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BMC Bioinformatics

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Editor-in-Chief
Melissa Norton, MD

Biology Editor
Penelope Webb, PhD

In-house Editor
Danielle Burgess PhD


Welcome to BMC Bioinformatics published by BioMed Central
BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics (ISSN 1471-2105) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, EMBASE, Scopus, Thomson Reuters (ISI) and Google Scholar.



BMC Featured articles

Credit: Adapted from Krishna et al. BMC Systems Biol 11_68
BMC Bioinformatics 2010, 11:68
A new method for clustering time-course microarray gene expression datasets, using a Granger causality approach to test the temporal relationships between genes, provides a promising way to group functionally related genes.
DNA sequencing trace, by Loris, source Wikipedia
BMC Bioinformatics 2009, 10:447
Next generation sequencing technologies have resulted in an explosion of transcriptome projects in non-model organisms and est2assembly is a useful tool for the assembly, annotation, analysis and visualization of such data.
Annalees Pics Flikr cc
BMC Bioinformatics 2009, 10:421
With the advent of more complete genomes BLAST has been re-written to include a new set of command line searches and a new modular structure, giving substantial speed improvements for long queries and an improved user interface.
BMC Bioinformatics 2009, 10:402
Double filtering using fold change and t test to find differentially expressed genes loses power due to differing assumptions about variance, whereas combining Bayesian mixture models with SAM approaches the performance of the theoretically best likelihood ratio test statistic.
Darwin's picture, source Wikipedia
BMC Bioinformatics 2009, 10:S6
Scratchpads, a new social networking tool for natural history researchers and enthusiasts, links information from disparate sources, encourages data sharing, and promotes the ultimate goal of describing and synthesising all facets of the diversity of life.


BMC  Latest supplements published in BMC Bioinformatics


Volume 11 Suppl 1
Research
Bangalore, India. 18-21 January 2010

Volume 10 Suppl 15
Proceedings
Singapore. 7-11 September 2009

Volume 10 Suppl 14
Research





BMC  Latest articles published in BMC Bioinformatics        [more info]


Software
Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays
Hedda Hovik, Tsute Chen
BMC Bioinformatics 2010, 11:82 (9February2010)
[Abstract] [Provisional PDF]

Research article
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, Dabing Zhang
BMC Bioinformatics 2010, 11:81 (9February2010)
[Abstract] [Provisional PDF]

Research article
Parameters for accurate genome alignment
Martin C Frith, Michiaki Hamada, Paul Horton
BMC Bioinformatics 2010, 11:80 (9February2010)
[Abstract] [Provisional PDF]

Research article
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies
Maria Pamela C David, Gisela P Concepcion, Eduardo A Padlan
BMC Bioinformatics 2010, 11:79 (8February2010)
[Abstract] [Provisional PDF]

Methodology article
Testing the additional predictive value of high-dimensional molecular data
Anne-Laure Boulesteix, Torsten Hothorn
BMC Bioinformatics 2010, 11:78 (8February2010)
[Abstract] [Provisional PDF]

Methodology article
A random effect multiplicative heteroscedastic model for bacterial growth
Ricardo Cao, Mario Francisco-Fernandez, Emiliano J Quinto
BMC Bioinformatics 2010, 11:77 (8February2010)
[Abstract] [Provisional PDF]

Research article
Extracting consistent knowledge from highly inconsistent cancer gene data sources
Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, Zheng Guo
BMC Bioinformatics 2010, 11:76 (5February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Research article
Mining protein loops using a structural alphabet and statistical exceptionality
Leslie Regad, Juliette Martin, Gregory Nuel, Anne-claude Camproux
BMC Bioinformatics 2010, 11:75 (4February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Software
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics
Xiaowu Gai, Juan C Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M Xie, Eric F Rappaport, Tamim H Shaikh, Peter S White
BMC Bioinformatics 2010, 11:74 (4February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Software
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Mark J Alston, John Seers, Jay CD Hinton, Sacha Lucchini
BMC Bioinformatics 2010, 11:73 (3February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]


BMC  Latest relevant articles from other journals in BioMed Central


Research
2X genomes - depth does matter
Michel C Milinkovitch, Raphael Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldon
Genome Biology 2010, 11:R16 (9February2010)
[Abstract] [Provisional PDF]

Research article
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita, Akio Kanai
BMC Genomics 2010, 11:101 (9February2010)
[Abstract] [Provisional PDF]

Research article
Variability of gene expression profiles in human blood and lymphoblastoid cell lines
Josine L Min, Amy Barrett, Tim Watts, Fredrik H Pettersson, Helen E Lockstone, Cecilia M Lindgren, Jennifer M Taylor, Maxine Allen, Krina T Zondervan, Mark I McCarthy
BMC Genomics 2010, 11:96 (8February2010)
[Abstract] [Provisional PDF]

Research article
Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
Chi Nam Ignatius Pang, Elisabeth Gasteiger, Marc R Wilkins
BMC Genomics 2010, 11:92 (5February2010)
[Abstract] [Provisional PDF]

Method
Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack
Genome Biology 2010, 11:R14 (4February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Software article
Jane: A new tool for the cophylogeny reconstruction problem
Chris Conow, Daniel Fielder, Yaniv Ovadia, Ran Libeskind-Hadas
Algorithms for Molecular Biology 2010, 5:16 (3February2010)
[Abstract] [Provisional PDF]

Method
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
Kristen Fortney, Max Kotlyar, Igor Jurisica
Genome Biology 2010, 11:R13 (3February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Research
Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
Kankshita Swaminathan, Magdy Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan S Rokhsar, Aru K Arumuganathan, Ray Ming, Pamela J Green, Blake C Meyers, Stephen P Moose, Matthew E Hudson
Genome Biology 2010, 11:R12 (3February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Methodology article
A general co-expression network-based approach to gene expression analysis: comparison and applications
Jianhua Ruan, Angela K Dean, Weixiong Zhang
BMC Systems Biology 2010, 4:8 (2February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

Research article
Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules
Sherri L Schwartz, Mark L Farman
BMC Genomics 2010, 11:87 (2February2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]

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