Table of Contents

February 2014; 24 (2)

Research

  • Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization

    • Kasper D. Hansen,
    • Sarven Sabunciyan,
    • Ben Langmead,
    • Noemi Nagy,
    • Rebecca Curley,
    • Georg Klein,
    • Eva Klein,
    • Daniel Salamon,
    • and Andrew P. Feinberg
    Genome Res. February 2014 24: 177-184; Published in Advance September 25, 2013, doi:10.1101/gr.157743.113
    OPEN ACCESS ARTICLE

  • Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

    • Keiko Akagi,
    • Jingfeng Li,
    • Tatevik R. Broutian,
    • Hesed Padilla-Nash,
    • Weihong Xiao,
    • Bo Jiang,
    • James W. Rocco,
    • Theodoros N. Teknos,
    • Bhavna Kumar,
    • Danny Wangsa,
    • Dandan He,
    • Thomas Ried,
    • David E. Symer,
    • and Maura L. Gillison
    Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113

  • Genomic and transcriptomic plasticity in treatment-naïve ovarian cancer

    • Marlous Hoogstraat,
    • Mirjam S. de Pagter,
    • Geert A. Cirkel,
    • Markus J. van Roosmalen,
    • Timothy T. Harkins,
    • Karen Duran,
    • Jennifer Kreeftmeijer,
    • Ivo Renkens,
    • Petronella O. Witteveen,
    • Clarence C. Lee,
    • Isaac J. Nijman,
    • Tanisha Guy,
    • Ruben van ’t Slot,
    • Trudy N. Jonges,
    • Martijn P. Lolkema,
    • Marco J. Koudijs,
    • Ronald P. Zweemer,
    • Emile E. Voest,
    • Edwin Cuppen,
    • and Wigard P. Kloosterman
    Genome Res. February 2014 24: 200-211; Published in Advance November 12, 2013, doi:10.1101/gr.161026.113

  • Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

    • Pedro G. Ferreira,
    • Pedro Jares,
    • Daniel Rico,
    • Gonzalo Gómez-López,
    • Alejandra Martínez-Trillos,
    • Neus Villamor,
    • Simone Ecker,
    • Abel González-Pérez,
    • David G. Knowles,
    • Jean Monlong,
    • Rory Johnson,
    • Victor Quesada,
    • Sarah Djebali,
    • Panagiotis Papasaikas,
    • Mónica López-Guerra,
    • Dolors Colomer,
    • Cristina Royo,
    • Maite Cazorla,
    • Magda Pinyol,
    • Guillem Clot,
    • Marta Aymerich,
    • Maria Rozman,
    • Marta Kulis,
    • David Tamborero,
    • Anaïs Gouin,
    • Julie Blanc,
    • Marta Gut,
    • Ivo Gut,
    • Xose S. Puente,
    • David G. Pisano,
    • José Ignacio Martin-Subero,
    • Nuria López-Bigas,
    • Armando López-Guillermo,
    • Alfonso Valencia,
    • Carlos López-Otín,
    • Elías Campo,
    • and Roderic Guigó
    Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
    OPEN ACCESS ARTICLE

  • An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease

    • Farhoud Faraji,
    • Ying Hu,
    • Gang Wu,
    • Natalie E. Goldberger,
    • Renard C. Walker,
    • Jinghui Zhang,
    • and Kent W. Hunter
    Genome Res. February 2014 24: 227-240; Published in Advance December 9, 2013, doi:10.1101/gr.166223.113

  • Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

    • Jeremy M. Simon,
    • Kathryn E. Hacker,
    • Darshan Singh,
    • A. Rose Brannon,
    • Joel S. Parker,
    • Matthew Weiser,
    • Thai H. Ho,
    • Pei-Fen Kuan,
    • Eric Jonasch,
    • Terrence S. Furey,
    • Jan F. Prins,
    • Jason D. Lieb,
    • W. Kimryn Rathmell,
    • and Ian J. Davis
    Genome Res. February 2014 24: 241-250; Published in Advance October 24, 2013, doi:10.1101/gr.158253.113

  • The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed

    • Brittany S. Sexton,
    • Denis Avey,
    • Brooke R. Druliner,
    • Justin A. Fincher,
    • Daniel L. Vera,
    • Daniel J. Grau,
    • Mark L. Borowsky,
    • Shobhit Gupta,
    • Senthil B. Girimurugan,
    • Eric Chicken,
    • Jinfeng Zhang,
    • William S. Noble,
    • Fanxiu Zhu,
    • Robert E. Kingston,
    • and Jonathan H. Dennis
    Genome Res. February 2014 24: 251-259; Published in Advance December 5, 2013, doi:10.1101/gr.160150.113

  • Canonical nucleosome organization at promoters forms during genome activation

    • Yong Zhang,
    • Nadine L. Vastenhouw,
    • Jianxing Feng,
    • Kai Fu,
    • Chenfei Wang,
    • Ying Ge,
    • Andrea Pauli,
    • Paul van Hummelen,
    • Alexander F. Schier,
    • and X. Shirley Liu
    Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
    OPEN ACCESS ARTICLE

  • Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells

    • Timothy J. Looney,
    • Li Zhang,
    • Chih-Hsin Chen,
    • Jae Hyun Lee,
    • Sheila Chari,
    • Frank Fuxiang Mao,
    • Mattia Pelizzola,
    • Lu Zhang,
    • Ryan Lister,
    • Samuel W. Baker,
    • Croydon J. Fernandes,
    • Jedidiah Gaetz,
    • Kara M. Foshay,
    • Kayla L. Clift,
    • Zhenyu Zhang,
    • Wei-Qiang Li,
    • Eric J. Vallender,
    • Ulrich Wagner,
    • Jane Yuxia Qin,
    • Katelyn J. Michelini,
    • Branimir Bugarija,
    • Donghyun Park,
    • Emmanuel Aryee,
    • Thomas Stricker,
    • Jie Zhou,
    • Kevin P. White,
    • Bing Ren,
    • Gary P. Schroth,
    • Joseph R. Ecker,
    • Andy Peng Xiang,
    • and Bruce T. Lahn
    Genome Res. February 2014 24: 267-280; Published in Advance December 5, 2013, doi:10.1101/gr.143891.112

  • Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network

    • Marcos Simões-Costa,
    • Joanne Tan-Cabugao,
    • Igor Antoshechkin,
    • Tatjana Sauka-Spengler,
    • and Marianne E. Bronner
    Genome Res. February 2014 24: 281-290; Published in Advance January 3, 2014, doi:10.1101/gr.161182.113

  • Genomic analysis of primordial dwarfism reveals novel disease genes

    • Ranad Shaheen,
    • Eissa Faqeih,
    • Shinu Ansari,
    • Ghada Abdel-Salam,
    • Zuhair N. Al-Hassnan,
    • Tarfa Al-Shidi,
    • Rana Alomar,
    • Sameera Sogaty,
    • and Fowzan S. Alkuraya
    Genome Res. February 2014 24: 291-299; Published in Advance January 3, 2014, doi:10.1101/gr.160572.113

Methods

  • Discovery of recurrent structural variants in nasopharyngeal carcinoma

    • Anton Valouev,
    • Ziming Weng,
    • Robert T. Sweeney,
    • Sushama Varma,
    • Quynh-Thu Le,
    • Christina Kong,
    • Arend Sidow,
    • and Robert B. West
    Genome Res. February 2014 24: 300-309; Published in Advance November 8, 2013, doi:10.1101/gr.156224.113

  • TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

    • Ken Chen,
    • Lei Chen,
    • Xian Fan,
    • John Wallis,
    • Li Ding,
    • and George Weinstock
    Genome Res. February 2014 24: 310-317; Published in Advance December 4, 2013, doi:10.1101/gr.162883.113

  • Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations

    • Anand Patel,
    • Richard Schwab,
    • Yu-Tsueng Liu,
    • and Vineet Bafna
    Genome Res. February 2014 24: 318-328; Published in Advance December 4, 2013, doi:10.1101/gr.161497.113

  • Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

    • Nancy H. Nabilsi,
    • Loic P. Deleyrolle,
    • Russell P. Darst,
    • Alberto Riva,
    • Brent A. Reynolds,
    • and Michael P. Kladde
    Genome Res. February 2014 24: 329-339; Published in Advance October 8, 2013, doi:10.1101/gr.161737.113

Resources

  • Improved exome prioritization of disease genes through cross-species phenotype comparison

    • Peter N. Robinson,
    • Sebastian Köhler,
    • Anika Oellrich,
    • Sanger Mouse Genetics Project,
    • Kai Wang,
    • Christopher J. Mungall,
    • Suzanna E. Lewis,
    • Nicole Washington,
    • Sebastian Bauer,
    • Dominik Seelow,
    • Peter Krawitz,
    • Christian Gilissen,
    • Melissa Haendel,
    • and Damian Smedley
    Genome Res. February 2014 24: 340-348; Published in Advance October 25, 2013, doi:10.1101/gr.160325.113
    OPEN ACCESS ARTICLE

  • Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster

    • Federico A. Santoni,
    • Periklis Makrythanasis,
    • Sergey Nikolaev,
    • Michel Guipponi,
    • Daniel Robyr,
    • Armand Bottani,
    • and Stylianos E. Antonarakis
    Genome Res. February 2014 24: 349-355; Published in Advance January 3, 2014, doi:10.1101/gr.163832.113

  • Variation Ontology for annotation of variation effects and mechanisms

    • Mauno Vihinen
    Genome Res. February 2014 24: 356-364; Published in Advance October 25, 2013, doi:10.1101/gr.157495.113
    OPEN ACCESS ARTICLE
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This Issue

February 2014; 24 (2)
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