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Previous Next 		Contents: Volume 24, Number 21, 1 November 2008   [Index by Author] 
Down DISCOVERY NOTES
     SEQUENCE ANALYSIS
Down ORIGINAL PAPERS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     PHYLOGENETICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down LETTERS TO THE EDITOR
     GENE EXPRESSION
     SYSTEMS BIOLOGY
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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 NOTES Back

SEQUENCE ANALYSIS Back

Robson Francisco de Souza, Vivek Anantharaman, Sandro José de Souza, L. Aravind, and Frederico J. Gueiros-Filho
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2423-2426; doi:10.1093/bioinformatics/btn449 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

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 Back

SEQUENCE ANALYSIS Back

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]  

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]  

Sriram Sankararaman and Kimmen Sjölander
INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification
Bioinformatics Advance Access published on September 6, 2008
Bioinformatics 2008 24: 2445-2452; doi:10.1093/bioinformatics/btn474 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

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]  

Mirabela Rusu, Stefan Birmanns, and Willy Wriggers
Biomolecular pleiomorphism probed by spatial interpolation of coarse models
Bioinformatics Advance Access published on August 30, 2008
Bioinformatics 2008 24: 2460-2466; doi:10.1093/bioinformatics/btn461 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

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]  

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]  

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]  

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 Back

Zachary A. Szpiech, Mattias Jakobsson, and Noah A. Rosenberg
ADZE: a rarefaction approach for counting alleles private to combinations of populations
Bioinformatics Advance Access published on September 8, 2008
Bioinformatics 2008 24: 2498-2504; doi:10.1093/bioinformatics/btn478 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

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 Back

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]  

Justin Klekota and Frederick P. Roth
Chemical substructures that enrich for biological activity
Bioinformatics Advance Access published on September 10, 2008
Bioinformatics 2008 24: 2518-2525; doi:10.1093/bioinformatics/btn479 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

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 Back

GENOME ANALYSIS Back

Darren Kessner, Matt Chambers, Robert Burke, David Agus, and Parag Mallick
ProteoWizard: open source software for rapid proteomics tools development
Bioinformatics Advance Access published on July 7, 2008
Bioinformatics 2008 24: 2534-2536; doi:10.1093/bioinformatics/btn323 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Alan P. Boyle, Justin Guinney, Gregory E. Crawford, and Terrence S. Furey
F-Seq: a feature density estimator for high-throughput sequence tags
Bioinformatics Advance Access published on September 10, 2008
Bioinformatics 2008 24: 2537-2538; doi:10.1093/bioinformatics/btn480 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

PHYLOGENETICS Back

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]  

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 Back

Denis C. Bauer and Timothy L. Bailey
STREAM: Static Thermodynamic REgulAtory Model of transcription
Bioinformatics Advance Access published on September 6, 2008
Bioinformatics 2008 24: 2544-2545; doi:10.1093/bioinformatics/btn467 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Dorothea Emig, Melissa S. Cline, Thomas Lengauer, and Mario Albrecht
Integrating expression data with domain interaction networks
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2546-2548; doi:10.1093/bioinformatics/btn437 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

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]  

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]  

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]  

Tian Xia and Julie A. Dickerson
OmicsViz: Cytoscape plug-in for visualizing omics data across species
Bioinformatics Advance Access published on September 8, 2008
Bioinformatics 2008 24: 2557-2558; doi:10.1093/bioinformatics/btn473 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATA AND TEXT MINING Back

Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou
FACTA: a text search engine for finding associated biomedical concepts
Bioinformatics Advance Access published on September 4, 2008
Bioinformatics 2008 24: 2559-2560; doi:10.1093/bioinformatics/btn469 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

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]  

C. Nelson Hayes, Diego Diez, Nicolas Joannin, Wataru Honda, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, and Susumu Goto
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
Bioinformatics Advance Access published on September 6, 2008
Bioinformatics 2008 24: 2564-2565; doi:10.1093/bioinformatics/btn477 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

LETTERS TO THE EDITOR Back

GENE EXPRESSION Back

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 Back

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]  

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.