Table of Contents

January 2005; 15 (1)

ARTICLE

  • Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

    • Stephen Richards,
    • Yue Liu,
    • Brian R. Bettencourt,
    • Pavel Hradecky,
    • Stan Letovsky,
    • Rasmus Nielsen,
    • Kevin Thornton,
    • Melissa J. Hubisz,
    • Rui Chen,
    • Richard P. Meisel,
    • Olivier Couronne,
    • Sujun Hua,
    • Mark A. Smith,
    • Peili Zhang,
    • Jing Liu,
    • Harmen J. Bussemaker,
    • Marinus F. van Batenburg,
    • Sally L. Howells,
    • Steven E. Scherer,
    • Erica Sodergren,
    • Beverly B. Matthews,
    • Madeline A. Crosby,
    • Andrew J. Schroeder,
    • Daniel Ortiz-Barrientos,
    • Catharine M. Rives,
    • Michael L. Metzker,
    • Donna M. Muzny,
    • Graham Scott,
    • David Steffen,
    • David A. Wheeler,
    • Kim C. Worley,
    • Paul Havlak,
    • K. James Durbin,
    • Amy Egan,
    • Rachel Gill,
    • Jennifer Hume,
    • Margaret B. Morgan,
    • George Miner,
    • Cerissa Hamilton,
    • Yanmei Huang,
    • Lenée Waldron,
    • Daniel Verduzco,
    • Kerstin P. Clerc-Blankenburg,
    • Inna Dubchak,
    • Mohamed A.F. Noor,
    • Wyatt Anderson,
    • Kevin P. White,
    • Andrew G. Clark,
    • Stephen W. Schaeffer,
    • William Gelbart,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
    OPEN ACCESS ARTICLE

LETTERS

  • High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium

    • Luísa Pereira,
    • Martin Richards,
    • Ana Goios,
    • Antonio Alonso,
    • Cristina Albarrán,
    • Oscar Garcia,
    • Doron M. Behar,
    • Mukaddes Gölge,
    • Jiři Hatina,
    • Lihadh Al-Gazali,
    • Daniel G. Bradley,
    • Vincent Macaulay,
    • and António Amorim
    Genome Res. January 2005 15: 19-24; doi:10.1101/gr.3182305

  • Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

    • Jennifer G. Sambrook,
    • Arman Bashirova,
    • Sophie Palmer,
    • Sarah Sims,
    • John Trowsdale,
    • Laurent Abi-Rached,
    • Peter Parham,
    • Mary Carrington,
    • and Stephan Beck
    Genome Res. January 2005 15: 25-35; doi:10.1101/gr.2381205

  • Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional “strand-switch” domain as a major feature

    • Samson O. Obado,
    • Martin C. Taylor,
    • Shane R. Wilkinson,
    • Elizabeth V. Bromley,
    • and John M. Kelly
    Genome Res. January 2005 15: 36-43; doi:10.1101/gr.2895105

Methods

  • High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification

    • Eric Chiao,
    • Jeff Leonard,
    • Kari Dickinson,
    • and Julie C. Baker
    Genome Res. January 2005 15: 44-53; doi:10.1101/gr.2993405

  • Gene and alternative splicing annotation with AIR

    • Liliana Florea,
    • Valentina Di Francesco,
    • Jason Miller,
    • Russell Turner,
    • Alison Yao,
    • Michael Harris,
    • Brian Walenz,
    • Clark Mobarry,
    • Gennady V. Merkulov,
    • Rosane Charlab,
    • Ian Dew,
    • Zuoming Deng,
    • Sorin Istrail,
    • Peter Li,
    • and Granger Sutton
    Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405

  • Identification of polymorphic motifs using probabilistic search algorithms

    • Analabha Basu,
    • Probal Chaudhuri,
    • and Partha P. Majumder
    Genome Res. January 2005 15: 67-77; doi:10.1101/gr.2358005

  • Computational prediction of miRNAs in Arabidopsis thaliana

    • Alex Adai,
    • Cameron Johnson,
    • Sizolwenkosi Mlotshwa,
    • Sarah Archer-Evans,
    • Varun Manocha,
    • Vicki Vance,
    • and Venkatesan Sundaresan
    Genome Res. January 2005 15: 78-91; doi:10.1101/gr.2908205

