Bioinformatics

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract K. Cartharius, K. Frech, K. Grote, B. Klocke, M. Haltmeier, A. Klingenhoff, M. Frisch, M. Bayerlein, and T. Werner

MatInspector and beyond: promoter analysis based on transcription factor binding sites
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 2933-2942; doi:10.1093/bioinformatics/bti473 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract G. D'Avenio, M. Grigioni, G. Orefici, and R. Creti

SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 2943-2949; doi:10.1093/bioinformatics/bti468 [Abstract] [Full Text] [Print PDF] [supplementary data] [Request Permissions]  

Get checked abstract Milana Frenkel-Morgenstern, Hillary Voet, and Shmuel Pietrokovski

Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure
Bioinformatics Advance Access published on May 3, 2005
Bioinformatics 2005 21: 2950-2956; doi:10.1093/bioinformatics/bti462 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Mark DeLong, Guang Yao, Quanli Wang, Adrian Dobra, Esther P. Black, Jeffrey T. Chang, Andrea Bild, Mike West, Joseph R. Nevins, and Holly Dressman

DIG—a system for gene annotation and functional discovery
Bioinformatics Advance Access published on May 3, 2005
Bioinformatics 2005 21: 2957-2959; doi:10.1093/bioinformatics/bti467 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Marco Punta and Burkhard Rost

PROFcon: novel prediction of long-range contacts
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 2960-2968; doi:10.1093/bioinformatics/bti454 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kai Wang and Ram Samudrala

FSSA: a novel method for identifying functional signatures from structural alignments
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 2969-2977; doi:10.1093/bioinformatics/bti471 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Lee-Wei Yang, Xiong Liu, Christopher J. Jursa, Mark Holliman, A.J. Rader, Hassan A. Karimi, and Ivet Bahar

iGNM: a database of protein functional motions based on Gaussian Network Model
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 2978-2987; doi:10.1093/bioinformatics/bti469 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Fátima Al-Shahrour, Ramón Díaz-Uriarte, and Joaquín Dopazo

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 2988-2993; doi:10.1093/bioinformatics/bti457 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Omer Demirkaya, Musa H. Asyali, and Mohamed M. Shoukri

Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 2994-3000; doi:10.1093/bioinformatics/bti455 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jiang Gui and Hongzhe Li

Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 3001-3008; doi:10.1093/bioinformatics/bti422 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yulan Liang, Bamidele Tayo, Xueya Cai, and Arpad Kelemen

Differential and trajectory methods for time course gene expression data
Bioinformatics Advance Access published on May 10, 2005
Bioinformatics 2005 21: 3009-3016; doi:10.1093/bioinformatics/bti465 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, and Alexander Ploner

False discovery rate, sensitivity and sample size for microarray studies
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 3017-3024; doi:10.1093/bioinformatics/bti448 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrew E. Teschendorff, Yanzhong Wang, Nuno L. Barbosa-Morais, James D. Brenton, and Carlos Caldas

A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 3025-3033; doi:10.1093/bioinformatics/bti466 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Vladimir N. Minin, Karin S. Dorman, Fang Fang, and Marc A. Suchard

Dual multiple change-point model leads to more accurate recombination detection
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3034-3042; doi:10.1093/bioinformatics/bti459 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Age K. Smilde, Jeroen J. Jansen, Huub C. J. Hoefsloot, Robert-Jan A. N. Lamers, Jan van der Greef, and Marieke E. Timmerman

ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3043-3048; doi:10.1093/bioinformatics/bti476 [Abstract] [Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Dequan Li, Yan Fu, Ruixiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Simin He, and Wen Gao

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 3049-3050; doi:10.1093/bioinformatics/bti439 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Grégory Nuel

S-SPatt: simple statistics for patterns on Markov chains
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 3051-3052; doi:10.1093/bioinformatics/bti451 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract M. W. J. van Passel, A. C. M. Luyf, A. H. C. van Kampen, A. Bart, and A. van der Ende

-Web, an online tool to assess composition similarity of individual nucleic acid sequences
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 3053-3055; doi:10.1093/bioinformatics/bti460 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Jeng-Sheng Yeh, Ding-Yun Chen, Bing-Yu Chen, and Ming Ouhyoung

A web-based three-dimensional protein retrieval system by matching visual similarity
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 3056-3057; doi:10.1093/bioinformatics/bti458 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ian John Donaldson, Michael Chapman, and Berthold Göttgens

TFBScluster: a resource for the characterization of transcriptional regulatory networks
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 3058-3059; doi:10.1093/bioinformatics/bti461 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Emily L. Webb, Gabrielle S. Sellick, and Richard S. Houlston

SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 3060-3061; doi:10.1093/bioinformatics/bti449 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 3062; doi:10.1093/bioinformatics/bti510 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 3063; doi:10.1093/bioinformatics/bti518 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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