Skip Navigation

Receive this page by email each issue: [Sign up for eTOCs]

Cover Image
Other Issues:
Previous 		Contents: Volume 26, Number 3, 1 February 2010   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATION NOTES
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down LETTERS TO THE EDITOR
Find articles in this issue containing these words:
[Search ALL Issues]

Front Matter (Print PDF) | Back Matter (Print PDF) | Table of Contents (Print PDF)

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides
Estimating DNA coverage and abundance in metagenomes using a gamma approximation
Bioinformatics Advance Access published on December 14, 2009
Bioinformatics 2010 26: 295-301; doi:10.1093/bioinformatics/btp687 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Thanh Le, Tom Altman, and Katheleen Gardiner
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
Bioinformatics Advance Access published on December 8, 2009
Bioinformatics 2010 26: 302-309; doi:10.1093/bioinformatics/btp676 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Daniel T. Lavelle and William R. Pearson
Globally, unrelated protein sequences appear random
Bioinformatics Advance Access published on November 30, 2009
Bioinformatics 2010 26: 310-318; doi:10.1093/bioinformatics/btp660 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

N. A. Temiz, A. Trapp, O. A. Prokopyev, and C. J. Camacho
Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 319-325; doi:10.1093/bioinformatics/btp664 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, and Oxana V. Galzitskaya
FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence
Bioinformatics Advance Access published on December 17, 2009
Bioinformatics 2010 26: 326-332; doi:10.1093/bioinformatics/btp691 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Shuya Lu, Jia Li, Chi Song, Kui Shen, and George C. Tseng
Biomarker detection in the integration of multiple multi-class genomic studies
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 333-340; doi:10.1093/bioinformatics/btp669 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Yijing Shen, Wei Sun, and Ker-Chau Li
Dynamically weighted clustering with noise set
Bioinformatics Advance Access published on December 9, 2009
Bioinformatics 2010 26: 341-347; doi:10.1093/bioinformatics/btp671 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Rui Hu, Xing Qiu, and Galina Glazko
A new gene selection procedure based on the covariance distance
Bioinformatics Advance Access published on December 8, 2009
Bioinformatics 2010 26: 348-354; doi:10.1093/bioinformatics/btp672 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Steven J. Kiddle, Oliver P. F. Windram, Stuart McHattie, Andrew Mead, Jim Beynon, Vicky Buchanan-Wollaston, Katherine J. Denby, and Sach Mukherjee
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
Bioinformatics Advance Access published on December 8, 2009
Bioinformatics 2010 26: 355-362; doi:10.1093/bioinformatics/btp673 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Thang V. Pham, Sander R. Piersma, Marc Warmoes, and Connie R. Jimenez
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
Bioinformatics Advance Access published on December 9, 2009
Bioinformatics 2010 26: 363-369; doi:10.1093/bioinformatics/btp677 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Theresa Scharl, Bettinan Grü, and Friedrich Leisch
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects
Bioinformatics Advance Access published on December 29, 2009
Bioinformatics 2010 26: 370-377; doi:10.1093/bioinformatics/btp686 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Monica Chagoyen and Florencio Pazos
Quantifying the biological significance of gene ontology biological processes—implications for the analysis of systems-wide data
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 378-384; doi:10.1093/bioinformatics/btp663 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Suk Hoon Jung, Bora Hyun, Woo-Hyuk Jang, Hee-Young Hur, and Dong-Soo Han
Protein complex prediction based on simultaneous protein interaction network
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 385-391; doi:10.1093/bioinformatics/btp668 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, and Yvan Saeys
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods
Bioinformatics Advance Access published on November 25, 2009
Bioinformatics 2010 26: 392-398; doi:10.1093/bioinformatics/btp630 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATION NOTES Back

