Bioinformatics

PAG MEETING PREFACE:

Richard Bruskiewich

Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition
Bioinformatics 2004 20: 139; doi:10.1093/bioinformatics/bth016 [Print PDF][Screen PDF] [Request Permissions]  

PAG MEETING ORIGINAL PAPERS:

Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, and Patrick S. Schnable

A strategy for assembling the maize (Zea mays L.) genome
Bioinformatics 2004 20: 140-147; doi:10.1093/bioinformatics/bth017 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lei Liu, George Gong, Yong Liu, Shreedhar Natarajan, Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, and Jonathan E. Beever

Multi-species comparative mapping in silico using the COMPASS strategy
Bioinformatics 2004 20: 148-154; doi:10.1093/bioinformatics/bth018 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nikoleta Juretic, Thomas E. Bureau, and Richard M. Bruskiewich

Transposable element annotation of the rice genome
Bioinformatics 2004 20: 155-160; doi:10.1093/bioinformatics/bth019 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, and Karl J. Kramer

Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome
Bioinformatics 2004 20: 161-169; doi:10.1093/bioinformatics/bth020 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kimmen Sjölander

Phylogenomic inference of protein molecular function: advances and challenges
Bioinformatics 2004 20: 170-179; doi:10.1093/bioinformatics/bth021 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

PAG MEETING APPLICATIONS NOTES:

Brad A. Chapman, John E. Bowers, Stefan R. Schulze, and Andrew H. Paterson

A comparative phylogenetic approach for dating whole genome duplication events
Bioinformatics 2004 20: 180-185; doi:10.1093/bioinformatics/bth022 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

I. L. Hofacker, B. Priwitzer, and P. F. Stadler

Prediction of locally stable RNA secondary structures for genome-wide surveys
Bioinformatics 2004 20: 186-190; doi:10.1093/bioinformatics/btg388 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan D. Wren and Harold R. Garner

Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
Bioinformatics 2004 20: 191-198; doi:10.1093/bioinformatics/btg390 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Brylinski, W. Jurkowski, L. Konieczny, and I. Roterman

Limited conformational space for early-stage protein folding simulation
Bioinformatics 2004 20: 199-205; doi:10.1093/bioinformatics/btg391 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Susana Vinga, Rodrigo Gouveia-Oliveira, and Jonas S. Almeida

Comparative evaluation of word composition distances for the recognition of SCOP relationships
Bioinformatics 2004 20: 206-215; doi:10.1093/bioinformatics/btg392 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey T. Chang, Hinrich Schütze, and Russ B. Altman

GAPSCORE: finding gene and protein names one word at a time
Bioinformatics 2004 20: 216-225; doi:10.1093/bioinformatics/btg393 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Steffen Klamt and Ernst Dieter Gilles

Minimal cut sets in biochemical reaction networks
Bioinformatics 2004 20: 226-234; doi:10.1093/bioinformatics/btg395 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Susmita Datta, Glen A. Satten, Dale J. Benos, Jiazeng Xia, Martin J. Heslin, and Somnath Datta

An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments
Bioinformatics 2004 20: 235-242; doi:10.1093/bioinformatics/btg396 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hideya Kawaji, Yoichi Takenaka, and Hideo Matsuda

Graph-based clustering for finding distant relationships in a large set of protein sequences
Bioinformatics 2004 20: 243-252; doi:10.1093/bioinformatics/btg397 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ulisses Braga-Neto, Ronaldo Hashimoto, Edward R. Dougherty, Danh V. Nguyen, and Raymond J. Carroll

Is cross-validation better than resubstitution for ranking genes?
Bioinformatics 2004 20: 253-258; doi:10.1093/bioinformatics/btg399 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Albert Burger, Duncan Davidson, and Richard Baldock

Formalization of mouse embryo anatomy
Bioinformatics 2004 20: 259-267; doi:10.1093/bioinformatics/btg400 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claußen, C. Ebeling, P. Ernst, V. Gailus-Durner, K.-H. Glatting, R. Gohla, F. Gößling, K. Grote, K. Heidtke, A. Herrmann, S. O'Keeffe, O. Kießlich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H.-T. Mevissen, H.-W. Mewes, H. Michael, M. Mokrejs, T. Müller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender, and R. Zimmer

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
Bioinformatics 2004 20: 268-270; doi:10.1093/bioinformatics/btg398 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, and Jean-Michel Fayard

ROSO: optimizing oligonucleotide probes for microarrays
Bioinformatics 2004 20: 271-273; doi:10.1093/bioinformatics/btg401 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. Barker

LVB: parsimony and simulated annealing in the search for phylogenetic trees
Bioinformatics 2004 20: 274-275; doi:10.1093/bioinformatics/btg402 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shir-Ly Huang, Li-Cheng Wu, Han-Kuen Liang, Kuan-Ting Pan, Jorng-Tzong Horng, and Ming-Tat Ko

PGTdb: a database providing growth temperatures of prokaryotes
Bioinformatics 2004 20: 276-278; doi:10.1093/bioinformatics/btg403 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ryan Brodie, Rachel L. Roper, and Chris Upton

JDotter: a Java interface to multiple dotplots generated by dotter
Bioinformatics 2004 20: 279-281; doi:10.1093/bioinformatics/btg406 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, and Michael F. Ochs

FGDP: functional genomics data pipeline for automated, multiple microarray data analyses
Bioinformatics 2004 20: 282-283; doi:10.1093/bioinformatics/btg407 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. J. Orton, W. I. Sellers, and D. L. Gerloff

YETI: Yeast Exploration Tool Integrator
Bioinformatics 2004 20: 284-285; doi:10.1093/bioinformatics/btg408 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lakshmi K. Matukumalli, John J. Grefenstette, Tad S. Sonstegard, and Curtis P. Van Tassell

EST-PAGE—managing and analyzing EST data
Bioinformatics 2004 20: 286-288; doi:10.1093/bioinformatics/btg411 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Emmanuel Paradis, Julien Claude, and Korbinian Strimmer

APE: Analyses of Phylogenetics and Evolution in R language
Bioinformatics 2004 20: 289-290; doi:10.1093/bioinformatics/btg412 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. J. Pérez, G. Thode, and O. Trelles

AnaGram: protein function assignment
Bioinformatics 2004 20: 291-292; doi:10.1093/bioinformatics/btg414 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

CORRIGENDA:

Torgeir R. Hvidsten, Andriy Kryshtafovych, Jan Komorowski, and Krzysztof Fidelis

A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins
Bioinformatics 2004 20: 293; doi:10.1093/bioinformatics/bth062 [Print PDF][Screen PDF] [Request Permissions]  

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