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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
 
A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data
Bjoern H Menze, Michael Kelm, Ralf Masuch, Uwe Himmelreich, Peter Bachert, Wolfgang Petrich, Fred A Hamprecht
BMC Bioinformatics 2009, 10:213 (10July2009)
[Abstract] [Provisional PDF]
Methodology article
Error statistics of hidden Markov model and hidden Boltzmann model results
Lee A Newberg
BMC Bioinformatics 2009, 10:212 (9July2009)
[Abstract] [Provisional PDF]
Software
puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis
Richard D Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D Lawrence, Magnus Rattray
BMC Bioinformatics 2009, 10:211 (9July2009)
[Abstract] [Provisional PDF]
Research article
Iterative refinement of structure-based sequence alignments by Seed Extension
Changhoon Kim, Chin-Hsien Tai, Byungkook Lee
BMC Bioinformatics 2009, 10:210 (9July2009)
[Abstract] [Provisional PDF]
Methodology article
A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
Antonio Carvajal-Rodriguez, Jacobo de Una-Alvarez, Emilio Rolan-Alvarez
BMC Bioinformatics 2009, 10:209 (8July2009)
[Abstract] [Provisional PDF]
Research article
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif
Amar Drawid, Nupur Gupta, Vijayalakshmi H Nagaraj, Celine Gelinas, Anirvan M Sengupta
BMC Bioinformatics 2009, 10:208 (7July2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Ensemble approach to predict specificity determinants: benchmarking and validation
Saikat Chakrabarti, Anna R Panchenko
BMC Bioinformatics 2009, 10:207 (2July2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Representative transcript sets for evaluating a translational initiation sites predictor
Jia Zeng, Reda Alhajj, Douglas J Demetrick
BMC Bioinformatics 2009, 10:206 (2July2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Clique-based data mining for related genes in a biomedical database
Tsutomu Matsunaga, Chikara Yonemori, Etsuji Tomita, Masaaki Muramatsu
BMC Bioinformatics 2009, 10:205 (1July2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Comparison of sequence-dependent tiling array normalization approaches
Ho-Ryun Chung, Martin Vingron
BMC Bioinformatics 2009, 10:204 (30June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Integrated analysis of DNA copy number and gene expression microarray data using gene sets
Renee X Menezes, Marten Boetzer, Melle Sieswerda, Gert-Jan B VAN Ommen, Judith M Boer
BMC Bioinformatics 2009, 10:203 (29June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
Alex N Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, Alan M Moses
BMC Bioinformatics 2009, 10:202 (29June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
A-MADMAN: annotation-based microarray data meta-analysis tool
Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
BMC Bioinformatics 2009, 10:201 (29June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis
Ming Yi, Uma Mudunuri, Anney Che, Robert M Stephens
BMC Bioinformatics 2009, 10:200 (29June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
DOTcvpSB, a software toolbox for dynamic optimization in systems biology
Tomas Hirmajer, Eva Balsa-Canto, Julio R. Banga
BMC Bioinformatics 2009, 10:199 (29June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
A Bayesian approach to efficient differential allocation for resampling-based significance testing
Shane T Jensen, Sameer Soi, Li-San Wang
BMC Bioinformatics 2009, 10:198 (28June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
ResBoost: characterizing and predicting catalytic residues in enzymes
Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjolander
BMC Bioinformatics 2009, 10:197 (27June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
BMC Bioinformatics 2009, 10:196 (27June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Ab initio and homology based prediction of protein domains by recursive neural networks
Ian Walsh, Alberto JM Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri
BMC Bioinformatics 2009, 10:195 (26June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis
Otavio JB Brustolini, Luciano G Fietto, Cosme D Cruz, Flavia ML Passos
BMC Bioinformatics 2009, 10:194 (25June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
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