Volume 14, Issue 3 | March 2004

ARTICLES
- - 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
    ...[+3 authors]...,
    Stefan Bekiranov
    Gregg Helt
    Hari Tammana
    Thomas R. Gingeras
    First Published March 1, 2004
  - Comparative Analysis of Protein Domain Organization
    Yuzhen Ye
    Adam Godzik
    First Published March 1, 2004
LETTERS
- - Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
    James P. Noonan
    Jane Grimwood
    Jeremy Schmutz
    Mark Dickson
    Richard M. Myers
    First Published March 1, 2004
  - 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
    First Published February 12, 2004
  - Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans
    José M. Ranz
    Kalsang Namgyal
    Greg Gibson
    Daniel L. Hartl
    First Published February 12, 2004
  - Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network
    Susanne Prinz
    Iliana Avila-Campillo
    Christine Aldridge
    Ajitha Srinivasan
    Krassen Dimitrov
    First Published March 1, 2004
  - Quantifying Modularity in the Evolution of Biomolecular Systems
    Berend Snel
    Martijn A. Huynen
    First Published March 1, 2004
Methods
- - 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
    First Published March 1, 2004
  - 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
    ...[+5 authors]...,
    Gary Temple
    Michel Caboche
    Jean Weissenbach
    Marcel Salanoubat
    First Published March 1, 2004
  - 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
    ...[+10 authors]...,
    Mark D. Shriver
    Jennifer M. Puck
    Keith W. Jones
    Rui Mei
    First Published March 1, 2004
  - The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
    Yi Xing
    Alissa Resch
    Christopher Lee
    First Published February 12, 2004
  - MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
    Peter D. Keightley
    Toby Johnson
    First Published March 1, 2004
  - Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
    Yueyi Liu
    X. Shirley Liu
    Liping Wei
    Russ B. Altman
    Serafim Batzoglou
    First Published March 1, 2004
  - Correct Estimation of Preferential Chromosome Pairing in Autotetraploids
    Dachuang Cao
    Thomas C. Osborn
    Rebecca W. Doerge
    First Published February 12, 2004
RESOURCES
- - 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
    ...[+5 authors]...,
    William Saurin
    Gabor Gyapay
    Marcel Salanoubat
    Jean Weissenbach
    First Published February 12, 2004
  - zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
    Ivan Ovcharenko
    Gabriela G. Loots
    Ross C. Hardison
    Webb Miller
    Lisa Stubbs
    First Published March 1, 2004
  - 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
    ...[+15 authors]...,
    Jeff M. Stott
    Siemon H.S. Ng
    William S. Davidson
    Ben F. Koop
    First Published February 12, 2004

Table of Contents

Volume 14, Issue 3 | March 2004

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

Table of Contents

Volume 14, Issue 3 | March 2004

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ARTICLES

LETTERS

Methods

RESOURCES