Volume 14, Issue 4 | April 2004

ARTICLES
- - Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat
    Eray Tuzun
    Jeffrey A. Bailey
    Evan E. Eichler
    First Published April 1, 2004
  - Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes
    Guillaume Bourque
    Pavel A. Pevzner
    Glenn Tesler
    First Published April 1, 2004
  - Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
    Shan Yang
    Arian F. Smit
    Scott Schwartz
    Francesca Chiaromonte
    Krishna M. Roskin
    First Published April 1, 2004
  - Comparative Recombination Rates in the Rat, Mouse, and Human Genomes
    Michael I. Jensen-Seaman
    Terrence S. Furey
    Bret A. Payseur
    Yontao Lu
    Krishna M. Roskin
    First Published April 1, 2004
LETTERS
- - Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
    Gregory M. Cooper
    Michael Brudno
    Eric A. Stone
    Inna Dubchak
    Serafim Batzoglou
    First Published April 1, 2004
  - Comparative Analysis of Amino Acid Repeats in Rodents and Humans
    M. Mar Albà
    Roderic Guigó
    First Published April 1, 2004
  - Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
    Martin S. Taylor
    Chris P. Ponting
    Richard R. Copley
    First Published April 1, 2004
  - Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
    Kateryna D. Makova
    Shan Yang
    Francesca Chiaromonte
    First Published April 1, 2004
  - Identification of Evolutionary Hotspots in the Rodent Genomes
    Von Bing Yap
    Lior Pachter
    First Published April 1, 2004
  - Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome
    Zhengdong Zhang
    Paula E. Burch
    Austin J. Cooney
    Rainer B. Lanz
    Fred A. Pereira
    First Published April 1, 2004
  - Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents
    Richard D. Emes
    Scott A. Beatson
    Chris P. Ponting
    Leo Goodstadt
    First Published April 1, 2004
  - Species Specificity in Rodent Pheromone Receptor Repertoires
    Robert P. Lane
    Janet Young
    Tera Newman
    Barbara J. Trask
    First Published April 1, 2004
  - A Genomic Analysis of Rat Proteases and Protease Inhibitors
    Xose S. Puente
    Carlos López-Otín
    First Published April 1, 2004
  - Comparative Analysis of the α-Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny
    Cristina Tufarelli
    Ross Hardison
    Webb Miller
    Jim Hughes
    Kevin Clark
    First Published April 1, 2004
  - The Genomic Sequence and Comparative Analysis of the Rat Major Histocompatibility Complex
    Peter Hurt
    Lutz Walter
    Ralf Sudbrak
    Sven Klages
    Ines Müller
    Takashi Shiina Hidetoshi Inoko
    ...[+2 authors]...,
    Hans Lehrach
    Eberhard Günther
    Richard Reinhardt
    Heinz Himmelbauer
    First Published April 1, 2004
  - Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54
    Ursula Vitt
    Darryl Gietzen
    Kristian Stevens
    Jim Wingrove
    Shanya Becha
    Sean Bulloch John Burrill Narinder Chawla Jennifer Chien Matthew Crawford Craig Ison Liam Kearney Mary Kwong Joe Park Jennifer Policky Mark Weiler Renee White Yuming Xu Sue Daniels Howard Jacob
    ...[+15 authors]...,
    Michael I. Jensen-Seaman
    Jozef Lazar
    Laura Stuve
    Jeanette Schmidt
    First Published April 1, 2004
Methods
- - Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human Data
    Simon N. Twigger
    Jeff Nie
    Victor Ruotti
    Jiaming Yu
    Dan Chen
    Dawei Li Jed Mathis Vijay Narayanasamy Gopal R. Gopinath Dean Pasko Mary Shimoyama Norberto de la Cruz
    ...[+7 authors]...,
    Susan Bromberg
    Anne E. Kwitek
    Howard J. Jacob
    Peter J. Tonellato
    First Published April 1, 2004
  - Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat
    Colin Dewey
    Jia Qian Wu
    Simon Cawley
    Marina Alexandersson
    Richard Gibbs
    First Published April 1, 2004
  - Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing
    Jia Qian Wu
    David Shteynberg
    Manimozhiyan Arumugam
    Richard A. Gibbs
    Michael R. Brent
    First Published April 1, 2004
  - Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing
    Ken J. Kalafus
    Andrew R. Jackson
    Aleksandar Milosavljevic
    First Published April 1, 2004
  - Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project
    Rui Chen
    Erica Sodergren
    George M. Weinstock
    Richard A. Gibbs
    First Published April 1, 2004
  - Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
