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Previous Next 		Contents: Volume 25, Number 21, 1 November 2009   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down ISMB/ECCB 2009 SPECIAL INTEREST GROUP ON SHORT READ SEQUENCING
     REPORT
     ORIGINAL PAPERS
         GENOME ANALYSIS
         SEQUENCE ANALYSIS
         GENE EXPRESSION
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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

Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, and Hiroshi Mamitsuka
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data
Bioinformatics Advance Access published on September 7, 2009
Bioinformatics 2009 25: 2735-2743; doi:10.1093/bioinformatics/btp531 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, and Predrag Radivojac
Automated inference of molecular mechanisms of disease from amino acid substitutions
Bioinformatics Advance Access published on September 3, 2009
Bioinformatics 2009 25: 2744-2750; doi:10.1093/bioinformatics/btp528 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Aleksandar Poleksic
Algorithms for optimal protein structure alignment
Bioinformatics Advance Access published on September 4, 2009
Bioinformatics 2009 25: 2751-2756; doi:10.1093/bioinformatics/btp530 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Lisa Bartoli, Piero Fariselli, Anders Krogh, and Rita Casadio
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information
Bioinformatics Advance Access published on September 10, 2009
Bioinformatics 2009 25: 2757-2763; doi:10.1093/bioinformatics/btp539 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Sandra Waaijenborg and Aeilko H. Zwinderman
Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis
Bioinformatics Advance Access published on August 17, 2009
Bioinformatics 2009 25: 2764-2771; doi:10.1093/bioinformatics/btp491 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Michael Dannemann, Anna Lorenc, Ines Hellmann, Philipp Khaitovich, and Michael Lachmann
The effects of probe binding affinity differences on gene expression measurements and how to deal with them
Bioinformatics Advance Access published on August 18, 2009
Bioinformatics 2009 25: 2772-2779; doi:10.1093/bioinformatics/btp492 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

YounJeong Choi and Christina Kendziorski
Statistical methods for gene set co-expression analysis
Bioinformatics Advance Access published on August 18, 2009
Bioinformatics 2009 25: 2780-2786; doi:10.1093/bioinformatics/btp502 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Andreas Keller, Christina Backes, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, and Hans-Peter Lenhof
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Bioinformatics Advance Access published on August 27, 2009
Bioinformatics 2009 25: 2787-2794; doi:10.1093/bioinformatics/btp510 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Anindya Bhattacharya and Rajat K. De
Bi-correlation clustering algorithm for determining a set of co-regulated genes
Bioinformatics Advance Access published on September 3, 2009
Bioinformatics 2009 25: 2795-2801; doi:10.1093/bioinformatics/btp526 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Zhi Wei, Wenguang Sun, Kai Wang, and Hakon Hakonarson
Multiple testing in genome-wide association studies via hidden Markov models
Bioinformatics Advance Access published on August 4, 2009
Bioinformatics 2009 25: 2802-2808; doi:10.1093/bioinformatics/btp476 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Moritz Gerstung, Michael Baudis, Holger Moch, and Niko Beerenwinkel
Quantifying cancer progression with conjunctive Bayesian networks
Bioinformatics Advance Access published on August 19, 2009
Bioinformatics 2009 25: 2809-2815; doi:10.1093/bioinformatics/btp505 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Irina Surovtsova, Natalia Simus, Thomas Lorenz, Artjom König, Sven Sahle, and Ursula Kummer
Accessible methods for the dynamic time-scale decomposition of biochemical systems
Bioinformatics Advance Access published on July 24, 2009
Bioinformatics 2009 25: 2816-2823; doi:10.1093/bioinformatics/btp451 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Victor Olariu, Daniel Coca, Stephen A. Billings, Peter Tonge, Paul Gokhale, Peter W. Andrews, and Visakan Kadirkamanathan
Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2824-2830; doi:10.1093/bioinformatics/btp456 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ze Tian, TaeHyun Hwang, and Rui Kuang
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2831-2838; doi:10.1093/bioinformatics/btp467 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Timo Lassmann, Yoshihide Hayashizaki, and Carsten O. Daub
TagDust—a program to eliminate artifacts from next generation sequencing data
Bioinformatics Advance Access published on September 7, 2009
Bioinformatics 2009 25: 2839-2840; doi:10.1093/bioinformatics/btp527 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Andrew D. Smith, Wen-Yu Chung, Emily Hodges, Jude Kendall, Greg Hannon, James Hicks, Zhenyu Xuan, and Michael Q. Zhang
Updates to the RMAP short-read mapping software
Bioinformatics Advance Access published on September 7, 2009
Bioinformatics 2009 25: 2841-2842; doi:10.1093/bioinformatics/btp533 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