  • Linkage group selection: Rapid gene discovery in malaria parasites

    • Richard Culleton,
    • Axel Martinelli,
    • Paul Hunt,
    • and Richard Carter
    Genome Res. January 2005 15: 92-97; doi:10.1101/gr.2866205

Chicken Special/Letters

  • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

    • Guillaume Bourque,
    • Evgeny M. Zdobnov,
    • Peer Bork,
    • Pavel A. Pevzner,
    • and Glenn Tesler
    Genome Res. January 2005 15: 98-110; Published in Advance December 8, 2004, doi:10.1101/gr.3002305

  • Comparison of splice sites in mammals and chicken

    • Josep F. Abril,
    • Robert Castelo,
    • and Roderic Guigó
    Genome Res. January 2005 15: 111-119; Published in Advance December 8, 2004, doi:10.1101/gr.3108805

  • Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes

    • Erik Axelsson,
    • Matthew T. Webster,
    • Nick G.C. Smith,
    • David W. Burt,
    • and Hans Ellegren
    Genome Res. January 2005 15: 120-125; Published in Advance December 8, 2004, doi:10.1101/gr.3021305

  • The repetitive landscape of the chicken genome

    • Thomas Wicker,
    • Jon S. Robertson,
    • Stefan R. Schulze,
    • F. Alex Feltus,
    • Vincent Magrini,
    • Jason A. Morrison,
    • Elaine R. Mardis,
    • Richard K. Wilson,
    • Daniel G. Peterson,
    • Andrew H. Paterson,
    • and Robert Ivarie
    Genome Res. January 2005 15: 126-136; Published in Advance July 15, 2004, doi:10.1101/gr.2438004

  • Evolution and functional classification of vertebrate gene deserts

    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Marcelo A. Nobrega,
    • Ross C. Hardison,
    • Webb Miller,
    • and Lisa Stubbs
    Genome Res. January 2005 15: 137-145; Published in Advance December 8, 2004, doi:10.1101/gr.3015505

  • Evolution of the Beckwith-Wiedemann syndrome region in vertebrates

    • Martina Paulsen,
    • Tarang Khare,
    • Christopher Burgard,
    • Sascha Tierling,
    • and Jörn Walter
    Genome Res. January 2005 15: 146-153; Published in Advance December 8, 2004, doi:10.1101/gr.2689805

  • Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region

    • Takaaki Yokomine,
    • Hisao Shirohzu,
    • Wahyu Purbowasito,
    • Atsushi Toyoda,
    • Hisakazu Iwama,
    • Kazuho Ikeo,
    • Tetsuya Hori,
    • Shigeki Mizuno,
    • Masaoki Tsudzuki,
    • Yoh-ichi Matsuda,
    • Masahira Hattori,
    • Yoshiyuki Sakaki,
    • and Hiroyuki Sasaki
    Genome Res. January 2005 15: 154-165; Published in Advance December 8, 2004, doi:10.1101/gr.2609605

Chicken Special/Resources

  • Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates

    • Wendy A. Kellner,
    • Robert T. Sullivan,
    • Brian H. Carlson,
    • and James W. Thomas
    Genome Res. January 2005 15: 166-173; Published in Advance December 8, 2004, doi:10.1101/gr.3066805

  • Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

    • Simon J. Hubbard,
    • Darren V. Grafham,
    • Kevin J. Beattie,
    • Ian M. Overton,
    • Stuart R. McLaren,
    • Michael D.R. Croning,
    • Paul E. Boardman,
    • James K. Bonfield,
    • Joan Burnside,
    • Robert M. Davies,
    • Elizabeth R. Farrell,
    • Matthew D. Francis,
    • Sam Griffiths-Jones,
    • Sean J. Humphray,
    • Christopher Hyland,
    • Carol E. Scott,
    • Haizhou Tang,
    • Ruth G. Taylor,
    • Cheryll Tickle,
    • William R.A. Brown,
    • Ewan Birney,
    • Jane Rogers,
    • and Stuart A. Wilson
    Genome Res. January 2005 15: 174-183; Published in Advance December 8, 2004, doi:10.1101/gr.3011405

  • Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Belinda M. Giardine,
    • Minmei Hou,
    • Jian Ma,
    • Ross C. Hardison,
    • Lisa Stubbs,
    • and Webb Miller
    Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
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This Issue

January 2005; 15 (1)
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  1. ARTICLE
  2. LETTERS
  3. Methods
  4. Chicken Special/Letters
  5. Chicken Special/Resources

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