Table of Contents

March 2015; 25 (3)

Research

  • Actionable exomic incidental findings in 6503 participants: challenges of variant classification

    • Laura M. Amendola,
    • Michael O. Dorschner,
    • Peggy D. Robertson,
    • Joseph S. Salama,
    • Ragan Hart,
    • Brian H. Shirts,
    • Mitzi L. Murray,
    • Mari J. Tokita,
    • Carlos J. Gallego,
    • Daniel Seung Kim,
    • James T. Bennett,
    • David R. Crosslin,
    • Jane Ranchalis,
    • Kelly L. Jones,
    • Elisabeth A. Rosenthal,
    • Ella R. Jarvik,
    • Andy Itsara,
    • Emily H. Turner,
    • Daniel S. Herman,
    • Jennifer Schleit,
    • Amber Burt,
    • Seema M. Jamal,
    • Jenica L. Abrudan,
    • Andrew D. Johnson,
    • Laura K. Conlin,
    • Matthew C. Dulik,
    • Avni Santani,
    • Danielle R. Metterville,
    • Melissa Kelly,
    • Ann Katherine M. Foreman,
    • Kristy Lee,
    • Kent D. Taylor,
    • Xiuqing Guo,
    • Kristy Crooks,
    • Lesli A. Kiedrowski,
    • Leslie J. Raffel,
    • Ora Gordon,
    • Kalotina Machini,
    • Robert J. Desnick,
    • Leslie G. Biesecker,
    • Steven A. Lubitz,
    • Surabhi Mulchandani,
    • Greg M. Cooper,
    • Steven Joffe,
    • C. Sue Richards,
    • Yaoping Yang,
    • Jerome I. Rotter,
    • Stephen S. Rich,
    • Christopher J. O’Donnell,
    • Jonathan S. Berg,
    • Nancy B. Spinner,
    • James P. Evans,
    • Stephanie M. Fullerton,
    • Kathleen A. Leppig,
    • Robin L. Bennett,
    • Thomas Bird,
    • Virginia P. Sybert,
    • William M. Grady,
    • Holly K. Tabor,
    • Jerry H. Kim,
    • Michael J. Bamshad,
    • Benjamin Wilfond,
    • Arno G. Motulsky,
    • C. Ronald Scott,
    • Colin C. Pritchard,
    • Tom D. Walsh,
    • Wylie Burke,
    • Wendy H. Raskind,
    • Peter Byers,
    • Fuki M. Hisama,
    • Heidi Rehm,
    • Debbie A. Nickerson,
    • and Gail P. Jarvik
    Genome Res. March 2015 25: 305-315; Published in Advance January 30, 2015, doi:10.1101/gr.183483.114
    OPEN ACCESS ARTICLE

  • Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

    • Hoon Kim,
    • Siyuan Zheng,
    • Seyed S. Amini,
    • Selene M. Virk,
    • Tom Mikkelsen,
    • Daniel J. Brat,
    • Jonna Grimsby,
    • Carrie Sougnez,
    • Florian Muller,
    • Jian Hu,
    • Andrew E. Sloan,
    • Mark L. Cohen,
    • Erwin G. Van Meir,
    • Lisa Scarpace,
    • Peter W. Laird,
    • John N. Weinstein,
    • Eric S. Lander,
    • Stacey Gabriel,
    • Gad Getz,
    • Matthew Meyerson,
    • Lynda Chin,
    • Jill S. Barnholtz-Sloan,
    • and Roel G.W. Verhaak
    Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114

  • DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences

    • Yoshiyuki Watanabe,
    • Hiroyuki Yamamoto,
    • Ritsuko Oikawa,
    • Minoru Toyota,
    • Masakazu Yamamoto,
    • Norihiro Kokudo,
    • Shinji Tanaka,
    • Shigeki Arii,
    • Hiroshi Yotsuyanagi,
    • Kazuhiko Koike,
    • and Fumio Itoh
    Genome Res. March 2015 25: 328-337; Published in Advance February 4, 2015, doi:10.1101/gr.175240.114

  • Methylomic trajectories across human fetal brain development

    • Helen Spiers,
    • Eilis Hannon,
    • Leonard C. Schalkwyk,
    • Rebecca Smith,
    • Chloe C.Y. Wong,
    • Michael C. O’Donovan,
    • Nicholas J. Bray,
    • and Jonathan Mill
    Genome Res. March 2015 25: 338-352; Published in Advance February 3, 2015, doi:10.1101/gr.180273.114
    OPEN ACCESS ARTICLE