David La, Juan Esquivel-Rodríguez, Vishwesh Venkatraman, Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, and Daisuke Kihara
3D-SURFER: software for high-throughput protein surface comparison and analysis
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 2843-2844; doi:10.1093/bioinformatics/btp542 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Mattias Jakobsson
COMPASS: a program for generating serial samples under an infinite sites model
Bioinformatics Advance Access published on September 17, 2009
Bioinformatics 2009 25: 2845-2847; doi:10.1093/bioinformatics/btp534 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Chris J. Myers, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, and Nam-Phuong D. Nguyen
iBioSim: a tool for the analysis and design of genetic circuits
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2848-2849; doi:10.1093/bioinformatics/btp457 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tae-Sung Jung, Hock Chuan Yeo, Satty G. Reddy, Wan-Sup Cho, and Dong-Yup Lee
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model
Bioinformatics Advance Access published on August 17, 2009
Bioinformatics 2009 25: 2850-2852; doi:10.1093/bioinformatics/btp496 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nicola Soranzo and Claudio Altafini
ERNEST: a toolbox for chemical reaction network theory
Bioinformatics Advance Access published on August 27, 2009
Bioinformatics 2009 25: 2853-2854; doi:10.1093/bioinformatics/btp513 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kim-Anh Lê Cao, Ignacio González, and Sébastien Déjean
integrOmics: an R package to unravel relationships between two omics datasets
Bioinformatics Advance Access published on August 25, 2009
Bioinformatics 2009 25: 2855-2856; doi:10.1093/bioinformatics/btp515 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Giovanni Scardoni, Michele Petterlini, and Carlo Laudanna
Analyzing biological network parameters with CentiScaPe
Bioinformatics Advance Access published on September 2, 2009
Bioinformatics 2009 25: 2857-2859; doi:10.1093/bioinformatics/btp517 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Kumaran Kandasamy, Shivakumar Keerthikumar, Rajesh Raju, T. S. Keshava Prasad, Y. L. Ramachandra, Sujatha Mohan, and Akhilesh Pandey
PathBuilder—open source software for annotating and developing pathway resources
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2860-2862; doi:10.1093/bioinformatics/btp453 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ISMB/ECCB 2009 SPECIAL INTEREST GROUP ON SHORT READ SEQUENCING Back

REPORT Back

Michael Brudno, Paul Medvedev, Jens Stoye, and Francisco M. De La Vega
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Bioinformatics Advance Access published on September 24, 2009
Bioinformatics 2009 25: 2863-2864; doi:10.1093/bioinformatics/btp525 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, and Zemin Ning
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2865-2871; doi:10.1093/bioinformatics/btp394 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Inanç Birol, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, and Steven J. M. Jones
De novo transcriptome assembly with ABySS
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 2872-2877; doi:10.1093/bioinformatics/btp367 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Bas E. Dutilh, Martijn A. Huynen, and Marc Strous
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2878-2881; doi:10.1093/bioinformatics/btp377 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

Gerald Quon and Quaid Morris
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2882-2889; doi:10.1093/bioinformatics/btp378 [Abstract] [FREE Full Text] [Print PDF]   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.