- Joke Allemeersch
- Steven Van Vooren
- Yves Moreau
- Content type: Methodology article
- Open Access
- Published: 19 November 2009
- Article: 380
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SitesIdentify: a protein functional site prediction tool
Authors (first, second and last of 6)
- Tracey Bray
- Pedro Chan
- Jim Warwicker
- Content type: Software
- Open Access
- Published: 18 November 2009
- Article: 379
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Nonlinear preprocessing method for detecting peaks from gas chromatograms
Authors
- Byonghyo Shim
- Hyeyoung Min
- Sungroh Yoon
- Content type: Methodology article
- Open Access
- Published: 18 November 2009
- Article: 378
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The ontology of biological sequences
Authors
- Robert Hoehndorf
- Janet Kelso
- Heinrich Herre
- Content type: Methodology article
- Open Access
- Published: 18 November 2009
- Article: 377
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Algorithms for effective querying of compound graph-based pathway databases
Authors (first, second and last of 4)
- Ugur Dogrusoz
- Ahmet Cetintas
- Ozgun Babur
- Content type: Methodology article
- Open Access
- Published: 16 November 2009
- Article: 376
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A generic algorithm for layout of biological networks
Authors (first, second and last of 4)
- Falk Schreiber
- Tim Dwyer
- Michael Wybrow
- Content type: Research article
- Open Access
- Published: 12 November 2009
- Article: 375
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Linguistic feature analysis for protein interaction extraction
Authors (first, second and last of 4)
- Timur Fayruzov
- Martine De Cock
- Veronique Hoste
- Content type: Research article
- Open Access
- Published: 12 November 2009
- Article: 374
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A theoretical approach to spot active regions in antimicrobial proteins
Authors
- Marc Torrent
- Victòria M Nogués
- Ester Boix
- Content type: Methodology article
- Open Access
- Published: 11 November 2009
- Article: 373
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Illumina WG-6 BeadChip strips should be normalized separately
Authors (first, second and last of 5)
- Wei Shi
- Ashish Banerjee
- Gordon K Smyth
- Content type: Methodology article
- Open Access
- Published: 11 November 2009
- Article: 372
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An empirical Bayesian approach for model-based inference of cellular signaling networks
Authors
- David J Klinke II
- Content type: Methodology article
- Open Access
- Published: 09 November 2009
- Article: 371
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Elucidation of functional consequences of signalling pathway interactions
Authors
- Adaoha EC Ihekwaba
- Phuong T Nguyen
- Corrado Priami
- Content type: Research article
- Open Access
- Published: 06 November 2009
- Article: 370
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RNA folding on the 3D triangular lattice
Authors
- Joel Gillespie
- Martin Mayne
- Minghui Jiang
- Content type: Research article
- Open Access
- Published: 05 November 2009
- Article: 369
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A biosegmentation benchmark for evaluation of bioimage analysis methods
Authors (first, second and last of 5)
- Elisa Drelie Gelasca
- Boguslaw Obara
- BS Manjunath
- Content type: Database
- Open Access
- Published: 01 November 2009
- Article: 368
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GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs
Authors (first, second and last of 6)
- Robert Lawrence
- Aaron G Day-Williams
- Eleftheria Zeggini
- Content type: Database
- Open Access
- Published: 31 October 2009
- Article: 367
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(PS)2-v2: template-based protein structure prediction server
Authors
- Chih-Chieh Chen
- Jenn-Kang Hwang
- Jinn-Moon Yang
- Content type: Methodology article
- Open Access
- Published: 31 October 2009
- Article: 366
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Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
Authors (first, second and last of 4)
- Stefano Lise
- Cedric Archambeau
- David T Jones
- Content type: Research article
- Open Access
- Published: 30 October 2009
- Article: 365
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multiplierz: an extensible API based desktop environment for proteomics data analysis
Authors (first, second and last of 8)
- Jignesh R Parikh
- Manor Askenazi
- Jarrod A Marto
- Content type: Software
- Open Access
- Published: 29 October 2009
- Article: 364
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A novel R-package graphic user interface for the analysis of metabonomic profiles
Authors (first, second and last of 7)
- Jose L Izquierdo-GarcÃa
- Ignacio RodrÃguez
- Jesús Ruiz-Cabello
- Content type: Software
- Open Access
- Published: 29 October 2009
- Article: 363
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BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
Authors
- Daniel N Frank
- Content type: Software
- Open Access
- Published: 29 October 2009
- Article: 362
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Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy
Authors
- Zheng Rong Yang
- Content type: Research article
- Open Access
- Published: 29 October 2009
- Article: 361
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Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA
Authors (first, second and last of 6)
- Naoki Hasegawa
- Wataru Sugiura
- Hiroshi Tanaka
- Content type: Methodology article
- Open Access
- Published: 29 October 2009
- Article: 360
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Analysis and comparison of very large metagenomes with fast clustering and functional annotation
Authors
- Weizhong Li
- Content type: Methodology article
- Open Access
- Published: 28 October 2009
- Article: 359
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ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
Authors
- Enrico Glaab
- Jonathan M Garibaldi
- Natalio Krasnogor
- Content type: Software
- Open Access
- Published: 28 October 2009
- Article: 358
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AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
Authors (first, second and last of 9)
- Surendra Kumar
- Åsmund Skjæveland
- Kamran Shalchian-Tabrizi
- Content type: Software
- Open Access
- Published: 28 October 2009
- Article: 357
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phyloXML: XML for evolutionary biology and comparative genomics
Authors
- Mira V Han
- Christian M Zmasek
- Content type: Software
- Open Access
- Published: 27 October 2009
- Article: 356