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Previous Next 		Contents: Volume 24, Number 24, 15 December 2008   [Index by Author] 
Down REVIEW
     GENOME ANALYSIS
Down DISCOVERY NOTE
     SYSTEMS BIOLOGY
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENETICS AND POPULATION ANALYSIS
     DATA AND TEXT MINING
Down CORRIGENDUM
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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

GENOME ANALYSIS Back

Christophe Pichon and Brice Felden
Small RNA gene identification and mRNA target predictions in bacteria
Bioinformatics Advance Access published on October 29, 2008
Bioinformatics 2008 24: 2807-2813; doi:10.1093/bioinformatics/btn560 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE Back

SYSTEMS BIOLOGY Back

Alexander E. Vinogradov
Modularity of cellular networks shows general center-periphery polarization
Bioinformatics Advance Access published on October 25, 2008
Bioinformatics 2008 24: 2814-2817; doi:10.1093/bioinformatics/btn555 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Jason R. Miller, Arthur L. Delcher, Sergey Koren, Eli Venter, Brian P. Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, and Granger Sutton
Aggressive assembly of pyrosequencing reads with mates
Bioinformatics Advance Access published on October 24, 2008
Bioinformatics 2008 24: 2818-2824; doi:10.1093/bioinformatics/btn548 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Yu Zhang
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
Bioinformatics Advance Access published on October 25, 2008
Bioinformatics 2008 24: 2825-2831; doi:10.1093/bioinformatics/btn549 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. R. Demey, J. L. Vicente-Villardón, M. P. Galindo-Villardón, and A. Y. Zambrano
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots
Bioinformatics Advance Access published on October 29, 2008
Bioinformatics 2008 24: 2832-2838; doi:10.1093/bioinformatics/btn552 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Paolo Ribeca and Emanuele Raineri
Faster exact Markovian probability functions for motif occurrences: a DFA-only approach
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2839-2848; doi:10.1093/bioinformatics/btn525 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics Advance Access published on October 21, 2008
Bioinformatics 2008 24: 2849-2856; doi:10.1093/bioinformatics/btn544 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren, and Kris Laukens
Prediction of kinase-specific phosphorylation sites using conditional random fields
Bioinformatics Advance Access published on October 20, 2008
Bioinformatics 2008 24: 2857-2864; doi:10.1093/bioinformatics/btn546 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

Andrew J. Bordner
Predicting small ligand binding sites in proteins using backbone structure
Bioinformatics Advance Access published on October 21, 2008
Bioinformatics 2008 24: 2865-2871; doi:10.1093/bioinformatics/btn543 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu
Integrated search and alignment of protein structures
Bioinformatics Advance Access published on October 22, 2008
Bioinformatics 2008 24: 2872-2879; doi:10.1093/bioinformatics/btn545 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Ronglai Shen, Jeremy M. G. Taylor, and Debashis Ghosh
Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model
Bioinformatics Advance Access published on October 14, 2008
Bioinformatics 2008 24: 2880-2886; doi:10.1093/bioinformatics/btn536 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Karen Kapur, Hui Jiang, Yi Xing, and Wing Hung Wong
Cross-hybridization modeling on Affymetrix exon arrays
Bioinformatics Advance Access published on November 4, 2008
Bioinformatics 2008 24: 2887-2893; doi:10.1093/bioinformatics/btn571 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Simon Rogers, Mark Girolami, Walter Kolch, Katrina M. Waters, Tao Liu, Brian Thrall, and H. Steven Wiley
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
Bioinformatics Advance Access published on October 30, 2008
Bioinformatics 2008 24: 2894-2900; doi:10.1093/bioinformatics/btn553 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Bärbel Finkenstädt, Elizabeth A. Heron, Michal Komorowski, Kieron Edwards, Sanyi Tang, Claire V. Harper, Julian R. E. Davis, Michael R. H. White, Andrew J. Millar, and David A. Rand
Reconstruction of transcriptional dynamics from gene reporter data using differential equations
Bioinformatics Advance Access published on October 30, 2008
Bioinformatics 2008 24: 2901-2907; doi:10.1093/bioinformatics/btn562 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATA AND TEXT MINING Back

