Table of Contents

October 2017; 27 (10)

Research

  • Transposable elements are the primary source of novelty in primate gene regulation

    • Marco Trizzino,
    • YoSon Park,
    • Marcia Holsbach-Beltrame,
    • Katherine Aracena,
    • Katelyn Mika,
    • Minal Caliskan,
    • George H. Perry,
    • Vincent J. Lynch,
    • and Christopher D. Brown
    Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
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  • Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence

    • Christelle Lenain,
    • Carolyn A. de Graaf,
    • Ludo Pagie,
    • Nils L. Visser,
    • Marcel de Haas,
    • Sandra S. de Vries,
    • Daniel Peric-Hupkes,
    • Bas van Steensel,
    • and Daniel S. Peeper
    Genome Res. October 2017 27: 1634-1644; Published in Advance September 15, 2017, doi:10.1101/gr.225763.117

  • Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity

    • Zdenek Andrysik,
    • Matthew D. Galbraith,
    • Anna L. Guarnieri,
    • Sara Zaccara,
    • Kelly D. Sullivan,
    • Ahwan Pandey,
    • Morgan MacBeth,
    • Alberto Inga,
    • and Joaquín M. Espinosa
    Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
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  • Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

    • Stefano de Pretis,
    • Theresia R. Kress,
    • Marco J. Morelli,
    • Arianna Sabò,
    • Chiara Locarno,
    • Alessandro Verrecchia,
    • Mirko Doni,
    • Stefano Campaner,
    • Bruno Amati,
    • and Mattia Pelizzola
    Genome Res. October 2017 27: 1658-1664; Published in Advance September 13, 2017, doi:10.1101/gr.226035.117
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  • Redundant and incoherent regulations of multiple phenotypes suggest microRNAs’ role in stability control

    • Zhongqi Liufu,
    • Yixin Zhao,
    • Li Guo,
    • Guangxia Miao,
    • Juan Xiao,
    • Yang Lyu,
    • Yuxin Chen,
    • Suhua Shi,
    • Tian Tang,
    • and Chung-I Wu
    Genome Res. October 2017 27: 1665-1673; Published in Advance September 13, 2017, doi:10.1101/gr.222505.117

  • Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity

    • Peng Mao,
    • Alexander J. Brown,
    • Ewa P. Malc,
    • Piotr A. Mieczkowski,
    • Michael J. Smerdon,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. October 2017 27: 1674-1684; Published in Advance September 14, 2017, doi:10.1101/gr.225771.117

  • Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

    • Xiaochuan Liu,
    • Mainul Hoque,
    • Marc Larochelle,
    • Jean-François Lemay,
    • Nathan Yurko,
    • James L. Manley,
    • François Bachand,
    • and Bin Tian
    Genome Res. October 2017 27: 1685-1695; Published in Advance September 15, 2017, doi:10.1101/gr.222331.117

  • RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system

    • Dan Bar-Yaacov,
    • Ernest Mordret,
    • Ruth Towers,
    • Tammy Biniashvili,
    • Clara Soyris,
    • Schraga Schwartz,
    • Orna Dahan,
    • and Yitzhak Pilpel
    Genome Res. October 2017 27: 1696-1703; Published in Advance September 1, 2017, doi:10.1101/gr.222760.117

Methods

  • Detection of structural mosaicism from targeted and whole-genome sequencing data

    • Daniel A. King,
    • Alejandro Sifrim,
    • Tomas W. Fitzgerald,
    • Raheleh Rahbari,
    • Emma Hobson,
    • Tessa Homfray,
    • Sahar Mansour,
    • Sarju G. Mehta,
    • Mohammed Shehla,
    • Susan E. Tomkins,
    • Pradeep C. Vasudevan,
    • Matthew E. Hurles,
    • and The Deciphering Developmental Disorders Study
    Genome Res. October 2017 27: 1704-1714; Published in Advance August 30, 2017, doi:10.1101/gr.212373.116
    OPEN ACCESS ARTICLE

  • Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

    • Joshua Traynelis,
    • Michael Silk,
    • Quanli Wang,
    • Samuel F. Berkovic,
    • Liping Liu,
    • David B. Ascher,
    • David J. Balding,
    • and Slavé Petrovski
    Genome Res. October 2017 27: 1715-1729; Published in Advance September 1, 2017, doi:10.1101/gr.226589.117
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  • Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

    • Ron Schwessinger,
    • Maria C. Suciu,
    • Simon J. McGowan,
    • Jelena Telenius,
    • Stephen Taylor,
    • Doug R. Higgs,
    • and Jim R. Hughes
    Genome Res. October 2017 27: 1730-1742; Published in Advance September 13, 2017, doi:10.1101/gr.220202.117

  • Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies

    • Paul Geeleher,
    • Zhenyu Zhang,
    • Fan Wang,
    • Robert F. Gruener,
    • Aritro Nath,
    • Gladys Morrison,
    • Steven Bhutra,
    • Robert L. Grossman,
    • and R. Stephanie Huang
    Genome Res. October 2017 27: 1743-1751; Published in Advance August 28, 2017, doi:10.1101/gr.221077.117

  • Solid-phase reverse transfection for intracellular delivery of functionally active proteins

    • Ruben Bulkescher,
    • Vytaute Starkuviene,
    • and Holger Erfle
    Genome Res. October 2017 27: 1752-1758; Published in Advance September 5, 2017, doi:10.1101/gr.215103.116

Resources

  • An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

    • Javier Tapial,
    • Kevin C.H. Ha,
    • Timothy Sterne-Weiler,
    • André Gohr,
    • Ulrich Braunschweig,
    • Antonio Hermoso-Pulido,
    • Mathieu Quesnel-Vallières,
    • Jon Permanyer,
    • Reza Sodaei,
    • Yamile Marquez,
    • Luca Cozzuto,
    • Xinchen Wang,
    • Melisa Gómez-Velázquez,
    • Teresa Rayon,
    • Miguel Manzanares,
    • Julia Ponomarenko,
    • Benjamin J. Blencowe,
    • and Manuel Irimia
    Genome Res. October 2017 27: 1759-1768; Published in Advance August 30, 2017, doi:10.1101/gr.220962.117

  • Toward the human cellular microRNAome

    • Matthew N. McCall,
    • Min-Sik Kim,
    • Mohammed Adil,
    • Arun H. Patil,
    • Yin Lu,
    • Christopher J. Mitchell,
    • Pamela Leal-Rojas,
    • Jinchong Xu,
    • Manoj Kumar,
    • Valina L. Dawson,
    • Ted M. Dawson,
    • Alexander S. Baras,
    • Avi Z. Rosenberg,
    • Dan E. Arking,
    • Kathleen H. Burns,
    • Akhilesh Pandey,
    • and Marc K. Halushka
    Genome Res. October 2017 27: 1769-1781; Published in Advance September 6, 2017, doi:10.1101/gr.222067.117

Corrigendum

  • Corrigendum: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy

    • Ayesha Noorani,
    • Jan Bornschein,
    • Andy G. Lynch,
    • Maria Secrier,
    • Achilleas Achilleos,
    • Matthew Eldridge,
    • Lawrence Bower,
    • Jamie M.J. Weaver,
    • Jason Crawte,
    • Chin-Ann Ong,
    • Nicholas Shannon,
    • Shona MacRae,
    • Nicola Grehan,
    • Barbara Nutzinger,
    • Maria O'Donovan,
    • Richard Hardwick,
    • Simon Tavaré,
    • Rebecca C. Fitzgerald,
    • and on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
    Genome Res. October 2017 27: 1782; doi:10.1101/gr.229153.117
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This Issue

October 2017; 27 (10)
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  1. Research
  2. Methods
  3. Resources
  4. Corrigendum

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