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Previous Next 		Contents: Volume 22, Number 22, 15 November 2006   [Index by Author] 
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
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DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Mensur Dlakic
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2711-2714; doi:10.1093/bioinformatics/btl468 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Usman Roshan and Dennis R. Livesay
Probalign: multiple sequence alignment using partition function posterior probabilities
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2715-2721; doi:10.1093/bioinformatics/btl472 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xudong Xie, Shuanhu Wu, Kin-Man Lam, and Hong Yan
PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
Bioinformatics Advance Access published on September 25, 2006
Bioinformatics 2006 22: 2722-2728; doi:10.1093/bioinformatics/btl482 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

E. Capriotti, R. Calabrese, and R. Casadio
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2729-2734; doi:10.1093/bioinformatics/btl423 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, and Mark Gerstein
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
Bioinformatics Advance Access published on October 23, 2006
Bioinformatics 2006 22: 2735-2738; doi:10.1093/bioinformatics/btl274 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

J. E. Eckel-Passow, A. L. Oberg, T. M. Therneau, C. J. Mason, D. W. Mahoney, K. L. Johnson, J. E. Olson, and H. R. Bergen, III
Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2739-2745; doi:10.1093/bioinformatics/btl464 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

N. Morozova, J. Allers, J. Myers, and Y. Shamoo
Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2746-2752; doi:10.1093/bioinformatics/btl470 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Darrin P. Lewis, Tony Jebara, and William Stafford Noble
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2753-2760; doi:10.1093/bioinformatics/btl475 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stewart T. Chang, Debashis Ghosh, Denise E. Kirschner, and Jennifer J. Linderman
Peptide length-based prediction of peptide–MHC class II binding
Bioinformatics Advance Access published on September 25, 2006
Bioinformatics 2006 22: 2761-2767; doi:10.1093/bioinformatics/btl479 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yong Zhao, Daniel Stoffler, and Michel Sanner
Hierarchical and multi-resolution representation of protein flexibility
Bioinformatics Advance Access published on September 18, 2006
Bioinformatics 2006 22: 2768-2774; doi:10.1093/bioinformatics/btl481 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Guido Sanguinetti, Neil D. Lawrence, and Magnus Rattray
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2775-2781; doi:10.1093/bioinformatics/btl473 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Mark Griffith, Tod Courtney, Jean Peccoud, and William H. Sanders
Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2782-2789; doi:10.1093/bioinformatics/btl465 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Matthias Heinemann and Sven Panke
Synthetic biology—putting engineering into biology
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2790-2799; doi:10.1093/bioinformatics/btl469 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jianzhen Xu and Yongjin Li
Discovering disease-genes by topological features in human protein–protein interaction network
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2800-2805; doi:10.1093/bioinformatics/btl467 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Vitaly A. Selivanov, Silvia Marin, Paul W. N. Lee, and Marta Cascante
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
Bioinformatics Advance Access published on September 25, 2006
Bioinformatics 2006 22: 2806-2812; doi:10.1093/bioinformatics/btl484 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Wei Zhou, Vetle I. Torvik, and Neil R. Smalheiser
ADAM: another database of abbreviations in MEDLINE
Bioinformatics Advance Access published on September 18, 2006
Bioinformatics 2006 22: 2813-2818; doi:10.1093/bioinformatics/btl480 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTE:

SEQUENCE ANALYSIS:

A. Billion, R. Ghai, T. Chakraborty, and T. Hain
Augur—a computational pipeline for whole genome microbial surface protein prediction and classification
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2819-2820; doi:10.1093/bioinformatics/btl466 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Mario A. Fares and David McNally
CAPS: coevolution analysis using protein sequences
Bioinformatics Advance Access published on September 27, 2006
Bioinformatics 2006 22: 2821-2822; doi:10.1093/bioinformatics/btl493 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Luke Sheneman, Jason Evans, and James A. Foster
Clearcut: a fast implementation of relaxed neighbor joining
Bioinformatics Advance Access published on September 18, 2006
Bioinformatics 2006 22: 2823-2824; doi:10.1093/bioinformatics/btl478 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, and Joanne Chory
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
Bioinformatics Advance Access published on September 18, 2006
Bioinformatics 2006 22: 2825-2827; doi:10.1093/bioinformatics/btl476 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Torsten Hothorn and Peter Bühlmann
Model-based boosting in high dimensions
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2828-2829; doi:10.1093/bioinformatics/btl462 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Brendan MacLean, Jimmy K. Eng, Ronald C. Beavis, and Martin McIntosh
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2830-2832; doi:10.1093/bioinformatics/btl379 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Lei Zhang and Daiwen Yang
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2833-2834; doi:10.1093/bioinformatics/btl477 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Eric J. Vallender, Justin E. Paschall, Christine M. Malcom, Bruce T. Lahn, and Gerald J. Wyckoff
SPEED: a molecular-evolution-based database of mammalian orthologous groups
Bioinformatics Advance Access published on September 11, 2006
Bioinformatics 2006 22: 2835-2837; doi:10.1093/bioinformatics/btl471 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kris Laukens, Rune Matthiesen, Filip Lemière, Eddy Esmans, Harry Van Onckelen, Ole Nørregaard Jensen, and Erwin Witters
Integration of gel-based proteome data with pProRep
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2838-2840; doi:10.1093/bioinformatics/btl487 [Abstract] [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.