Table of Contents

March 2019; 29 (3)

Research

  • Ribosomal DNA harbors an evolutionarily conserved clock of biological aging

    • Meng Wang and
    • Bernardo Lemos
    Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118

  • Most chromatin interactions are not in linkage disequilibrium

    • Sean Whalen and
    • Katherine S. Pollard
    Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
    OPEN ACCESS ARTICLE

  • High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

    • Kaia Mattioli,
    • Pieter-Jan Volders,
    • Chiara Gerhardinger,
    • James C. Lee,
    • Philipp G. Maass,
    • Marta Melé,
    • and John L. Rinn
    Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
    OPEN ACCESS ARTICLE

  • The circular RNome of primary breast cancer

    • Marcel Smid,
    • Saskia M. Wilting,
    • Katharina Uhr,
    • F. Germán Rodríguez-González,
    • Vanja de Weerd,
    • Wendy J.C. Prager-Van der Smissen,
    • Michelle van der Vlugt-Daane,
    • Anne van Galen,
    • Serena Nik-Zainal,
    • Adam Butler,
    • Sancha Martin,
    • Helen R. Davies,
    • Johan Staaf,
    • Marc J. van de Vijver,
    • Andrea L. Richardson,
    • Gaëten MacGrogan,
    • Roberto Salgado,
    • Gert G.G.M. van den Eynden,
    • Colin A. Purdie,
    • Alastair M. Thompson,
    • Carlos Caldas,
    • Paul N. Span,
    • Fred C.G.J. Sweep,
    • Peter T. Simpson,
    • Sunil R. Lakhani,
    • Steven Van Laere,
    • Christine Desmedt,
    • Angelo Paradiso,
    • Jorunn Eyfjord,
    • Annegien Broeks,
    • Anne Vincent-Salomon,
    • Andrew P. Futreal,
    • Stian Knappskog,
    • Tari King,
    • Alain Viari,
    • Anne-Lise Børresen-Dale,
    • Hendrik G. Stunnenberg,
    • Mike Stratton,
    • John A. Foekens,
    • Anieta M. Sieuwerts,
    • and John W.M. Martens
    Genome Res. March 2019 29: 356-366; Published in Advance January 28, 2019, doi:10.1101/gr.238121.118

  • Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion

    • Brittany L. Daughtry,
    • Jimi L. Rosenkrantz,
    • Nathan H. Lazar,
    • Suzanne S. Fei,
    • Nash Redmayne,
    • Kristof A. Torkenczy,
    • Andrew Adey,
    • Melissa Yan,
    • Lina Gao,
    • Byung Park,
    • Kimberly A. Nevonen,
    • Lucia Carbone,
    • and Shawn L. Chavez
    Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118

  • Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

    • Marina Veil,
    • Lev Y. Yampolsky,
    • Björn Grüning,
    • and Daria Onichtchouk
    Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118

  • Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes

    • Monica R. Sanchez,
    • Celia Payen,
    • Frances Cheong,
    • Blake T. Hovde,
    • Sarah Bissonnette,
    • Adam P. Arkin,
    • Jeffrey M. Skerker,
    • Rachel B. Brem,
    • Amy A. Caudy,
    • and Maitreya J. Dunham
    Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117

  • Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

    • Josefina Ocampo,
    • Răzvan V. Chereji,
    • Peter R. Eriksson,
    • and David J. Clark
    Genome Res. March 2019 29: 407-417; Published in Advance January 25, 2019, doi:10.1101/gr.242032.118

Methods

  • Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin

    • Kun Sun,
    • Peiyong Jiang,
    • Suk Hang Cheng,
    • Timothy H.T. Cheng,
    • John Wong,
    • Vincent W.S. Wong,
    • Simon S.M. Ng,
    • Brigette B.Y. Ma,
    • Tak Y. Leung,
    • Stephen L. Chan,
    • Tony S.K. Mok,
    • Paul B.S. Lai,
    • Henry L.Y. Chan,
    • Hao Sun,
    • K.C. Allen Chan,
    • Rossa W.K. Chiu,
    • and Y.M. Dennis Lo
    Genome Res. March 2019 29: 418-427; Published in Advance February 26, 2019, doi:10.1101/gr.242719.118
    OPEN ACCESS ARTICLE

