Bioinformatics

EDITORIALS:

Werner Mewes

German Conference on Bioinformatics 2003 (GCB'03)
Bioinformatics 2004 20: 1481; doi:10.1093/bioinformatics/bth353 [Print PDF][Screen PDF] [Request Permissions]  

GCB CONFERENCE PAPERS:

Peter F. Arndt and Terence Hwa

Regional and time-resolved mutation patterns of the human genome
Bioinformatics 2004 20: 1482-1485; doi:10.1093/bioinformatics/bth105 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, and Michael Schroeder

Using convex hulls to extract interaction interfaces from known structures
Bioinformatics 2004 20: 1486-1490; doi:10.1093/bioinformatics/bth106 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Flöter, J. Nicolas, T. Schaub, and J. Selbig

Threshold extraction in metabolite concentration data
Bioinformatics 2004 20: 1491-1494; doi:10.1093/bioinformatics/bth107 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

I.L. Hofacker, P.F. Stadler, and R.R. Stocsits

Conserved RNA secondary structures in viral genomes: a survey
Bioinformatics 2004 20: 1495-1499; doi:10.1093/bioinformatics/bth108 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Rainer König and Roland Eils

Gene expression analysis on biochemical networks using the Potts spin model
Bioinformatics 2004 20: 1500-1505; doi:10.1093/bioinformatics/bth109 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Maciej Swat, Alexander Kel, and Hanspeter Herzel

Bifurcation analysis of the regulatory modules of the mammalian G₁/S transition
Bioinformatics 2004 20: 1506-1511; doi:10.1093/bioinformatics/bth110 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Kel, Y. Tikunov, N. Voss, and E. Wingender

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
Bioinformatics 2004 20: 1512-1516; doi:10.1093/bioinformatics/bth111 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Florian Sohler, Daniel Hanisch, and Ralf Zimmer

New methods for joint analysis of biological networks and expression data
Bioinformatics 2004 20: 1517-1521; doi:10.1093/bioinformatics/bth112 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, and Gerhard Klebe

Efficient similarity search in protein structure databases by k-clique hashing
Bioinformatics 2004 20: 1522-1526; doi:10.1093/bioinformatics/bth113 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Michael C. Wendl and Shiaw-Pyng Yang

Gap statistics for whole genome shotgun DNA sequencing projects
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1527-1534; doi:10.1093/bioinformatics/bth120 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Fazel Famili, Ganming Liu, and Ziying Liu

Evaluation and optimization of clustering in gene expression data analysis
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1535-1545; doi:10.1093/bioinformatics/bth124 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Catherine Grasso and Christopher Lee

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1546-1556; doi:10.1093/bioinformatics/bth126 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shane T. Jensen and Jun S. Liu

BioOptimizer: a Bayesian scoring function approach to motif discovery
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1557-1564; doi:10.1093/bioinformatics/bth127 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

John P. Dekker, Anthony Fodor, Richard W. Aldrich, and Gary Yellen

A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1565-1572; doi:10.1093/bioinformatics/bth128 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Björn Voss, Carsten Meyer, and Robert Giegerich

Evaluating the predictability of conformational switching in RNA
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1573-1582; doi:10.1093/bioinformatics/bth129 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrew Jones, Ela Hunt, Jonathan M. Wastling, Angel Pizarro, and Christian J. Stoeckert, Jr

An object model and database for functional genomics
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 1583-1590; doi:10.1093/bioinformatics/bth130 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yongmei Ji, Xing Xu, and Gary D. Stormo

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1591-1602; doi:10.1093/bioinformatics/bth131 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gavin E. Crooks and Steven E. Brenner

Protein secondary structure: entropy, correlations and prediction
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1603-1611; doi:10.1093/bioinformatics/bth132 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Rui Kuang, Christina S. Leslie, and An-Suei Yang

Protein backbone angle prediction with machine learning approaches
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1612-1621; doi:10.1093/bioinformatics/bth136 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alice C. McHardy, Alexander Goesmann, Alfred Pühler, and Folker Meyer

Development of joint application strategies for two microbial gene finders
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1622-1631; doi:10.1093/bioinformatics/bth137 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

DISCOVERY NOTES:

Aubrey Hill and Eric Sorscher

Common structural patterns in human genes
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1632-1635; doi:10.1093/bioinformatics/bth134 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Thomas Mailund and Christian N. S. Pedersen

QDist—quartet distance between evolutionary trees
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1636-1637; doi:10.1093/bioinformatics/bth097 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Leping Li, David M. Umbach, Paul Terry, and Jack A. Taylor

Application of the GA/KNN method to SELDI proteomics data
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1638-1640; doi:10.1093/bioinformatics/bth098 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

G. Golfier, M. Tran Dang, L. Dauphinot, E. Graison, J. Rossier, and M.-C. Potier

VARAN: a web server for Variability Analysis of DNA microarray experiments
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1641-1643; doi:10.1093/bioinformatics/bth117 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Simon N. Jarman

Amplicon: software for designing PCR primers on aligned DNA sequences
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1644-1645; doi:10.1093/bioinformatics/bth121 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, and Akihiko Konagaya

OBIYagns: a grid-based biochemical simulator with a parameter estimator
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1646-1648; doi:10.1093/bioinformatics/bth122 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

John Boyle

SeqExpress: desktop analysis and visualization tool for gene expression experiments
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1649-1650; doi:10.1093/bioinformatics/bth123 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wolfgang Huber and Robert Gentleman

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1651-1652; doi:10.1093/bioinformatics/bth133 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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