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Previous Next 		Contents: Volume 24, Number 4, 15 February 2008   [Index by Author] 
       DISCOVERY NOTES
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                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:

SEQUENCE ANALYSIS:

Sushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, and Toby J. Gibson
Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation
Bioinformatics Advance Access published on January 9, 2008
Bioinformatics 2008 24: 453-457; doi:10.1093/bioinformatics/btm624 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Saraswathi Abhiman, Lakshminarayan M. Iyer, and L. Aravind
BEN: a novel domain in chromatin factors and DNA viral proteins
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 458-461; doi:10.1093/bioinformatics/btn007 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

James Robert White, Michael Roberts, James A. Yorke, and Mihai Pop
Figaro: a novel statistical method for vector sequence removal
Bioinformatics Advance Access published on January 17, 2008
Bioinformatics 2008 24: 462-467; doi:10.1093/bioinformatics/btm632 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Xuehui Li, Tamer Kahveci, and A. Mark Settles
A novel genome-scale repeat finder geared towards transposons
Bioinformatics Advance Access published on December 18, 2007
Bioinformatics 2008 24: 468-476; doi:10.1093/bioinformatics/btm613 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, and Yoram Louzoun
Precise score for the prediction of peptides cleaved by the proteasome
Bioinformatics Advance Access published on January 23, 2008
Bioinformatics 2008 24: 477-483; doi:10.1093/bioinformatics/btm616 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Sumedha Gunewardena and Zhaolei Zhang
A hybrid model for robust detection of transcription factor binding sites
Bioinformatics Advance Access published on January 9, 2008
Bioinformatics 2008 24: 484-491; doi:10.1093/bioinformatics/btm629 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Walter Pirovano, K. Anton Feenstra, and Jaap Heringa
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins
Bioinformatics Advance Access published on January 2, 2008
Bioinformatics 2008 24: 492-497; doi:10.1093/bioinformatics/btm636 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Rotem Rubinstein and Andras Fiser
Predicting disulfide bond connectivity in proteins by correlated mutations analysis
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 498-504; doi:10.1093/bioinformatics/btm637 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yu-Chieh Liao, Min-Shi Lee, Chin-Yu Ko, and Chao A. Hsiung
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 505-512; doi:10.1093/bioinformatics/btm638 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Arlo Randall, Jianlin Cheng, Michael Sweredoski, and Pierre Baldi
TMBpro: secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 513-520; doi:10.1093/bioinformatics/btm548 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Konrad Hinsen
Structural flexibility in proteins: impact of the crystal environment
Bioinformatics Advance Access published on December 18, 2007
Bioinformatics 2008 24: 521-528; doi:10.1093/bioinformatics/btm625 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Jeffrey S. Morris, Brittan N. Clark, and Howard B. Gutstein
Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
Bioinformatics Advance Access published on January 14, 2008
Bioinformatics 2008 24: 529-536; doi:10.1093/bioinformatics/btm590 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Jelle J. Goeman and Ulrich Mansmann
Multiple testing on the directed acyclic graph of gene ontology
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 537-544; doi:10.1093/bioinformatics/btm628 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Debayan Datta and Hongyu Zhao
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae
Bioinformatics Advance Access published on November 7, 2007
Bioinformatics 2008 24: 545-552; doi:10.1093/bioinformatics/btm523 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hao Xiong and Yoonsuck Choe
Structural systems identification of genetic regulatory networks
Bioinformatics Advance Access published on January 5, 2008
Bioinformatics 2008 24: 553-560; doi:10.1093/bioinformatics/btm623 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Vasyl Pihur, Somnath Datta, and Susmita Datta
Reconstruction of genetic association networks from microarray data: a partial least squares approach
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 561-568; doi:10.1093/bioinformatics/btm640 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Yuntao Qian and Robert F. Murphy
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models
Bioinformatics Advance Access published on November 22, 2007
Bioinformatics 2008 24: 569-576; doi:10.1093/bioinformatics/btm561 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Niranjan Nagarajan and Uri Keich
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments
Bioinformatics Advance Access published on January 6, 2008
Bioinformatics 2008 24: 577-578; doi:10.1093/bioinformatics/btm594 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Yuri R. Bendaña and Ian H. Holmes
Colorstock, SScolor, Ratón: RNA alignment visualization tools
Bioinformatics Advance Access published on January 24, 2008
Bioinformatics 2008 24: 579-580; doi:10.1093/bioinformatics/btm635 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Johan A.A. Nylander, James C. Wilgenbusch, Dan L. Warren, and David L. Swofford
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
Bioinformatics Advance Access published on August 30, 2007
Bioinformatics 2008 24: 581-583; doi:10.1093/bioinformatics/btm388 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Dominik Gront and Andrzej Kolinski
Utility library for structural bioinformatics
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 584-585; doi:10.1093/bioinformatics/btm627 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Liam J. McGuffin
The ModFOLD server for the quality assessment of protein structural models
Bioinformatics Advance Access published on January 9, 2008
Bioinformatics 2008 24: 586-587; doi:10.1093/bioinformatics/btn014 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Priit Adler, Jüri Reimand, Jürgen Jänes, Raivo Kolde, Hedi Peterson, and Jaak Vilo
KEGGanim: pathway animations for high-throughput data
Bioinformatics Advance Access published on December 1, 2007
Bioinformatics 2008 24: 588-590; doi:10.1093/bioinformatics/btm581 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin, and Henner Sudek
DECOMP—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Bioinformatics Advance Access published on January 2, 2008
Bioinformatics 2008 24: 591-593; doi:10.1093/bioinformatics/btm631 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Maxim Kalaev, Mike Smoot, Trey Ideker, and Roded Sharan
NetworkBLAST: comparative analysis of protein networks
Bioinformatics Advance Access published on January 2, 2008
Bioinformatics 2008 24: 594-596; doi:10.1093/bioinformatics/btm630 [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.