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Previous Next 		Contents: Volume 25, Number 4, 15 February 2009   [Index by Author] 
Down REVIEW
     DATA AND TEXT MINING
Down EDITORIAL
Down DISCOVERY NOTE
     GENE EXPRESSION
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     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.

REVIEW Back

DATA AND TEXT MINING Back

Robert Guralnick and Andrew Hill
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 421-428; doi:10.1093/bioinformatics/btn659 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

EDITORIAL Back

Alex Bateman and John Quackenbush
Editorial
Bioinformatics Advance Access published on February 8, 2009
Bioinformatics 2009 25: 429; doi:10.1093/bioinformatics/btp037 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE Back

GENE EXPRESSION Back

Fuxiao Xin, Meng Li, Curt Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, and Kenneth P. Nephew
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance
Bioinformatics Advance Access published on December 17, 2008
Bioinformatics 2009 25: 430-434; doi:10.1093/bioinformatics/btn646 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, and Stefan A. Haas
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Bioinformatics Advance Access published on December 9, 2008
Bioinformatics 2009 25: 435-442; doi:10.1093/bioinformatics/btn627 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Norman E. Davey, Denis C. Shields, and Richard J. Edwards
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
Bioinformatics Advance Access published on January 9, 2009
Bioinformatics 2009 25: 443-450; doi:10.1093/bioinformatics/btn664 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Tala M. Bakheet and Andrew J. Doig
Properties and identification of human protein drug targets
Bioinformatics Advance Access published on January 21, 2009
Bioinformatics 2009 25: 451-457; doi:10.1093/bioinformatics/btp002 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

René L. Warren, Brad H. Nelson, and Robert A. Holt
Profiling model T-cell metagenomes with short reads
Bioinformatics Advance Access published on January 9, 2009
Bioinformatics 2009 25: 458-464; doi:10.1093/bioinformatics/btp010 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, and Kiyoshi Asai
Prediction of RNA secondary structure using generalized centroid estimators
Bioinformatics Advance Access published on December 18, 2008
Bioinformatics 2009 25: 465-473; doi:10.1093/bioinformatics/btn601 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Dirk Stratmann, Carine van Heijenoort, and Eric Guittet
NOEnet–Use of NOE networks for NMR resonance assignment of proteins with known 3D structure
Bioinformatics Advance Access published on December 12, 2008
Bioinformatics 2009 25: 474-481; doi:10.1093/bioinformatics/btn638 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

Daniel M. Gatti, Andrey A. Shabalin, Tieu-Chong Lam, Fred A. Wright, Ivan Rusyn, and Andrew B. Nobel
FastMap: Fast eQTL mapping in homozygous populations
Bioinformatics Advance Access published on December 17, 2008
Bioinformatics 2009 25: 482-489; doi:10.1093/bioinformatics/btn648 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, and Tom Michoel
Module networks revisited: computational assessment and prioritization of model predictions
Bioinformatics Advance Access published on January 9, 2009
Bioinformatics 2009 25: 490-496; doi:10.1093/bioinformatics/btn658 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Mingyao Li, Kai Wang, Struan F. A. Grant, Hakon Hakonarson, and Chun Li
ATOM: a powerful gene-based association test by combining optimally weighted markers
Bioinformatics Advance Access published on December 15, 2008
Bioinformatics 2009 25: 497-503; doi:10.1093/bioinformatics/btn641 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Can Yang, Zengyou He, Xiang Wan, Qiang Yang, Hong Xue, and Weichuan Yu
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies
Bioinformatics Advance Access published on December 19, 2008
Bioinformatics 2009 25: 504-511; doi:10.1093/bioinformatics/btn652 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Simon Rogers, Richard A. Scheltema, Mark Girolami, and Rainer Breitling
Probabilistic assignment of formulas to mass peaks in metabolomics experiments
Bioinformatics Advance Access published on December 18, 2008
Bioinformatics 2009 25: 512-518; doi:10.1093/bioinformatics/btn642 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Oliver Kotte and Matthias Heinemann
A divide-and-conquer approach to analyze underdetermined biochemical models
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 519-525; doi:10.1093/bioinformatics/btp004 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Bai Zhang, Huai Li, Rebecca B. Riggins, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, and Yue Wang
Differential dependency network analysis to identify condition-specific topological changes in biological networks
Bioinformatics Advance Access published on December 26, 2008
Bioinformatics 2009 25: 526-532; doi:10.1093/bioinformatics/btn660 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Sascha Steinbiss, Gordon Gremme, Christin Schärfer, Malte Mader, and Stefan Kurtz
AnnotationSketch: a genome annotation drawing library
Bioinformatics Advance Access published on December 23, 2008
Bioinformatics 2009 25: 533-534; doi:10.1093/bioinformatics/btn657 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Michael S. Barker, Katrina M. Dlugosch, A. Chaitanya C. Reddy, Sarah N. Amyotte, and Loren H. Rieseberg
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 535-536; doi:10.1093/bioinformatics/btp011 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

PHYLOGENETICS Back

Jeremy M. Brown and Robert ElDabaje
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
Bioinformatics Advance Access published on December 19, 2008
Bioinformatics 2009 25: 537-538; doi:10.1093/bioinformatics/btn651 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Benjamin M. Bulheller and Jonathan D. Hirst
DichroCalc—circular and linear dichroism online
Bioinformatics Advance Access published on January 7, 2009
Bioinformatics 2009 25: 539-540; doi:10.1093/bioinformatics/btp016 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn, Fred A. Wright, and William T. Barry
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy
Bioinformatics Advance Access published on December 19, 2008
Bioinformatics 2009 25: 541-542; doi:10.1093/bioinformatics/btn655 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Ryosuke R. Ishiwata, Masaki S. Morioka, Soichi Ogishima, and Hiroshi Tanaka
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 543-544; doi:10.1093/bioinformatics/btp008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Qihao Qi, Yingdong Zhao, MingChung Li, and Richard Simon
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools
Bioinformatics Advance Access published on January 8, 2009
Bioinformatics 2009 25: 545-547; doi:10.1093/bioinformatics/btp009 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

E. Ryder, H. Spriggs, E. Drummond, D. St Johnston, and S. Russell
The Flannotator—a gene and protein expression annotation tool for Drosophila melanogaster
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 548-549; doi:10.1093/bioinformatics/btp012 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers, and Sacha A. F. T. van Hijum
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data
Bioinformatics Advance Access published on January 25, 2009
Bioinformatics 2009 25: 550-551; doi:10.1093/bioinformatics/btp013 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Gilles Guillot and Matthieu Foll
Correcting for ascertainment bias in the inference of population structure
Bioinformatics Advance Access published on January 9, 2009
Bioinformatics 2009 25: 552-554; doi:10.1093/bioinformatics/btn665 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Uma Mudunuri, Anney Che, Ming Yi, and Robert M. Stephens
bioDBnet: the biological database network
Bioinformatics Advance Access published on January 7, 2009
Bioinformatics 2009 25: 555-556; doi:10.1093/bioinformatics/btn654 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jeff Heard, William Kaufmann, and Xiaojun Guan
A novel method for large tree visualization
Bioinformatics Advance Access published on January 7, 2009
Bioinformatics 2009 25: 557-558; doi:10.1093/bioinformatics/btn656 [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.