Skip Navigation

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

Cover Image
Other Issues:
Previous Next 		Contents: Volume 25, Number 13, 1 July 2009   [Index by Author] 
Down REVIEW
     DATA AND TEXT MINING
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
Down APPLICATIONS NOTE
     STRUCTURAL BIOINFORMATICS
     DATA AND TEXT MINING
Down CORRIGENDUM
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.

REVIEW Back

DATA AND TEXT MINING Back

Raffaele Giancarlo, Davide Scaturro, and Filippo Utro
Textual data compression in computational biology: a synopsis
Bioinformatics Advance Access published on February 27, 2009
Bioinformatics 2009 25: 1575-1586; doi:10.1093/bioinformatics/btp117 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

David V. Lu, Randall H. Brown, Manimozhiyan Arumugam, and Michael R. Brent
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1587-1593; doi:10.1093/bioinformatics/btp273 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jochen W. Klingelhoefer, Loukas Moutsianas, and Chris Holmes
Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency
Bioinformatics Advance Access published on May 6, 2009
Bioinformatics 2009 25: 1594-1601; doi:10.1093/bioinformatics/btp284 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Anoop Kumar and Lenore Cowen
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1602-1608; doi:10.1093/bioinformatics/btp265 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Zia Khan, Joshua S. Bloom, Leonid Kruglyak, and Mona Singh
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1609-1616; doi:10.1093/bioinformatics/btp275 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Dennis J. Hazelett, Daniel L. Lakeland, and Joseph B. Weiss
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets
Bioinformatics Advance Access published on April 28, 2009
Bioinformatics 2009 25: 1617-1624; doi:10.1093/bioinformatics/btp282 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

Jairo Rocha, Joan Segura, Richard C. Wilson, and Swagata Dasgupta
Flexible structural protein alignment by a sequence of local transformations
Bioinformatics Advance Access published on May 5, 2009
Bioinformatics 2009 25: 1625-1631; doi:10.1093/bioinformatics/btp296 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Christian Schillinger, Prisca Boisguerin, and Gerd Krause
Domain Interaction Footprint: a multi-classification approach to predict domain–peptide interactions
Bioinformatics Advance Access published on April 17, 2009
Bioinformatics 2009 25: 1632-1639; doi:10.1093/bioinformatics/btp264 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Denis C. Bauer and Timothy L. Bailey
Optimizing static thermodynamic models of transcriptional regulation
Bioinformatics Advance Access published on April 27, 2009
Bioinformatics 2009 25: 1640-1646; doi:10.1093/bioinformatics/btp283 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Fred P. Davis and Sean R. Eddy
A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1647-1654; doi:10.1093/bioinformatics/btp288 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Chunrong Cheng, Kui Shen, Chi Song, Jianhua Luo, and George C. Tseng
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1655-1661; doi:10.1093/bioinformatics/btp292 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Min Zhang, Lin Zhang, Jinfeng Zou, Chen Yao, Hui Xiao, Qing Liu, Jing Wang, Dong Wang, Chenguang Wang, and Zheng Guo
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
Bioinformatics Advance Access published on May 5, 2009
Bioinformatics 2009 25: 1662-1668; doi:10.1093/bioinformatics/btp295 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Long Yang Wu, Hugh A. Chipman, Shelley B. Bull, Laurent Briollais, and Kesheng Wang
A Bayesian segmentation approach to ascertain copy number variations at the population level
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1669-1679; doi:10.1093/bioinformatics/btp270 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Chao-Yi Dong, Jisoon Lim, Yoonkey Nam, and Kwang-Hyun Cho
Systematic analysis of synchronized oscillatory neuronal networks reveals an enrichment for coupled direct and indirect feedback motifs
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1680-1685; doi:10.1093/bioinformatics/btp271 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data 1] [Request Permissions]  

Janis Dingel and Olgica Milenkovic
List-decoding methods for inferring polynomials in finite dynamical gene network models
Bioinformatics Advance Access published on April 28, 2009
Bioinformatics 2009 25: 1686-1693; doi:10.1093/bioinformatics/btp281 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jonathan D. Wren
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1694-1701; doi:10.1093/bioinformatics/btp290 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Quanyu Zhao and Hiroyuki Kurata
Genetic modification of flux for flux prediction of mutants
Bioinformatics Advance Access published on May 25, 2009
Bioinformatics 2009 25: 1702-1708; doi:10.1093/bioinformatics/btp298 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

STRUCTURAL BIOINFORMATICS Back

Jordi Camps, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluís Gelpí, and Modesto Orozco
FlexServ: an integrated tool for the analysis of protein flexibility
Bioinformatics Advance Access published on May 7, 2009
Bioinformatics 2009 25: 1709-1710; doi:10.1093/bioinformatics/btp304 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING Back

Natalia Becker, Wiebke Werft, Grischa Toedt, Peter Lichter, and Axel Benner
penalizedSVM: a R-package for feature selection SVM classification
Bioinformatics Advance Access published on April 27, 2009
Bioinformatics 2009 25: 1711-1712; doi:10.1093/bioinformatics/btp286 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

CORRIGENDUM Back

Eric P. Nawrocki, Diana L. Kolbe, and Sean R. Eddy
Infernal 1.0: inference of RNA alignments
Bioinformatics 2009 25: 1713; doi:10.1093/bioinformatics/btp326 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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.