Melanie Osl, Stephan Dreiseitl, Bernhard Pfeifer, Klaus Weinberger, Helmut Klocker, Georg Bartsch, Georg Schäfer, Bernhard Tilg, Armin Graber, and Christian Baumgartner
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry
Bioinformatics Advance Access published on September 24, 2008
Bioinformatics 2008 24: 2908-2914; doi:10.1093/bioinformatics/btn506 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Robert T. Morris, Timothy R. O'Connor, and John J. Wyrick
Osiris: an integrated promoter database for Oryza sativa L.
Bioinformatics Advance Access published on October 15, 2008
Bioinformatics 2008 24: 2915-2917; doi:10.1093/bioinformatics/btn537 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Matteo Cesaroni, Davide Cittaro, Alessandro Brozzi, Pier Giuseppe Pelicci, and Lucilla Luzi
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data
Bioinformatics Advance Access published on October 21, 2008
Bioinformatics 2008 24: 2918-2920; doi:10.1093/bioinformatics/btn542 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. M. Cairns, M. J. Dunning, M. E. Ritchie, R. Russell, and A. G. Lynch
BASH: a tool for managing BeadArray spatial artefacts
Bioinformatics Advance Access published on October 25, 2008
Bioinformatics 2008 24: 2921-2922; doi:10.1093/bioinformatics/btn557 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Jun Kong, Fei Zhu, Jim Stalker, and David J. Adams
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes
Bioinformatics Advance Access published on October 30, 2008
Bioinformatics 2008 24: 2923-2925; doi:10.1093/bioinformatics/btn541 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Leming Zhou, Ingrid Mihai, and Liliana Florea
Effective cluster-based seed design for cross-species sequence comparisons
Bioinformatics Advance Access published on October 20, 2008
Bioinformatics 2008 24: 2926-2927; doi:10.1093/bioinformatics/btn547 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Håkan Viklund, Andreas Bernsel, Marcin Skwark, and Arne Elofsson
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
Bioinformatics Advance Access published on October 22, 2008
Bioinformatics 2008 24: 2928-2929; doi:10.1093/bioinformatics/btn550 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Vinhthuy Phan and Nicholas A. Furlotte
Motif Tool Manager: a web-based framework for motif discovery
Bioinformatics Advance Access published on November 18, 2008
Bioinformatics 2008 24: 2930-2931; doi:10.1093/bioinformatics/btn559 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS Back

Jeffrey C. Oliver
AUGIST: inferring species trees while accommodating gene tree uncertainty
Bioinformatics Advance Access published on October 25, 2008
Bioinformatics 2008 24: 2932-2933; doi:10.1093/bioinformatics/btn556 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

Hui Kian Ho, Michael J. Kuiper, and Ramamohanarao Kotagiri
PConPy—a Python module for generating 2D protein maps
Bioinformatics Advance Access published on October 31, 2008
Bioinformatics 2008 24: 2934-2935; doi:10.1093/bioinformatics/btn566 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Matthew J. Jobin and Joanna L. Mountain
REJECTOR: software for population history inference from genetic data via a rejection algorithm
Bioinformatics Advance Access published on October 20, 2008
Bioinformatics 2008 24: 2936-2937; doi:10.1093/bioinformatics/btn540 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Andrew D. Johnson, Robert E. Handsaker, Sara L. Pulit, Marcia M. Nizzari, Christopher J. O'Donnell, and Paul I. W. de Bakker
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
Bioinformatics Advance Access published on October 30, 2008
Bioinformatics 2008 24: 2938-2939; doi:10.1093/bioinformatics/btn564 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING Back

Nigel Collier, Son Doan, Ai Kawazoe, Reiko Matsuda Goodwin, Mike Conway, Yoshio Tateno, Quoc-Hung Ngo, Dinh Dien, Asanee Kawtrakul, Koichi Takeuchi, Mika Shigematsu, and Kiyosu Taniguchi
BioCaster: detecting public health rumors with a Web-based text mining system
Bioinformatics Advance Access published on October 15, 2008
Bioinformatics 2008 24: 2940-2941; doi:10.1093/bioinformatics/btn534 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

CORRIGENDUM Back

Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, and Alejandro A. Schäffer
Database indexing for production MegaBLAST searches
Bioinformatics 2008 24: 2942; doi:10.1093/bioinformatics/btn554 [Extract] [Full Text] [Print PDF] [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.