GENOME ANALYSIS Back

Kousuke Hanada, Kenji Akiyama, Tetsuya Sakurai, Tetsuro Toyoda, Kazuo Shinozaki, and Shin-Han Shiu
sORF finder: a program package to identify small open reading frames with high coding potential
Bioinformatics Advance Access published on December 14, 2009
Bioinformatics 2010 26: 399-400; doi:10.1093/bioinformatics/btp688 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Iain Milne, Micha Bayer, Linda Cardle, Paul Shaw, Gordon Stephen, Frank Wright, and David Marshall
Tablet—next generation sequence assembly visualization
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 401-402; doi:10.1093/bioinformatics/btp666 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Emese Meglécz, Caroline Costedoat, Vincent Dubut, André Gilles, Thibaut Malausa, Nicolas Pech, and Jean-François Martin
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects
Bioinformatics Advance Access published on December 10, 2009
Bioinformatics 2010 26: 403-404; doi:10.1093/bioinformatics/btp670 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu, and Hongwei Xie
Tmod: toolbox of motif discovery
Bioinformatics Advance Access published on December 10, 2009
Bioinformatics 2010 26: 405-407; doi:10.1093/bioinformatics/btp681 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS Back

Chi Ho Lin, Hao Zhao, Sean Harry Lowcay, Atif Shahab, and Guillaume Bourque
webMGR: an online tool for the multiple genome rearrangement problem
Bioinformatics Advance Access published on December 18, 2009
Bioinformatics 2010 26: 408-410; doi:10.1093/bioinformatics/btp689 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Nathan S. Watson-Haigh, Haja N. Kadarmideen, and Antonio Reverter
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
Bioinformatics Advance Access published on December 9, 2009
Bioinformatics 2010 26: 411-413; doi:10.1093/bioinformatics/btp674 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Keyan Salari, Robert Tibshirani, and Jonathan R. Pollack
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
Bioinformatics Advance Access published on December 22, 2009
Bioinformatics 2010 26: 414-416; doi:10.1093/bioinformatics/btp702 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Valery Terletskiy, Valentina Tyshchenko, Ilargi Martinez-Ballesteros, Javier Garaizar, and Joseba Bikandi
Validation of double digest selective label database for sequenced prokaryotic genomes
Bioinformatics Advance Access published on December 8, 2009
Bioinformatics 2010 26: 417-418; doi:10.1093/bioinformatics/btp675 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Emmanuel Paradis
pegas: an R package for population genetics with an integrated–modular approach
Bioinformatics Advance Access published on January 14, 2010
Bioinformatics 2010 26: 419-420; doi:10.1093/bioinformatics/btp696 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Falko Krause, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp, and Wolfram Liebermeister
Annotation and merging of SBML models with semanticSBML
Bioinformatics Advance Access published on November 17, 2009
Bioinformatics 2010 26: 421-422; doi:10.1093/bioinformatics/btp642 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kendell Clement, Nathaniel Gustafson, Amanda Berbert, Hyrum Carroll, Christopher Merris, Ammon Olsen, Mark Clement, Quinn Snell, Jared Allen, and Randall J. Roper
PathGen: a transitive gene pathway generator
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 423-425; doi:10.1093/bioinformatics/btp661 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Emmet Caulfield and Andreas Hellander
CellMC—a multiplatform model compiler for the Cell Broadband Engine and x86
Bioinformatics Advance Access published on December 8, 2009
Bioinformatics 2010 26: 426-428; doi:10.1093/bioinformatics/btp662 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ozgun Babur, Ugur Dogrusoz, Emek Demir, and Chris Sander
ChiBE: interactive visualization and manipulation of BioPAX pathway models
Bioinformatics Advance Access published on December 9, 2009
Bioinformatics 2010 26: 429-431; doi:10.1093/bioinformatics/btp665 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Bart S. Hendriks and Christopher W. Espelin
DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets
Bioinformatics Advance Access published on December 4, 2009
Bioinformatics 2010 26: 432-433; doi:10.1093/bioinformatics/btp667 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Carson M. Andorf, Carolyn J. Lawrence, Lisa C. Harper, Mary L. Schaeffer, Darwin A. Campbell, and Taner Z. Sen
The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps
Bioinformatics 2010 26: 434-436; doi:10.1093/bioinformatics/btp556 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTERS TO THE EDITOR Back

Anne-Laure Boulesteix
Over-optimism in bioinformatics research
Bioinformatics Advance Access published on November 26, 2009
Bioinformatics 2010 26: 437-439; doi:10.1093/bioinformatics/btp648 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Pawel Smialowski, Dmitrij Frishman, and Stefan Kramer
Pitfalls of supervised feature selection
Bioinformatics Advance Access published on October 29, 2009
Bioinformatics 2010 26: 440-443; doi:10.1093/bioinformatics/btp621 [Extract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.