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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Tim Sands PhD
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 BMC Bioinformatics, Volume 10
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Research article
 
Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
Yohan Kim, John Sidney, Clemencia Pinilla, Alessandro Sette, Bjoern Peters
BMC Bioinformatics 2009, 10:394 (30November2009)
[Abstract] [Provisional PDF]
Research article
Phylogeny-guided interaction mapping in seven eukaryotes
Janusz Dutkowski, Jerzy Tiuryn
BMC Bioinformatics 2009, 10:393 (30November2009)
[Abstract] [Provisional PDF]
Software
siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
Yuki Naito, Jun Yoshimura, Shinichi Morishita, Kumiko Ui-Tei
BMC Bioinformatics 2009, 10:392 (30November2009)
[Abstract] [Provisional PDF]
Software
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Chunguang Liang, Alexander Schmid, Maria JOSE Lopez-Sanchez, Andres Moya, Roy Gross, Jorg Bernhardt, Thomas Dandekar
BMC Bioinformatics 2009, 10:391 (29November2009)
[Abstract] [Provisional PDF]
Software
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis
Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G McNally, Zlatko Trajanoski
BMC Bioinformatics 2009, 10:390 (26November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
Herman MJ Sontrop, Perry D Moerland, Rene van den Ham, Marcel JT Reinders, Wim FJ Verhaegh
BMC Bioinformatics 2009, 10:389 (26November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices
Isabelle da Piedade, Man-Hung Eric Tang, Olivier Elemento
BMC Bioinformatics 2009, 10:388 (26November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Modeling lymphocytes homing and encounters in lymph nodes
Valentina Baldazzi, Paola Paci, Massimo Bernaschi, Filippo Castiglione
BMC Bioinformatics 2009, 10:387 (25November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses.
Gonzalo Guillen-Gosalbez, Albert Sorribas
BMC Bioinformatics 2009, 10:386 (24November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Automated vocabulary discovery for geo-parsing online epidemic intelligence
Mikaela Keller, Clark C Freifeld, John S Brownstein
BMC Bioinformatics 2009, 10:385 (24November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Regularized estimation of large-scale gene association networks using graphical Gaussian models
Nicole Kramer, Juliane Schafer, Anne-Laure Boulesteix
BMC Bioinformatics 2009, 10:384 (24November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Valentin Ruano-Rubio, Olivier Poch, Julie D Thompson
BMC Bioinformatics 2009, 10:383 (24November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Iterative Pruning PCA Improves Resolution of Highly Structured Populations
Apichart Intarapanich, Philip J Shaw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Kridsadakorn Chaichoompu, Jittima Piriyapongsa, Sissades Tongsima
BMC Bioinformatics 2009, 10:382 (23November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Prediction of protein binding sites in protein structures using hidden Markov support vector machine
Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qiwen Dong, Xuan Wang
BMC Bioinformatics 2009, 10:381 (20November2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH
Joke Allemeersch, Steven Van Vooren, Femke Hannes, Bart De Moor, Joris Robert Vermeesch, Yves Moreau
BMC Bioinformatics 2009, 10:380 (19November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
SitesIdentify: a protein functional site prediction tool
Tracey Bray, Pedro Chan, Salim Bougouffa, Richard Greaves, Andrew J Doig, Jim Warwicker
BMC Bioinformatics 2009, 10:379 (18November2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Nonlinear preprocessing method for detecting peaks from gas chromatograms
Byonghyo Shim, Hyeyoung Min, Sungroh Yoon
BMC Bioinformatics 2009, 10:378 (18November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
The ontology of biological sequences
Robert Hoehndorf, Janet Kelso, Heinrich Herre
BMC Bioinformatics 2009, 10:377 (18November2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Algorithms for effective querying of compound graph-based pathway databases
Ugur Dogrusoz, Ahmet Cetintas, Emek Demir, Ozgun Babur
BMC Bioinformatics 2009, 10:376 (16November2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A generic algorithm for layout of biological networks
Falk Schreiber, Tim Dwyer, Kim Marriott, Michael Wybrow
BMC Bioinformatics 2009, 10:375 (12November2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
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