Table of Contents

ARTICLES

Select this article
Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
- 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
Genome Res. March 2004 14: 331-342; doi:10.1101/gr.2094104
Select this article
Comparative Analysis of Protein Domain Organization
- Yuzhen Ye and
- Adam Godzik
Genome Res. March 2004 14: 343-353; doi:10.1101/gr.1610504

LETTERS

Select this article
Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
- James P. Noonan,
- Jane Grimwood,
- Jeremy Schmutz,
- Mark Dickson,
- and Richard M. Myers
Genome Res. March 2004 14: 354-366; doi:10.1101/gr.2133704
Select this article
Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
- Kelly A. Frazer,
- Heng Tao,
- Kazutoyo Osoegawa,
- Pieter J. de Jong,
- Xiyin Chen,
- Mark F. Doherty,
- and David R. Cox
Genome Res. March 2004 14: 367-372; Published in Advance February 12, 2004, doi:10.1101/gr.1961204
Select this article
Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans
- José M. Ranz,
- Kalsang Namgyal,
- Greg Gibson,
- and Daniel L. Hartl
Genome Res. March 2004 14: 373-379; Published in Advance February 12, 2004, doi:10.1101/gr.2019804
Select this article
Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network
- Susanne Prinz,
- Iliana Avila-Campillo,
- Christine Aldridge,
- Ajitha Srinivasan,
- Krassen Dimitrov,
- Andrew F. Siegel,
- and Timothy Galitski
Genome Res. March 2004 14: 380-390; doi:10.1101/gr.2020604
Select this article
Quantifying Modularity in the Evolution of Biomolecular Systems
- Berend Snel and
- Martijn A. Huynen
Genome Res. March 2004 14: 391-397; doi:10.1101/gr.1969504

Methods

Select this article
Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
- 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
Genome Res. March 2004 14: 398-405; doi:10.1101/gr.2141004
Select this article
Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
- 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
Genome Res. March 2004 14: 406-413; doi:10.1101/gr.1515604
Select this article
Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
- 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
Genome Res. March 2004 14: 414-425; doi:10.1101/gr.2014904
Select this article
The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
- Yi Xing,
- Alissa Resch,
- and Christopher Lee
Genome Res. March 2004 14: 426-441; Published in Advance February 12, 2004, doi:10.1101/gr.1304504
Select this article
MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
- Peter D. Keightley and
- Toby Johnson
Genome Res. March 2004 14: 442-450; doi:10.1101/gr.1571904
Select this article
Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
- Yueyi Liu,
- X. Shirley Liu,
- Liping Wei,
- Russ B. Altman,
- and Serafim Batzoglou
Genome Res. March 2004 14: 451-458; doi:10.1101/gr.1327604
Select this article
Correct Estimation of Preferential Chromosome Pairing in Autotetraploids
- Dachuang Cao,
- Thomas C. Osborn,
- and Rebecca W. Doerge
Genome Res. March 2004 14: 459-462; Published in Advance February 12, 2004, doi:10.1101/gr.1596604

RESOURCES

Select this article
Numerous Novel Annotations of the Human Genome Sequence Supported by a 5′-End–Enriched cDNA Collection
- 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
Genome Res. March 2004 14: 463-471; Published in Advance February 12, 2004, doi:10.1101/gr.1481104
Select this article
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Ross C. Hardison,
- Webb Miller,
- and Lisa Stubbs
Genome Res. March 2004 14: 472-477; doi:10.1101/gr.2129504
Select this article
Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
- 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
Genome Res. March 2004 14: 478-490; Published in Advance February 12, 2004, doi:10.1101/gr.1687304

ARTICLES

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Comparative Analysis of Protein Domain Organization

LETTERS

Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity

Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional

Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans

Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network

Quantifying Modularity in the Evolution of Biomolecular Systems

Methods

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures

MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution

Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics

Correct Estimation of Preferential Chromosome Pairing in Autotetraploids

RESOURCES

Numerous Novel Annotations of the Human Genome Sequence Supported by a 5′-End–Enriched cDNA Collection

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

This Issue

Preprint Server

Current Issue

In This Issue