  • A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation

    • Hala Al Adhami,
    • Brendan Evano,
    • Anne Le Digarcher,
    • Charlotte Gueydan,
    • Emeric Dubois,
    • Hugues Parrinello,
    • Christelle Dantec,
    • Tristan Bouschet,
    • Annie Varrault,
    • and Laurent Journot
    Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
    OPEN ACCESS ARTICLE

  • Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline

    • Toshiaki Watanabe,
    • Ee-chun Cheng,
    • Mei Zhong,
    • and Haifan Lin
    Genome Res. March 2015 25: 368-380; Published in Advance December 5, 2014, doi:10.1101/gr.180802.114

  • Asymmetric nucleosomes flank promoters in the budding yeast genome

    • Srinivas Ramachandran,
    • Gabriel E. Zentner,
    • and Steven Henikoff
    Genome Res. March 2015 25: 381-390; Published in Advance December 9, 2014, doi:10.1101/gr.182618.114
    OPEN ACCESS ARTICLE

  • The spatial and temporal organization of origin firing during the S-phase of fission yeast

    • Atanas Kaykov and
    • Paul Nurse
    Genome Res. March 2015 25: 391-401; Published in Advance February 3, 2015, doi:10.1101/gr.180372.114
    OPEN ACCESS ARTICLE

  • Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription

    • Elizabeth A. Hoffman,
    • Andrew McCulley,
    • Brian Haarer,
    • Remigiusz Arnak,
    • and Wenyi Feng
    Genome Res. March 2015 25: 402-412; Published in Advance January 21, 2015, doi:10.1101/gr.180497.114
    OPEN ACCESS ARTICLE

  • Genetic and phenotypic intra-species variation in Candida albicans

    • Matthew P. Hirakawa,
    • Diego A. Martinez,
    • Sharadha Sakthikumar,
    • Matthew Z. Anderson,
    • Aaron Berlin,
    • Sharvari Gujja,
    • Qiandong Zeng,
    • Ethan Zisson,
    • Joshua M. Wang,
    • Joshua M. Greenberg,
    • Judith Berman,
    • Richard J. Bennett,
    • and Christina A. Cuomo
    Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114

Methods

  • Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing

    • Brock A. Peters,
    • Bahram G. Kermani,
    • Oleg Alferov,
    • Misha R. Agarwal,
    • Mark A. McElwain,
    • Natali Gulbahce,
    • Daniel M. Hayden,
    • Y. Tom Tang,
    • Rebecca Yu Zhang,
    • Rick Tearle,
    • Birgit Crain,
    • Renata Prates,
    • Alan Berkeley,
    • Santiago Munné,
    • and Radoje Drmanac
    Genome Res. March 2015 25: 426-434; Published in Advance February 11, 2015, doi:10.1101/gr.181255.114
    OPEN ACCESS ARTICLE

  • Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling

    • Yo Suzuki,
    • Nacyra Assad-Garcia,
    • Maxim Kostylev,
    • Vladimir N. Noskov,
    • Kim S. Wise,
    • Bogumil J. Karas,
    • Jason Stam,
    • Michael G. Montague,
    • Timothy J. Hanly,
    • Nico J. Enriquez,
    • Adi Ramon,
    • Gregory M. Goldgof,
    • R. Alexander Richter,
    • Sanjay Vashee,
    • Ray-Yuan Chuang,
    • Elizabeth A. Winzeler,
    • Clyde A. Hutchison III,
    • Daniel G. Gibson,
    • Hamilton O. Smith,
    • John I. Glass,
    • and J. Craig Venter
    Genome Res. March 2015 25: 435-444; Published in Advance February 5, 2015, doi:10.1101/gr.182477.114

Resource

  • The Release 6 reference sequence of the Drosophila melanogaster genome

    • Roger A. Hoskins,
    • Joseph W. Carlson,
    • Kenneth H. Wan,
    • Soo Park,
    • Ivonne Mendez,
    • Samuel E. Galle,
    • Benjamin W. Booth,
    • Barret D. Pfeiffer,
    • Reed A. George,
    • Robert Svirskas,
    • Martin Krzywinski,
    • Jacqueline Schein,
    • Maria Carmela Accardo,
    • Elisabetta Damia,
    • Giovanni Messina,
    • María Méndez-Lago,
    • Beatriz de Pablos,
    • Olga V. Demakova,
    • Evgeniya N. Andreyeva,
    • Lidiya V. Boldyreva,
    • Marco Marra,
    • A. Bernardo Carvalho,
    • Patrizio Dimitri,
    • Alfredo Villasante,
    • Igor F. Zhimulev,
    • Gerald M. Rubin,
    • Gary H. Karpen,
    • and Susan E. Celniker
    Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
    OPEN ACCESS ARTICLE
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This Issue

March 2015; 25 (3)
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