Table of Contents

March 2006; 16 (3)

In this Issue

Forum

  • Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

    • Lutz Froenicke,
    • Montserrat Garcia Caldés,
    • Alexander Graphodatsky,
    • Stefan Müller,
    • Leslie A. Lyons,
    • Terence J. Robinson,
    • Marianne Volleth,
    • Fengtang Yang,
    • and Johannes Wienberg
    Genome Res. March 2006 16: 306-310; doi:10.1101/gr.3955206

  • The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction

    • Guillaume Bourque,
    • Glenn Tesler,
    • and Pavel A. Pevzner
    Genome Res. March 2006 16: 311-313; doi:10.1101/gr.4631806

COMMENTARY

  • Small open reading frames: Not so small anymore

    • Richelle Sopko and
    • Brenda Andrews
    Genome Res. March 2006 16: 314-315; doi:10.1101/gr.4976706

PERSPECTIVE

  • Application of sequence-based methods in human microbial ecology

    • Li Weng,
    • Edward M. Rubin,
    • and James Bristow
    Genome Res. March 2006 16: 316-322; Published in Advance February 6, 2006, doi:10.1101/gr.3676406

LETTERS

  • The portability of tagSNPs across populations: A worldwide survey

    • Anna González-Neira,
    • Xiayi Ke,
    • Oscar Lao,
    • Francesc Calafell,
    • Arcadi Navarro,
    • David Comas,
    • Howard Cann,
    • Suzannah Bumpstead,
    • Jilur Ghori,
    • Sarah Hunt,
    • Panos Deloukas,
    • Ian Dunham,
    • Lon R. Cardon,
    • and Jaume Bertranpetit
    Genome Res. March 2006 16: 323-330; Published in Advance February 8, 2006, doi:10.1101/gr.4138406

  • Analysis of allelic differential expression in human white blood cells

    • P.V. Krishna Pant,
    • Heng Tao,
    • Erica J. Beilharz,
    • Dennis G. Ballinger,
    • David R. Cox,
    • and Kelly A. Frazer
    Genome Res. March 2006 16: 331-339; Published in Advance February 8, 2006, doi:10.1101/gr.4559106

  • Callipyge mutation affects gene expression in cis: A potential role for chromatin structure

    • Susan K. Murphy,
    • Catherine M. Nolan,
    • Zhiqing Huang,
    • Katerina S. Kucera,
    • Brad A. Freking,
    • Timothy P.L. Smith,
    • Kreg A. Leymaster,
    • Jennifer R. Weidman,
    • and Randy L. Jirtle
    Genome Res. March 2006 16: 340-346; Published in Advance January 13, 2006, doi:10.1101/gr.4389306

  • “Genome design” model: Evidence from conserved intronic sequence in human–mouse comparison

    • Alexander E. Vinogradov
    Genome Res. March 2006 16: 347-354; Published in Advance February 3, 2006, doi:10.1101/gr.4318206

  • Dynamic evolution at pericentromeres

    • Anne E. Hall,
    • Gregory C. Kettler,
    • and Daphne Preuss
    Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206

  • Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae

    • James P. Kastenmayer,
    • Li Ni,
    • Angela Chu,
    • Lauren E. Kitchen,
    • Wei-Chun Au,
    • Hui Yang,
    • Carole D. Carter,
    • David Wheeler,
    • Ronald W. Davis,
    • Jef D. Boeke,
    • Michael A. Snyder,
    • and Munira A. Basrai
    Genome Res. March 2006 16: 365-373; doi:10.1101/gr.4355406

  • Identification and analysis of evolutionarily cohesive functional modules in protein networks

    • Mónica Campillos,
    • Christian von Mering,
    • Lars Juhl Jensen,
    • and Peer Bork
    Genome Res. March 2006 16: 374-382; Published in Advance January 31, 2006, doi:10.1101/gr.4336406

Methods

  • High-throughput DNA methylation profiling using universal bead arrays

    • Marina Bibikova,
    • Zhenwu Lin,
    • Lixin Zhou,
    • Eugene Chudin,
    • Eliza Wickham Garcia,
    • Bonnie Wu,
    • Dennis Doucet,
    • Neal J. Thomas,
    • Yunhua Wang,
    • Ekkehard Vollmer,
    • Torsten Goldmann,
    • Carola Seifart,
    • Wei Jiang,
    • David L. Barker,
    • Mark S. Chee,
    • Joanna Floros,
    • and Jian-Bing Fan
    Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
    OPEN ACCESS ARTICLE

