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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.
Featured articles
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.
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 Bioinformatics 2009, 10 :362
A tool that designs primers to tag genomic DNA with molecular barcodes, and another to analyze the results, will help metagenomics projects that use multiplexed DNA sequencing.
BMC Bioinformatics 2009, 10 :350
Methods for quantifying cell– cell contact often rely on global descriptors, such as overall cell density, but a new statistical model that accounts for local interactions, such as individual cell-cell distances, reduces noisy data and effectively describes contact inhibition effects.
Volume 10 Suppl 15
Proceedings
Singapore. 7-11 September 2009
Volume 10 Suppl 14
Research
Volume 10 Suppl 13
Meeting abstracts
Stockholm, Sweden. 27 June 2009
more info ]
Research article
Classification across gene expression microarray studies Andreas Buness, Markus Ruschhaupt, Ruprecht Kuner, Achim Tresch BMC Bioinformatics 2009, 10 :453 (30 [Abstract ] [Provisional PDF ]
Software
Skittle: A 2-Dimensional Genome Visualization Tool Josiah D. Seaman, John C. Sanford BMC Bioinformatics 2009, 10 :452 (30 [Abstract ] [Provisional PDF ]
Methodology article
Predicting functional upstream open reading frames in Saccharomyces cerevisiae Selpi Selpi, Christopher H Bryant, Graham JL Kemp, Janeli Sarv, Erik Kristiansson, Per Sunnerhagen BMC Bioinformatics 2009, 10 :451 (30 [Abstract ] [Provisional PDF ]
Software
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks Pedro T Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T Freitas, Hidde de Jong BMC Bioinformatics 2009, 10 :450 (30 [Abstract ] [Provisional PDF ]
Methodology article
A white-box approach to microarray probe response characterization: the BaFL pipeline Kevin J Thompson, Hrishikesh Deshmukh, Jeffrey L Solka, Jennifer W Weller BMC Bioinformatics 2009, 10 :449 (29 [Abstract ] [Provisional PDF ]
Research article
Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling Johanna Mazur, Daniel Ritter, Gerhard Reinelt, Lars Kaderali BMC Bioinformatics 2009, 10 :448 (28 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Software
Next generation transcriptomes for next generation genomes using est2assembly
Alexie Papanicolaou, Remo Stierli, Richard H ffrench-Constant, David G Heckel BMC Bioinformatics 2009, 10 :447 (24 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Methodology article
Data mining of enzymes using specific peptides Uri Weingart, Yair Lavi, David Horn BMC Bioinformatics 2009, 10 :446 (24 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Methodology article
LipocalinPred: a SVM-based method for prediction of lipocalins Jayashree Ramana, Dinesh Gupta BMC Bioinformatics 2009, 10 :445 (24 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Software
IRIS: a method for reverse engineering of regulatory relations in gene networks Sandro Morganella, Pietro Zoppoli, Michele Ceccarelli BMC Bioinformatics 2009, 10 :444 (23 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum Tarun KUMAR Bhatt, Charu Kapil, Sameena Khan, Mohamad AMAN Jairajpuri, Vinay Sharma, Daniele Santoni, Francesco Silvestrini, Elisabetta Pizzi, Amit Sharma BMC Genomics 2009, 10 :644 (31 [Abstract ] [Provisional PDF ]
Research article
MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana Robert Grant-Downton, Gael Le Trionnaire, Ralf Schmid, Josefina Rodriguez-Enriquez, Said Hafidh, Saher Mehdi, David Twell, Hugh Dickinson BMC Genomics 2009, 10 :643 (30 [Abstract ] [Provisional PDF ]
Method
Correlating measurements across samples improves accuracy of
large-scale expression profile experiments Mariano Javier Alvarez, Pavel Sumazin, Presha Rajbhandari, Andrea Califano Genome Biology 2009, 10 :R143 (30 [Abstract ] [Provisional PDF ]
Research
An asymmetric approach to preserve common intervals while sorting by reversals Marilia D V Braga, Christian Gautier, Marie-France Sagot Algorithms for Molecular Biology 2009, 4 :16 (30 [Abstract ] [Provisional PDF ]
Research article
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index Kazuharu Arakawa, Haruo Suzuki, Masaru Tomita BMC Genomics 2009, 10 :640 (30 [Abstract ] [Provisional PDF ]
Research article
Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli Rishi Jain, Ranjan Srivastava BMC Systems Biology 2009, 3 :121 (30 [Abstract ] [Provisional PDF ]
Research article
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions Konstantin V. Gunbin, Dmitry A. Afonnikov, Nikolay A. Kolchanov BMC Genomics 2009, 10 :639 (30 [Abstract ] [Provisional PDF ]
Research article
Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development William K. F. Tse, Birgit Eisenhaber, Steven H.-K. Ho, Qimei Ng, Frank Eisenhaber, Yun-Jin Jiang BMC Genomics 2009, 10 :637 (30 [Abstract ] [Provisional PDF ]
Software
3PD: Rapid design of optimal primers for chromosome conformation capture assays Sebastian Frohler, Christoph Dieterich BMC Genomics 2009, 10 :635 (29 [Abstract ] [Provisional PDF ]
Research
Proteomic analysis of regenerating mouse liver following 50% partial hepatectomy Hongcui Cao, Jiong Yu, Wei Xu, Xiaofei Jia, Jinfeng Yang, Qiaoling Pan, Qiyi Zhang, Guoping Sheng, Jun Li, Xiaoping Pan, Yingjie Wang, Lanjuan Li Proteome Science 2009, 7 :48 (29 [Abstract ] [Provisional PDF ]
Featured articles 
