Bioinformatics

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, and Zhaohui S. Qin

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
Bioinformatics Advance Access published on May 14, 2009
Bioinformatics 2009 25: 1715-1721; doi:10.1093/bioinformatics/btp312 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Request Permissions]  

Get checked abstract M. Monzoorul Haque, Tarini Shankar Ghosh, Dinakar Komanduri, and Sharmila S. Mande

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
Bioinformatics Advance Access published on May 13, 2009
Bioinformatics 2009 25: 1722-1730; doi:10.1093/bioinformatics/btp317 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Request Permissions]  

Get checked abstract Marty C. Brandon, Douglas C. Wallace, and Pierre Baldi

Data structures and compression algorithms for genomic sequence data
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1731-1738; doi:10.1093/bioinformatics/btp319 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Meghana Chitale, Troy Hawkins, Changsoon Park, and Daisuke Kihara

ESG: extended similarity group method for automated protein function prediction
Bioinformatics Advance Access published on May 12, 2009
Bioinformatics 2009 25: 1739-1745; doi:10.1093/bioinformatics/btp309 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Request Permissions]  

Get checked abstract Verónica Becher, Alejandro Deymonnaz, and Pablo Heiber

Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome
Bioinformatics Advance Access published on May 18, 2009
Bioinformatics 2009 25: 1746-1753; doi:10.1093/bioinformatics/btp321 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Anna Lobley, Michael I. Sadowski, and David T. Jones

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
Bioinformatics Advance Access published on May 7, 2009
Bioinformatics 2009 25: 1761-1767; doi:10.1093/bioinformatics/btp302 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION

Get checked abstract E. Steele, A. Tucker, P.A.C. 't Hoen, and M.J. Schuemie

Literature-based priors for gene regulatory networks
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1768-1774; doi:10.1093/bioinformatics/btp277 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Insuk Sohn, Jinseog Kim, Sin-Ho Jung, and Changyi Park

Gradient lasso for Cox proportional hazards model
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1775-1781; doi:10.1093/bioinformatics/btp322 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jun Wan, Jimmy Lin, Donald J. Zack, and Jiang Qian

Relating periodicity of nucleosome organization and gene regulation
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1782-1788; doi:10.1093/bioinformatics/btp323 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Gilles Guillot

On the inference of spatial structure from population genetics data
Bioinformatics 2009 25: 1796-1801; doi:10.1093/bioinformatics/btp267 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Request Permissions]  

LETTERS TO THE EDITOR

GENETICS AND POPULATION ANALYSIS

Get checked abstract Eric Durand, Chibiao Chen, and Olivier François

Comment on ‘On the inference of spatial structure from population genetics data’
Bioinformatics 2009 25: 1802-1804; doi:10.1093/bioinformatics/btp337 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Gilles Guillot

Response to comment on ‘On the inference of spatial structure from population genetics data’
Bioinformatics Advance Access published on June 10, 2009
Bioinformatics 2009 25: 1805-1806; doi:10.1093/bioinformatics/btp351 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

GENETICS AND POPULATION ANALYSIS

Get checked abstract József Bukszár, Joseph L. McClay, and Edwin J. C. G. van den Oord

Estimating the posterior probability that genome-wide association findings are true or false
Bioinformatics Advance Access published on May 6, 2009
Bioinformatics 2009 25: 1807-1813; doi:10.1093/bioinformatics/btp305 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Philip Bachman and Ying Liu

Structure discovery in PPI networks using pattern-based network decomposition
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1814-1821; doi:10.1093/bioinformatics/btp297 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Aziz Mithani, Gail M. Preston, and Jotun Hein

Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
Bioinformatics Advance Access published on April 27, 2009
Bioinformatics 2009 25: 1831-1832; doi:10.1093/bioinformatics/btp269 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu

MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 1843-1845; doi:10.1093/bioinformatics/btp272 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Seong-Hyeuk Nam, Dae-Won Kim, Tae-Sung Jung, Young-Sang Choi, Dong-Wook Kim, Han-Suk Choi, Sang-Haeng Choi, and Hong-Seog Park

PESTAS: a web server for EST analysis and sequence mining
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1846-1848; doi:10.1093/bioinformatics/btp293 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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