ARTICLES:

Dione Kampa, Jill Cheng, Philipp Kapranov, Mark Yamanaka, Shane Brubaker, Simon Cawley, Jorg Drenkow, Antonio Piccolboni, Stefan Bekiranov, Gregg Helt, Hari Tammana, and Thomas R. Gingeras

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
Genome Res. 2004 14: 331-342. [Abstract] [Full Text] [Supplemental Research Data]  

Yuzhen Ye and Adam Godzik

Comparative Analysis of Protein Domain Organization
Genome Res. 2004 14: 343-353. [Abstract] [Full Text]  

LETTERS:

James P. Noonan, Jane Grimwood, Jeremy Schmutz, Mark Dickson, and Richard M. Myers

Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
Genome Res. 2004 14: 354-366. [Abstract] [Full Text]  

Kelly A. Frazer, Heng Tao, Kazutoyo Osoegawa, Pieter J. de Jong, Xiyin Chen, Mark F. Doherty, and David R. Cox

Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
Genome Res. 2004 14: 367-372. Published in Advance February 12, 2004, 10.1101/gr.1961204 [Abstract] [Full Text] [Supplemental Research Data]  

José M. Ranz, Kalsang Namgyal, Greg Gibson, and Daniel L. Hartl

Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans
Genome Res. 2004 14: 373-379. Published in Advance February 12, 2004, 10.1101/gr.2019804 [Abstract] [Full Text] [Supplemental Research Data]  

Susanne Prinz, Iliana Avila-Campillo, Christine Aldridge, Ajitha Srinivasan, Krassen Dimitrov, Andrew F. Siegel, and Timothy Galitski

Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network
Genome Res. 2004 14: 380-390. [Abstract] [Full Text] [Supplemental Research Data]  

Berend Snel and Martijn A. Huynen

Quantifying Modularity in the Evolution of Biomolecular Systems
Genome Res. 2004 14: 391-397. [Abstract] [Full Text] [Supplemental Research Data]  

METHODS:

Christopher W. Wong, Thomas J. Albert, Vinsensius B. Vega, Jason E. Norton, David J. Cutler, Todd A. Richmond, Lawrence W. Stanton, Edison T. Liu, and Lance D. Miller

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
Genome Res. 2004 14: 398-405. [Abstract] [Full Text] [Supplemental Research Data]  

Vanina Castelli, Jean-Marc Aury, Olivier Jaillon, Patrick Wincker, Christian Clepet, Manuella Menard, Corinne Cruaud, Francis Quétier, Claude Scarpelli, Vincent Schächter, Gary Temple, Michel Caboche, Jean Weissenbach, and Marcel Salanoubat

Whole Genome Sequence Comparisons and "Full-Length" cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
Genome Res. 2004 14: 406-413. [Abstract] [Full Text] [Supplemental Research Data]  

Hajime Matsuzaki, Halina Loi, Shoulian Dong, Ya-Yu Tsai, Joy Fang, Jane Law, Xiaojun Di, Wei-Min Liu, Geoffrey Yang, Guoying Liu, Jing Huang, Giulia C. Kennedy, Thomas B. Ryder, Gregory A. Marcus, P. Sean Walsh, Mark D. Shriver, Jennifer M. Puck, Keith W. Jones, and Rui Mei

Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
Genome Res. 2004 14: 414-425. [Abstract] [Full Text] [Supplemental Research Data]  

Yi Xing, Alissa Resch, and Christopher Lee

The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
Genome Res. 2004 14: 426-441. Published in Advance February 12, 2004, 10.1101/gr.1304504 [Abstract] [Full Text]  

Peter D. Keightley and Toby Johnson

MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
Genome Res. 2004 14: 442-450. [Abstract] [Full Text]  

Yueyi Liu, X. Shirley Liu, Liping Wei, Russ B. Altman, and Serafim Batzoglou

Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
Genome Res. 2004 14: 451-458. [Abstract] [Full Text] [Supplemental Research Data]  

Dachuang Cao, Thomas C. Osborn, and Rebecca W. Doerge

Correct Estimation of Preferential Chromosome Pairing in Autotetraploids
Genome Res. 2004 14: 459-462. Published in Advance February 12, 2004, 10.1101/gr.1596604 [Abstract] [Full Text]  

RESOURCES:

Betina M. Porcel, Olivier Delfour, Vanina Castelli, Veronique De Berardinis, Lucie Friedlander, Corinne Cruaud, Abel Ureta-Vidal, Claude Scarpelli, Patrick Wincker, Vincent Schächter, William Saurin, Gabor Gyapay, Marcel Salanoubat, and Jean Weissenbach

Numerous Novel Annotations of the Human Genome Sequence Supported by a 5'-End–Enriched cDNA Collection
Genome Res. 2004 14: 463-471. Published in Advance February 12, 2004, 10.1101/gr.1481104 [Abstract] [Full Text]  

Ivan Ovcharenko, Gabriela G. Loots, Ross C. Hardison, Webb Miller, and Lisa Stubbs

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Genome Res. 2004 14: 472-477. [Abstract] [Full Text]  

Matthew L. Rise, Kristian R. von Schalburg, Gordon D. Brown, Melanie A. Mawer, Robert H. Devlin, Nathanael Kuipers, Maura Busby, Marianne Beetz-Sargent, Roberto Alberto, A. Ross Gibbs, Peter Hunt, Robert Shukin, Jeffrey A. Zeznik, Colleen Nelson, Simon R.M. Jones, Duane E. Smailus, Steven J.M. Jones, Jacqueline E. Schein, Marco A. Marra, Yaron S.N. Butterfield, Jeff M. Stott, Siemon H.S. Ng, William S. Davidson, and Ben F. Koop

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
Genome Res. 2004 14: 478-490. Published in Advance February 12, 2004, 10.1101/gr.1687304 [Abstract] [Full Text]  

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