  • Decoding the fine-scale structure of a breast cancer genome and transcriptome

    • Stanislav Volik,
    • Benjamin J. Raphael,
    • Guiqing Huang,
    • Michael R. Stratton,
    • Graham Bignel,
    • John Murnane,
    • John H. Brebner,
    • Krystyna Bajsarowicz,
    • Pamela L. Paris,
    • Quanzhou Tao,
    • David Kowbel,
    • Anna Lapuk,
    • Dmitri A. Shagin,
    • Irina A. Shagina,
    • Joe W. Gray,
    • Jan-Fang Cheng,
    • Pieter J. de Jong,
    • Pavel Pevzner,
    • and Colin Collins
    Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306

  • A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles

    • Li-Wei Chang,
    • Rakesh Nagarajan,
    • Jeffrey A. Magee,
    • Jeffrey Milbrandt,
    • and Gary D. Stormo
    Genome Res. March 2006 16: 405-413; Published in Advance January 31, 2006, doi:10.1101/gr.4303406

  • Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine

    • Yunhai Li,
    • Kee Khoon Lee,
    • Sean Walsh,
    • Caroline Smith,
    • Sophie Hadingham,
    • Karim Sorefan,
    • Gavin Cawley,
    • and Michael W. Bevan
    Genome Res. March 2006 16: 414-427; Published in Advance January 19, 2006, doi:10.1101/gr.4237406

  • Systematic identification of functional orthologs based on protein network comparison

    • Sourav Bandyopadhyay,
    • Roded Sharan,
    • and Trey Ideker
    Genome Res. March 2006 16: 428-435; Published in Advance April 4, 2006, doi:10.1101/gr.4526006

RESOURCES

  • Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse

    • Jennifer L. Moran,
    • Andrew D. Bolton,
    • Pamela V. Tran,
    • Alison Brown,
    • Noelle D. Dwyer,
    • Danielle K. Manning,
    • Bryan C. Bjork,
    • Cheng Li,
    • Kate Montgomery,
    • Sandra M. Siepka,
    • Martha Hotz Vitaterna,
    • Joseph S. Takahashi,
    • Tim Wiltshire,
    • David J. Kwiatkowski,
    • Raju Kucherlapati,
    • and David R. Beier
    Genome Res. March 2006 16: 436-440; Published in Advance February 3, 2006, doi:10.1101/gr.4563306

  • A global assembly of cotton ESTs

    • Joshua A. Udall,
    • Jordan M. Swanson,
    • Karl Haller,
    • Ryan A. Rapp,
    • Michael E. Sparks,
    • Jamie Hatfield,
    • Yeisoo Yu,
    • Yingru Wu,
    • Caitriona Dowd,
    • Aladdin B. Arpat,
    • Brad A. Sickler,
    • Thea A. Wilkins,
    • Jin Ying Guo,
    • Xiao Ya Chen,
    • Jodi Scheffler,
    • Earl Taliercio,
    • Ricky Turley,
    • Helen McFadden,
    • Paxton Payton,
    • Natalya Klueva,
    • Randell Allen,
    • Deshui Zhang,
    • Candace Haigler,
    • Curtis Wilkerson,
    • Jinfeng Suo,
    • Stefan R. Schulze,
    • Margaret L. Pierce,
    • Margaret Essenberg,
    • HyeRan Kim,
    • Danny J. Llewellyn,
    • Elizabeth S. Dennis,
    • David Kudrna,
    • Rod Wing,
    • Andrew H. Paterson,
    • Cari Soderlund,
    • and Jonathan F. Wendel
    Genome Res. March 2006 16: 441-450; Published in Advance February 14, 2006, doi:10.1101/gr.4602906
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This Issue

March 2006; 16 (3)
Cover
  1. In this Issue
  2. Forum
  3. COMMENTARY
  4. PERSPECTIVE
  5. LETTERS
  6. Methods
  7. RESOURCES

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