Table of Contents

April 2004; 14 (4)

ARTICLES

  • Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat

    • Eray Tuzun,
    • Jeffrey A. Bailey,
    • and Evan E. Eichler
    Genome Res. April 2004 14: 493-506; doi:10.1101/gr.1907504

  • Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes

    • Guillaume Bourque,
    • Pavel A. Pevzner,
    • and Glenn Tesler
    Genome Res. April 2004 14: 507-516; doi:10.1101/gr.1975204

  • 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,
    • David Haussler,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. April 2004 14: 517-527; doi:10.1101/gr.1984404

  • 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,
    • Chin-Fu Chen,
    • Michael A. Thomas,
    • David Haussler,
    • and Howard J. Jacob
    Genome Res. April 2004 14: 528-538; doi:10.1101/gr.1970304

LETTERS

  • Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

    • Gregory M. Cooper,
    • Michael Brudno,
    • Eric A. Stone,
    • Inna Dubchak,
    • Serafim Batzoglou,
    • and Arend Sidow
    Genome Res. April 2004 14: 539-548; doi:10.1101/gr.2034704

  • Comparative Analysis of Amino Acid Repeats in Rodents and Humans

    • M. Mar Albà and
    • Roderic Guigó
    Genome Res. April 2004 14: 549-554; doi:10.1101/gr.1925704

  • Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes

    • Martin S. Taylor,
    • Chris P. Ponting,
    • and Richard R. Copley
    Genome Res. April 2004 14: 555-566; doi:10.1101/gr.1977804

  • Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents

    • Kateryna D. Makova,
    • Shan Yang,
    • and Francesca Chiaromonte
    Genome Res. April 2004 14: 567-573; doi:10.1101/gr.1971104

  • Identification of Evolutionary Hotspots in the Rodent Genomes

    • Von Bing Yap and
    • Lior Pachter
    Genome Res. April 2004 14: 574-579; doi:10.1101/gr.1967904

  • 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,
    • Jiaqian Wu,
    • Richard A. Gibbs,
    • George Weinstock,
    • and David A. Wheeler
    Genome Res. April 2004 14: 580-590; doi:10.1101/gr.2160004

  • Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents

    • Richard D. Emes,
    • Scott A. Beatson,
    • Chris P. Ponting,
    • and Leo Goodstadt
    Genome Res. April 2004 14: 591-602; doi:10.1101/gr.1940604

  • Species Specificity in Rodent Pheromone Receptor Repertoires

    • Robert P. Lane,
    • Janet Young,
    • Tera Newman,
    • and Barbara J. Trask
    Genome Res. April 2004 14: 603-608; doi:10.1101/gr.2117004

  • A Genomic Analysis of Rat Proteases and Protease Inhibitors

    • Xose S. Puente and
    • Carlos López-Otín
    Genome Res. April 2004 14: 609-622; doi:10.1101/gr.1946304

  • 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,
    • Nicki Ventress,
    • Anna Maria Frischauf,
    • and Douglas R. Higgs
    Genome Res. April 2004 14: 623-630; doi:10.1101/gr.2143604

  • 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,
    • Hans Lehrach,
    • Eberhard Günther,
    • Richard Reinhardt,
    • and Heinz Himmelbauer
    Genome Res. April 2004 14: 631-639; doi:10.1101/gr.1987704

  • 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,
    • Michael I. Jensen-Seaman,
    • Jozef Lazar,
    • Laura Stuve,
    • and Jeanette Schmidt
    Genome Res. April 2004 14: 640-650; doi:10.1101/gr.1932304

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,
    • Susan Bromberg,
    • Anne E. Kwitek,
    • Howard J. Jacob,
    • and Peter J. Tonellato
    Genome Res. April 2004 14: 651-660; doi:10.1101/gr.1974504

  • 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,
    • and Lior Pachter
    Genome Res. April 2004 14: 661-664; doi:10.1101/gr.1939804

  • Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing

    • Jia Qian Wu,
    • David Shteynberg,
    • Manimozhiyan Arumugam,
    • Richard A. Gibbs,
    • and Michael R. Brent
    Genome Res. April 2004 14: 665-671; doi:10.1101/gr.1959604

  • Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing

    • Ken J. Kalafus,
    • Andrew R. Jackson,
    • and Aleksandar Milosavljevic
    Genome Res. April 2004 14: 672-678; doi:10.1101/gr.1963804

  • Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project

    • Rui Chen,
    • Erica Sodergren,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. April 2004 14: 679-684; doi:10.1101/gr.2171704

  • Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

    • Michael Brudno,
    • Alexander Poliakov,
    • Asaf Salamov,
    • Gregory M. Cooper,
    • Arend Sidow,
    • Edward M. Rubin,
    • Victor Solovyev,
    • Serafim Batzoglou,
    • and Inna Dubchak
    Genome Res. April 2004 14: 685-692; doi:10.1101/gr.2067704

  • MAVID: Constrained Ancestral Alignment of Multiple Sequences

    • Nicolas Bray and
    • Lior Pachter
    Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404

  • Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

    • Diana Kolbe,
    • James Taylor,
    • Laura Elnitski,
    • Pallavi Eswara,
    • Jia Li,
    • Webb Miller,
    • Ross Hardison,
    • and Francesca Chiaromonte
    Genome Res. April 2004 14: 700-707; doi:10.1101/gr.1976004

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,
    • Hiram Clawson,
    • Eric D. Green,
    • David Haussler,
    • and Webb Miller
    Genome Res. April 2004 14: 708-715; doi:10.1101/gr.1933104

  • Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER

    • Kushal Chakrabarti and
    • Lior Pachter
    Genome Res. April 2004 14: 716-720; doi:10.1101/gr.1957004

  • The Atlas Genome Assembly System

    • Paul Havlak,
    • Rui Chen,
    • K. James Durbin,
    • Amy Egan,
    • Yanru Ren,
    • Xing-Zhi Song,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. April 2004 14: 721-732; doi:10.1101/gr.2264004

  • High-Throughput Gene Discovery in the Rat

    • Todd E. Scheetz,
    • Jennifer J. Laffin,
    • Brian Berger,
    • Sara Holte,
    • Susan A. Baumes,
    • Robert Brown II,
    • 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,
    • Maria F. Bonaldo,
    • Thomas L. Casavant,
    • Val C. Sheffield,
    • and M. Bento Soares
    Genome Res. April 2004 14: 733-741; doi:10.1101/gr.1414204

  • Applications of a Rat Multiple Tissue Gene Expression Data Set

    • John R. Walker,
    • Andrew I. Su,
    • David W. Self,
    • John B. Hogenesch,
    • Hilmar Lapp,
    • Rainer Maier,
    • Daniel Hoyer,
    • and Graeme Bilbe
    Genome Res. April 2004 14: 742-749; doi:10.1101/gr.2161804

  • 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,
    • M. Bento Soares,
    • Val C. Sheffield,
    • Peter J. Tonellato,
    • and Howard J. Jacob
    Genome Res. April 2004 14: 750-757; doi:10.1101/gr.1968704

  • 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,
    • and Dominique Gauguier
    Genome Res. April 2004 14: 758-765; doi:10.1101/gr.2001604

  • 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,
    • Norbert Hübner,
    • Steven Jones,
    • Marco Marra,
    • and Jacqueline Schein
    Genome Res. April 2004 14: 766-779; doi:10.1101/gr.2336604

  • BAC Resources for the Rat Genome Project

    • Kazutoyo Osoegawa,
    • Baoli Zhu,
    • Chung Li Shu,
    • Teresa Ren,
    • Qing Cao,
    • Gery M. Vessere,
    • Michelle M. Lutz,
    • Michael I. Jensen-Seaman,
    • Shaying Zhao,
    • and Pieter J. de Jong
    Genome Res. April 2004 14: 780-785; doi:10.1101/gr.2033904

ERRATA

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This Issue

April 2004; 14 (4)
Cover
  1. ARTICLES
  2. LETTERS
  3. Methods
  4. RESOURCES
  5. ERRATA

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