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Editor-in-Chief Melissa Norton, MD
Biology Editor Penelope Webb, PhD
In-house Editor Tim Sands, 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, Scopus, EMBASE, Thomson Reuters (ISI) and Google Scholar.
BMC Bioinformatics 2009, 10 :171
A new software, T-REX, facilitates the cumbersome analysis of terminal restriction fragment length polymorphisms (T-RFLPs) including the processing of raw data, identification of true peaks and the comparative analysis of terminal restriction fragments in all samples.
BMC Bioinformatics 2009, 10 :156
The Affymetrix GeneChip microarray platform, widely used to assay gene expression, can also detect differential splicing events with the help of a new statistical method called FIRMAGene that analyses information from poorly fitting adjacent probes.
BMC Bioinformatics 2009, 10 :151
An international collaboration of software developers, computer scientists, life scientists and research technicians has extended a database tool that manages microarray data from various sources to include data from the latest ultra-high throughput DNA sequencing technologies.
BMC Bioinformatics 2009, 10 :130
Massive amounts of SNP data can now be analysed with three different tree-based methods
classification tree, random forest, deterministic forest
by using a new, memory-efficient software called Willows.
BMC Bioinformatics 2009, 10 :120
Reconstruction of ancestral genomes with algorithms that estimate genome rearrangements is easier for multichromosomal versus unichromosomal genomes, and most of the theoretical issues with the combinatorial optimization problems of genome rearrangement have been resolved.
Volume 10 Suppl 7
Meeting abstracts
Pikeville, TN, USA. 20 Volume 10 Suppl 6
Proceedings
Martina Franca, Italy. 18 Volume 10 Suppl 5
Proceedings
Toronto, ON, Canada. 20 July 2008
more info ]
Research article
Ensemble approach to predict specificity determinants: benchmarking and validation Saikat Chakrabarti, Anna R Panchenko BMC Bioinformatics 2009, 10 :207 (2 [Abstract ] [Provisional PDF ]
Research article
Representative transcript sets for evaluating a translational initiation sites predictor Jia Zeng, Reda Alhajj, Douglas J Demetrick BMC Bioinformatics 2009, 10 :206 (2 [Abstract ] [Provisional PDF ]
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 (1 [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 (30 [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 (29 [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 (29 [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 (29 [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 (29 [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 (29 [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 (28 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research
Ranking candidate genes in rat models of type 2 diabetes Lars Andersson, Greta Petersen, Fredrik Stahl Theoretical Biology and Medical Modelling 2009, 6 :12 (3 [Abstract ] [Provisional PDF ]
Research article
Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus Christian Obermeier, Bashir Hosseini, Wolfgang Friedt, Rod Snowdon BMC Genomics 2009, 10 :295 (3 [Abstract ] [Provisional PDF ]
Research article
Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards Christy A Hipsley, Lin Himmelmann, Dirk Metzler, Johannes Mueller BMC Evolutionary Biology 2009, 9 :151 (1 [Abstract ] [Provisional PDF ]
Research
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons Rui Liu, Sridhar Hannenhalli, Maja Bucan Genome Biology 2009, 10 :R72 (1 [Abstract ] [Provisional PDF ]
Research
Morphogenesis signaling components influence cell cycle regulation by cyclin dependent kinase Brian TD Tobe, Ana A Kitazono, Jacqueline Suen Garcia, Renee A Gerber, Brooke J Bevis, John S Choy, Daniel Chasman, Stephen J Kron Cell Division 2009, 4 :12 (1 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
Improved estimation of structure predictor quality Kevin W DeRonne, George Karypis BMC Structural Biology 2009, 9 :41 (30 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Methodology article
BowTieBuilder: modeling signal transduction pathways Jochen Supper, Lucia Spangenberg, Hannes Planatscher, Andreas Draeger, Adrian Schroeder, Andreas Zell BMC Systems Biology 2009, 3 :67 (30 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouze, Yves Van de Peer BMC Genomics 2009, 10 :288 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research
Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome Srilatha Kuntumalla, John C Braisted, Shih-Ting Huang, Prashanth P Parmar, David J Clark, Hamid Alami, Quanshun Zhang, Arthur Donohue-Rolfe, Saul Tzipori, Robert D Fleischmann, Scott N Peterson, Rembert Pieper Proteome Science 2009, 7 :22 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Database
Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs Barbara Lazzari, Andrea Caprera, Alessandro Cestaro, Ivan Merelli, Marcello Del Corvo, Paolo Fontana, Luciano Milanesi, Riccardo Velasco, Alessandra Stella BMC Plant Biology 2009, 9 :82 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Featured articles
classification tree, random forest, deterministic forest 
