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Previous Next 		Contents: Volume 25, Number 7, 1 April 2009   [Index by Author] 
Down DISCOVERY NOTE
     GENOME ANALYSIS
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     STRUCTURAL BIOINFORMATICS
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
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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.

DISCOVERY NOTE Back

GENOME ANALYSIS Back

Xiaohua Douglas Zhang and Joseph F. Heyse
Determination of sample size in genome-scale RNAi screens
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 841-844; doi:10.1093/bioinformatics/btp082 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Kuo-Ho Yen, Chung-Liang Ho, and Chiang Lee
The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding
Bioinformatics Advance Access published on December 20, 2008
Bioinformatics 2009 25: 845-852; doi:10.1093/bioinformatics/btn649 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, and Yasubumi Sakakibara
Accurate identification of orthologous segments among multiple genomes
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 853-860; doi:10.1093/bioinformatics/btp070 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Henrik Bengtsson, Amrita Ray, Paul Spellman, and Terence P. Speed
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
Bioinformatics Advance Access published on February 4, 2009
Bioinformatics 2009 25: 861-867; doi:10.1093/bioinformatics/btp074 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Chen Yanover, Mona Singh, and Elena Zaslavsky
M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 868-874; doi:10.1093/bioinformatics/btp090 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

João Pedro de Magalhães, João Curado, and George M. Church
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 875-881; doi:10.1093/bioinformatics/btp073 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

Shuangge Ma and Michael R. Kosorok
Identification of differential gene pathways with principal component analysis
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 882-889; doi:10.1093/bioinformatics/btp085 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Harald Binder, Arthur Allignol, Martin Schumacher, and Jan Beyersmann
Boosting for high-dimensional time-to-event data with competing risks
Bioinformatics Advance Access published on February 25, 2009
Bioinformatics 2009 25: 890-896; doi:10.1093/bioinformatics/btp088 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Chen-An Tsai and James J. Chen
Multivariate analysis of variance test for gene set analysis
Bioinformatics Advance Access published on March 2, 2009
Bioinformatics 2009 25: 897-903; doi:10.1093/bioinformatics/btp098 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ruth Heller, Elisabetta Manduchi, and Dylan S. Small
Matching methods for observational microarray studies
Bioinformatics Advance Access published on December 19, 2008
Bioinformatics 2009 25: 904-909; doi:10.1093/bioinformatics/btn650 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Joshua Colvin, Michael I. Monine, James R. Faeder, William S. Hlavacek, Daniel D. Von Hoff, and Richard G. Posner
Simulation of large-scale rule-based models
Bioinformatics Advance Access published on February 11, 2009
Bioinformatics 2009 25: 910-917; doi:10.1093/bioinformatics/btp066 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Shuhei Kimura, Satoshi Nakayama, and Mariko Hatakeyama
Genetic network inference as a series of discrimination tasks
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 918-925; doi:10.1093/bioinformatics/btp072 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Géraldine Del Mondo, Damien Eveillard, and Irena Rusu
Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 926-932; doi:10.1093/bioinformatics/btp083 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, and Koji Tsuda
Enumeration of condition-dependent dense modules in protein interaction networks
Bioinformatics Advance Access published on February 11, 2009
Bioinformatics 2009 25: 933-940; doi:10.1093/bioinformatics/btp080 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

M. Netzer, G. Millonig, M. Osl, B. Pfeifer, S. Praun, J. Villinger, W. Vogel, and C. Baumgartner
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 941-947; doi:10.1093/bioinformatics/btp093 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Hiromi Arai, Satoru Watanabe, Takanori Kigawa, and Masayuki Yamamura
A new modeling method in feature construction for the HSQC spectra screening problem
Bioinformatics Advance Access published on July 4, 2008
Bioinformatics 2009 25: 948-953; doi:10.1093/bioinformatics/btn345 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Touati Benoukraf, Pierre Cauchy, Romain Fenouil, Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe Andrau, Salvatore Spicuglia, and Pierre Ferrier
CoCAS: a ChIP-on-chip analysis suite
Bioinformatics Advance Access published on February 4, 2009
Bioinformatics 2009 25: 954-955; doi:10.1093/bioinformatics/btp075 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Kashi Vishwanath Revanna, Vivek Krishnakumar, and Qunfeng Dong
A web-based software system for dynamic gene cluster comparison across multiple genomes
Bioinformatics Advance Access published on February 9, 2009
Bioinformatics 2009 25: 956-957; doi:10.1093/bioinformatics/btp078 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Masumi Itoh and Hidemi Watanabe
CGAS: comparative genomic analysis server
Bioinformatics Advance Access published on February 13, 2009
Bioinformatics 2009 25: 958-959; doi:10.1093/bioinformatics/btp086 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Andrés Esteban-Marcos, Aaron E. Darling, and Mark A. Ragan
Seevolution: visualizing chromosome evolution
Bioinformatics Advance Access published on February 20, 2009
Bioinformatics 2009 25: 960-961; doi:10.1093/bioinformatics/btp096 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Andrew C. Stewart, Brian Osborne, and Timothy D. Read
DIYA: a bacterial annotation pipeline for any genomics lab
Bioinformatics Advance Access published on March 2, 2009
Bioinformatics 2009 25: 962-963; doi:10.1093/bioinformatics/btp097 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Lukas Käll, John D. Storey, and William Stafford Noble
QVALITY: non-parametric estimation of q-values and posterior error probabilities
Bioinformatics Advance Access published on February 4, 2009
Bioinformatics 2009 25: 964-966; doi:10.1093/bioinformatics/btp021 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Davide Campagna, Alessandro Albiero, Alessandra Bilardi, Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, and Giorgio Valle
PASS: a program to align short sequences
Bioinformatics Advance Access published on February 13, 2009
Bioinformatics 2009 25: 967-968; doi:10.1093/bioinformatics/btp087 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hugh L. Eaves and Yuan Gao
MOM: maximum oligonucleotide mapping
Bioinformatics Advance Access published on February 19, 2009
Bioinformatics 2009 25: 969-970; doi:10.1093/bioinformatics/btp092 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS Back

Laura S. Kubatko, Bryan C. Carstens, and L. Lacey Knowles
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
Bioinformatics Advance Access published on February 10, 2009
Bioinformatics 2009 25: 971-973; doi:10.1093/bioinformatics/btp079 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

David J. States, Alex S. Ade, Zachary C. Wright, Aaron V. Bookvich, and Brian D. Athey
MiSearch adaptive pubMed search tool
Bioinformatics Advance Access published on March 6, 2008
Bioinformatics 2009 25: 974-976; doi:10.1093/bioinformatics/btn033 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Georgios A. Pavlopoulos, Evangelos Pafilis, M. Kuhn, Sean D. Hooper, and Reinhard Schneider
OnTheFly: a tool for automated document-based text annotation, data linking and network generation
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 977-978; doi:10.1093/bioinformatics/btp081 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Joo Chuan Tong, Shen Jean Lim, Hon Cheng Muh, Fook Tim Chew, and Martti T. Tammi
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
Bioinformatics Advance Access published on February 11, 2009
Bioinformatics 2009 25: 979-980; doi:10.1093/bioinformatics/btp077 [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.