  • Bayesian-based noninvasive prenatal diagnosis of single-gene disorders

    • Tom Rabinowitz,
    • Avital Polsky,
    • David Golan,
    • Artem Danilevsky,
    • Guy Shapira,
    • Chen Raff,
    • Lina Basel-Salmon,
    • Reut Tomashov Matar,
    • and Noam Shomron
    Genome Res. March 2019 29: 428-438; Published in Advance February 20, 2019, doi:10.1101/gr.235796.118
    OPEN ACCESS ARTICLE

  • Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes

    • Dana Sherill-Rofe,
    • Dolev Rahat,
    • Steven Findlay,
    • Anna Mellul,
    • Irene Guberman,
    • Maya Braun,
    • Idit Bloch,
    • Alon Lalezari,
    • Arash Samiei,
    • Ruslan Sadreyev,
    • Michal Goldberg,
    • Alexandre Orthwein,
    • Aviad Zick,
    • and Yuval Tabach
    Genome Res. March 2019 29: 439-448; Published in Advance February 4, 2019, doi:10.1101/gr.241414.118

  • Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

    • Emily R. Miraldi,
    • Maria Pokrovskii,
    • Aaron Watters,
    • Dayanne M. Castro,
    • Nicholas De Veaux,
    • Jason A. Hall,
    • June-Yong Lee,
    • Maria Ciofani,
    • Aviv Madar,
    • Nick Carriero,
    • Dan R. Littman,
    • and Richard Bonneau
    Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
    OPEN ACCESS ARTICLE

  • JACKS: joint analysis of CRISPR/Cas9 knockout screens

    • Felicity Allen,
    • Fiona Behan,
    • Anton Khodak,
    • Francesco Iorio,
    • Kosuke Yusa,
    • Mathew Garnett,
    • and Leopold Parts
    Genome Res. March 2019 29: 464-471; Published in Advance January 23, 2019, doi:10.1101/gr.238923.118
    OPEN ACCESS ARTICLE

Resources

  • Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

    • Bo Zhou,
    • Steve S. Ho,
    • Stephanie U. Greer,
    • Xiaowei Zhu,
    • John M. Bell,
    • Joseph G. Arthur,
    • Noah Spies,
    • Xianglong Zhang,
    • Seunggyu Byeon,
    • Reenal Pattni,
    • Noa Ben-Efraim,
    • Michael S. Haney,
    • Rajini R. Haraksingh,
    • Giltae Song,
    • Hanlee P. Ji,
    • Dimitri Perrin,
    • Wing H. Wong,
    • Alexej Abyzov,
    • and Alexander E. Urban
    Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118

  • PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations

    • Bo Wen,
    • Xiaojing Wang,
    • and Bing Zhang
    Genome Res. March 2019 29: 485-493; Published in Advance January 4, 2019, doi:10.1101/gr.235028.118

  • Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis

    • Leslie O. Goodwin,
    • Erik Splinter,
    • Tiffany L. Davis,
    • Rachel Urban,
    • Hao He,
    • Robert E. Braun,
    • Elissa J. Chesler,
    • Vivek Kumar,
    • Max van Min,
    • Juliet Ndukum,
    • Vivek M. Philip,
    • Laura G. Reinholdt,
    • Karen Svenson,
    • Jacqueline K. White,
    • Michael Sasner,
    • Cathleen Lutz,
    • and Stephen A. Murray
    Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
    OPEN ACCESS ARTICLE

  • Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

    • Michal Pawlak,
    • Katarzyna Z. Kedzierska,
    • Maciej Migdal,
    • Karim Abu Nahia,
    • Jordan A. Ramilowski,
    • Lukasz Bugajski,
    • Kosuke Hashimoto,
    • Aleksandra Marconi,
    • Katarzyna Piwocka,
    • Piero Carninci,
    • and Cecilia L. Winata
    Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
    OPEN ACCESS ARTICLE

Corrigendum

  • Corrigendum: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

    • Guifen Liu,
    • Wen Wang,
    • Shengen Hu,
    • Xiangxiu Wang,
    • and Yong Zhang
    Genome Res. March 2019 29: 520; doi:10.1101/gr.248732.119
    OPEN ACCESS ARTICLE
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This Issue

March 2019; 29 (3)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Corrigendum

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