Bioinformatics

DISCOVERY NOTES

SEQUENCE ANALYSIS

Get checked abstract Fanny Jadeau, Emmanuelle Bechet, Alain J. Cozzone, Gilbert Deléage, Christophe Grangeasse, and Christophe Combet

Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature
Bioinformatics Advance Access published on September 3, 2008
Bioinformatics 2008 24: 2427-2430; doi:10.1093/bioinformatics/btn462 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

SEQUENCE ANALYSIS

Get checked abstract Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, and Ming Li

ZOOM! Zillions of oligos mapped
Bioinformatics Advance Access published on August 6, 2008
Bioinformatics 2008 24: 2431-2437; doi:10.1093/bioinformatics/btn416 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Osamu Gotoh

Direct mapping and alignment of protein sequences onto genomic sequence
Bioinformatics Advance Access published on August 26, 2008
Bioinformatics 2008 24: 2438-2444; doi:10.1093/bioinformatics/btn460 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and Kevin Karplus

PREDICT-2ND: a tool for generalized protein local structure prediction
Bioinformatics Advance Access published on August 30, 2008
Bioinformatics 2008 24: 2453-2459; doi:10.1093/bioinformatics/btn438 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Chang-Tsun Li, Yinyin Yuan, and Roland Wilson

An unsupervised conditional random fields approach for clustering gene expression time series
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2467-2473; doi:10.1093/bioinformatics/btn375 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Xi Chen, Lily Wang, Jonathan D. Smith, and Bing Zhang

Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
Bioinformatics Advance Access published on August 27, 2008
Bioinformatics 2008 24: 2474-2481; doi:10.1093/bioinformatics/btn458 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Elissa J. Cosgrove, Yingchun Zhou, Timothy S. Gardner, and Eric D. Kolaczyk

Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia
Bioinformatics Advance Access published on September 8, 2008
Bioinformatics 2008 24: 2482-2490; doi:10.1093/bioinformatics/btn476 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Antonio Reverter and Eva K. F. Chan

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
Bioinformatics Advance Access published on September 10, 2008
Bioinformatics 2008 24: 2491-2497; doi:10.1093/bioinformatics/btn482 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

SYSTEMS BIOLOGY

Get checked abstract Gautam Goel, I-Chun Chou, and Eberhard O. Voit

System estimation from metabolic time-series data
Bioinformatics Advance Access published on September 4, 2008
Bioinformatics 2008 24: 2505-2511; doi:10.1093/bioinformatics/btn470 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner, and Paul Lu

Improving subcellular localization prediction using text classification and the gene ontology
Bioinformatics Advance Access published on August 26, 2008
Bioinformatics 2008 24: 2512-2517; doi:10.1093/bioinformatics/btn463 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, and Zehra Meral Ozsoyoglu

PathCase: pathways database system
Bioinformatics Advance Access published on August 26, 2008
Bioinformatics 2008 24: 2526-2533; doi:10.1093/bioinformatics/btn459 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

GENOME ANALYSIS

PHYLOGENETICS

Get checked abstract Salvador Ramírez-Flandes and Osvaldo Ulloa

Bosque: integrated phylogenetic analysis software
Bioinformatics Advance Access published on September 1, 2008
Bioinformatics 2008 24: 2539-2541; doi:10.1093/bioinformatics/btn466 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Liang Liu

BEST: Bayesian estimation of species trees under the coalescent model
Bioinformatics Advance Access published on September 17, 2008
Bioinformatics 2008 24: 2542-2543; doi:10.1093/bioinformatics/btn484 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

SYSTEMS BIOLOGY

Get checked abstract Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, and F. Markowetz

Analyzing gene perturbation screens with nested effects models in R and bioconductor
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2549-2550; doi:10.1093/bioinformatics/btn446 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, and Yiannis N. Kaznessis

SynBioSS: the synthetic biology modeling suite
Bioinformatics Advance Access published on August 30, 2008
Bioinformatics 2008 24: 2551-2553; doi:10.1093/bioinformatics/btn468 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Guillermo Rodrigo, Javier Carrera, Kristala Jones Prather, and Alfonso Jaramillo

DESHARKY: automatic design of metabolic pathways for optimal cell growth
Bioinformatics Advance Access published on September 5, 2008
Bioinformatics 2008 24: 2554-2556; doi:10.1093/bioinformatics/btn471 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

DATABASES AND ONTOLOGIES

Get checked abstract Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, and Youping Deng

GOfetcher: a database with complex searching facility for gene ontology
Bioinformatics Advance Access published on August 26, 2008
Bioinformatics 2008 24: 2561-2563; doi:10.1093/bioinformatics/btn441 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTERS TO THE EDITOR

GENE EXPRESSION

Get checked abstract Harald Binder and Martin Schumacher

Comment on ‘network-constrained regularization and variable selection for analysis of genomic data’
Bioinformatics Advance Access published on August 4, 2008
Bioinformatics 2008 24: 2566-2568; doi:10.1093/bioinformatics/btn412 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Caiyan Li and Hongzhe Li

In Response to Comment on ‘Network-constrained regularization and variable selection for analysis of genomic data’
Bioinformatics Advance Access published on September 11, 2008
Bioinformatics 2008 24: 2569; doi:10.1093/bioinformatics/btn485 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

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