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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Maria Kowalczuk
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 BMC Bioinformatics, Volume 9
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Software
 
GenomeMatcher: A graphical user interface for DNA sequence comparison
Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda
BMC Bioinformatics 2008, 9:376 (16September2008)
[Abstract] [Provisional PDF]
Research article
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Groepl
BMC Bioinformatics 2008, 9:375 (15September2008)
[Abstract] [Provisional PDF]
Methodology article
Large-scale identification of polymorphic microsatellites
using an in silico approach
Jifeng Tang, Samantha J Baldwin, Jeanne ME Jacobs, C GERARD van der Linden, Roeland E Voorrips, Jack AM Leunissen, Herman van Eck, Ben Vosman
BMC Bioinformatics 2008, 9:374 (15September2008)
[Abstract] [Provisional PDF]
Research article
Increasing the efficiency of bacterial transcription simulations: when to exclude the genome without loss of accuracy
Marco A. J. Iafolla, Guang Qiang Dong, David R McMillen
BMC Bioinformatics 2008, 9:373 (12September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, Bik K Tye
BMC Bioinformatics 2008, 9:372 (12September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Kismeth: Analyzer of plant methylation states through bisulfite sequencing
Eyal Gruntman, Yijun Qi, Richard KEITH Slotkin, Ted Roeder, Robert A Martienssen, Ravi Sachidanandam
BMC Bioinformatics 2008, 9:371 (11September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Mixture models for analysis of melting temperature data.
Christoffer Nellaker, Fredrik Uhrzander, Joanna Tyrcha, Hakan Karlsson
BMC Bioinformatics 2008, 9:370 (11September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Automatic detection of exonic splicing enhancers (ESEs) using SVMs
Britta Mersch, Alexander Gepperth, Sandor Suhai, Agnes Hotz-Wagenblatt
BMC Bioinformatics 2008, 9:369 (10September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens
Wah Heng Lee, Christopher W Wong, Wan Yee Leong, Lance D Miller, Wing Kin Sung
BMC Bioinformatics 2008, 9:368 (10September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
IgTM: an algorithm to predict transmembrane domains and topology in proteins
Piedachu Peris, Damian Lopez, Marcelino Campos
BMC Bioinformatics 2008, 9:367 (10September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
Thomas D Otto, Leonardo H F Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda, Wim M Degrave
BMC Bioinformatics 2008, 9:366 (9September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions
E ANDRES Houseman, Brock C Christensen, Ru-Fang Yeh, Carmen J Marsit, Margaret R Karagas, Margaret Wrensch, Heather H Nelson, Joseph Wiemels, Shichun Zheng, John K Wiencke, Karl T Kelsey
BMC Bioinformatics 2008, 9:365 (9September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Fregene: Simulation of realistic sequence-level data in populations and ascertained samples.
Marc Chadeau-Hyam, Clive J Hoggart, Paul F O'Reilly, John C Whittaker, Maria De Iorio, David J Balding
BMC Bioinformatics 2008, 9:364 (8September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Virtual screening of GPCRs: an in silico chemogenomics approach
Laurent Jacob, Brice Hoffmann, Veronique Stoven, Jean-Philippe Vert
BMC Bioinformatics 2008, 9:363 (6September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Testing gene set enrichment for subset of genes:Sub-GSE
Xiting Yan, Fengzhu Sun
BMC Bioinformatics 2008, 9:362 (2September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution
Stefano Moretti, Danitsja van Leeuwen, Hans Gmuender, Stefano Bonassi, Joost van Delft, Jos Kleinjans, Fioravante Patrone, Domenico Franco Merlo
BMC Bioinformatics 2008, 9:361 (2September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
The C1C2: A framework for simultaneous model selection and assessment
Martin Eklund, Ola Spjuth, Jarl ES Wikberg
BMC Bioinformatics 2008, 9:360 (2September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Methodology capture: discriminating between the "best" and the rest of community practice
James M Eales, John W Pinney, Robert D Stevens, David L Robertson
BMC Bioinformatics 2008, 9:359 (1September2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
BMC Bioinformatics 2008, 9:358 (31August2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Impact of residue accessible surface area on the prediction of protein secondary structures
Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi
BMC Bioinformatics 2008, 9:357 (31August2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
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