    Michael Brudno
    Alexander Poliakov
    Asaf Salamov
    Gregory M. Cooper
    Arend Sidow
    First Published April 1, 2004
  - MAVID: Constrained Ancestral Alignment of Multiple Sequences
    Nicolas Bray
    Lior Pachter
    First Published April 1, 2004
  - Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
    Diana Kolbe
    James Taylor
    Laura Elnitski
    Pallavi Eswara
    Jia Li
    First Published April 1, 2004
RESOURCES
- - Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
    Mathieu Blanchette
    W. James Kent
    Cathy Riemer
    Laura Elnitski
    Arian F.A. Smit
    Krishna M. Roskin Robert Baertsch Kate Rosenbloom
    ...[+3 authors]...,
    Hiram Clawson
    Eric D. Green
    David Haussler
    Webb Miller
    First Published April 1, 2004
  - Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER
    Kushal Chakrabarti
    Lior Pachter
    First Published April 1, 2004
  - The Atlas Genome Assembly System
    Paul Havlak
    Rui Chen
    K. James Durbin
    Amy Egan
    Yanru Ren
    First Published April 1, 2004
  - High-Throughput Gene Discovery in the Rat
    Todd E. Scheetz
    Jennifer J. Laffin
    Brian Berger
    Sara Holte
    Susan A. Baumes
    Robert Brown Shereen Chang Justin Coco Jim Conklin Keith Crouch Micca Donohue Greg Doonan Chris Estes Mari Eyestone Katrina Fishler Jack Gardiner Lankai Guo Brad Johnson Catherine Keppel Rikki Kreger Mark Lebeck Rudy Marcelino Vladan Miljkovich Mindee Perdue Ling Qui Joshua Rehmann Rebecca S. Reiter Bridgette Rhoads Kelly Schaefer Christina Smith Ivana Sunjevaric Kurtis Trout Ning Wu Clayton L. Birkett Jared Bischof Barry Gackle Allen Gavin A. Jason Grundstad Brian Mokrzycki Chris Moressi Brian O'Leary Kevin Pedretti Chad Roberts Natalie L. Robinson Michael Smith Dylan Tack Nishank Trivedi Tamara Kucaba Tom Freeman Jim J.-C. Lin
    ...[+45 authors]...,
    Maria F. Bonaldo
    Thomas L. Casavant
    Val C. Sheffield
    M. Bento Soares
    First Published April 1, 2004
  - Applications of a Rat Multiple Tissue Gene Expression Data Set
    John R. Walker
    Andrew I. Su
    David W. Self
    John B. Hogenesch
    Hilmar Lapp
    First Published April 1, 2004
  - High-Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence
    Anne E. Kwitek
    Jo Gullings-Handley
    Jiaming Yu
    Danilo C. Carlos
    Kimberly Orlebeke
    Jeff Nie Jeffrey Eckert Angela Lemke Jaime Wendt Andrae Susan Bromberg Dean Pasko Dan Chen Todd E. Scheetz Thomas L. Casavant
    ...[+9 authors]...,
    M. Bento Soares
    Val C. Sheffield
    Peter J. Tonellato
    Howard J. Jacob
    First Published April 1, 2004
  - Integration of the Rat Recombination and EST Maps in the Rat Genomic Sequence and Comparative Mapping Analysis With the Mouse Genome
    Steven P. Wilder
    Marie-Thérèse Bihoreau
    Karène Argoud
    Takeshi K. Watanabe
    Mark Lathrop
    First Published April 1, 2004
  - Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
    Martin Krzywinski
    John Wallis
    Claudia Gösele
    Ian Bosdet
    Readman Chiu
    Tina Graves Oliver Hummel Dan Layman Carrie Mathewson Natasja Wye Baoli Zhu Derek Albracht Jennifer Asano Sarah Barber Mabel Brown-John Susanna Chan Steve Chand Alison Cloutier Jonathon Davito Chris Fjell Tony Gaige Detlev Ganten Noreen Girn Kurtis Guggenheimer Heinz Himmelbauer Thomas Kreitler Stephen Leach Darlene Lee Hans Lehrach Michael Mayo Kelly Mead Teika Olson Pawan Pandoh Anna-Liisa Prabhu Heesun Shin Simone Tänzer Jason Thompson Miranda Tsai Jason Walker George Yang Mandeep Sekhon LaDeana Hillier Heike Zimdahl Andre Marziali Kazutoyo Osoegawa Shaying Zhao Asim Siddiqui Pieter J. de Jong Wes Warren Elaine Mardis John D. McPherson Richard Wilson
    ...[+47 authors]...,
    Norbert Hübner
    Steven Jones
    Marco Marra
    Jacqueline Schein
    First Published April 1, 2004
  - BAC Resources for the Rat Genome Project
    Kazutoyo Osoegawa
    Baoli Zhu
    Chung Li Shu
    Teresa Ren
    Qing Cao
    Gery M. Vessere
    ...[+1 authors]...,
    Michelle M. Lutz
    Michael I. Jensen-Seaman
    Shaying Zhao
    Pieter J. de Jong
    First Published April 1, 2004
ERRATA
- - Correction for Volume 13, p. 103
    First Published April 1, 2004
  - Correction for Volume 14, p. 414
    First Published April 1, 2004

Table of Contents

Volume 14, Issue 4 | April 2004

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ARTICLES

LETTERS

Methods

RESOURCES

ERRATA