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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
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) GenomeMatcher: A graphical user interface for DNA sequence comparison Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda BMC Bioinformatics 2008, 9:376 (16 September 2008) [Abstract] [Provisional PDF] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (15 September 2008) [Abstract] [Provisional PDF] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (15 September 2008) [Abstract] [Provisional PDF] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (12 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (12 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Software
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (11 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) Mixture models for analysis of melting temperature data. Christoffer Nellaker, Fredrik Uhrzander, Joanna Tyrcha, Hakan Karlsson BMC Bioinformatics 2008, 9:370 (11 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) Automatic detection of exonic splicing enhancers (ESEs) using SVMs Britta Mersch, Alexander Gepperth, Sandor Suhai, Agnes Hotz-Wagenblatt BMC Bioinformatics 2008, 9:369 (10 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Software
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (10 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) IgTM: an algorithm to predict transmembrane domains and topology in proteins Piedachu Peris, Damian Lopez, Marcelino Campos BMC Bioinformatics 2008, 9:367 (10 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (9 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (9 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Software
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (8 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Research article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) Virtual screening of GPCRs: an in silico chemogenomics approach Laurent Jacob, Brice Hoffmann, Veronique Stoven, Jean-Philippe Vert BMC Bioinformatics 2008, 9:363 (6 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif) Testing gene set enrichment for subset of genes:Sub-GSE Xiting Yan, Fengzhu Sun BMC Bioinformatics 2008, 9:362 (2 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) 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 (2 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Methodology article
![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/entities/160.gif) ![](https://webarchive.library.unt.edu/eot2008/20080917070401im_/http://www.biomedcentral.com/bmcimages/browse/OA.gif) The C1C2: A framework for simultaneous model selection and assessment Martin Eklund, Ola Spjuth, Jarl ES Wikberg BMC Bioinformatics 2008, 9:360 (2 September 2008) [Abstract] [Provisional PDF] [PubMed] [Related articles] Research article
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