Table of Contents

September 2018; 28 (9)

Perspective

  • Realizing the potential of blockchain technologies in genomics

    • Halil Ibrahim Ozercan,
    • Atalay Mert Ileri,
    • Erman Ayday,
    • and Can Alkan
    Genome Res. September 2018 28: 1255-1263; Published in Advance August 3, 2018, doi:10.1101/gr.207464.116
    OPEN ACCESS ARTICLE

Research

  • Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

    • Ilias Georgakopoulos-Soares,
    • Sandro Morganella,
    • Naman Jain,
    • Martin Hemberg,
    • and Serena Nik-Zainal
    Genome Res. September 2018 28: 1264-1271; Published in Advance August 13, 2018, doi:10.1101/gr.231688.117

  • Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

    • Ian C. McDowell,
    • Alejandro Barrera,
    • Anthony M. D'Ippolito,
    • Christopher M. Vockley,
    • Linda K. Hong,
    • Sarah M. Leichter,
    • Luke C. Bartelt,
    • William H. Majoros,
    • Lingyun Song,
    • Alexias Safi,
    • D. Dewran Koçak,
    • Charles A. Gersbach,
    • Alexander J. Hartemink,
    • Gregory E. Crawford,
    • Barbara E. Engelhardt,
    • and Timothy E. Reddy
    Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
    OPEN ACCESS ARTICLE

  • Tracing human stem cell lineage during development using DNA methylation

    • Lucas A. Salas,
    • John K. Wiencke,
    • Devin C. Koestler,
    • Ze Zhang,
    • Brock C. Christensen,
    • and Karl T. Kelsey
    Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
    OPEN ACCESS ARTICLE

  • Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels

    • Arwen W. Gao,
    • Mark G. Sterken,
    • Jelmi uit de Bos,
    • Jelle van Creij,
    • Rashmi Kamble,
    • Basten L. Snoek,
    • Jan E. Kammenga,
    • and Riekelt H. Houtkooper
    Genome Res. September 2018 28: 1296-1308; Published in Advance August 14, 2018, doi:10.1101/gr.232322.117
    OPEN ACCESS ARTICLE

  • Death of new microRNA genes in Drosophila via gradual loss of fitness advantages

    • Guang-An Lu,
    • Yixin Zhao,
    • Hao Yang,
    • Ao Lan,
    • Suhua Shi,
    • Zhongqi Liufu,
    • Yumei Huang,
    • Tian Tang,
    • Jin Xu,
    • Xu Shen,
    • and Chung-I Wu
    Genome Res. September 2018 28: 1309-1318; Published in Advance July 26, 2018, doi:10.1101/gr.233809.117

  • Hidden variation in polyploid wheat drives local adaptation

    • Laura-Jayne Gardiner,
    • Ryan Joynson,
    • Jimmy Omony,
    • Rachel Rusholme-Pilcher,
    • Lisa Olohan,
    • Daniel Lang,
    • Caihong Bai,
    • Malcolm Hawkesford,
    • David Salt,
    • Manuel Spannagl,
    • Klaus F.X. Mayer,
    • John Kenny,
    • Michael Bevan,
    • Neil Hall,
    • and Anthony Hall
    Genome Res. September 2018 28: 1319-1332; Published in Advance August 9, 2018, doi:10.1101/gr.233551.117
    OPEN ACCESS ARTICLE

  • Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots

    • Atul Kakrana,
    • Sandra M. Mathioni,
    • Kun Huang,
    • Reza Hammond,
    • Lee Vandivier,
    • Parth Patel,
    • Siwaret Arikit,
    • Olga Shevchenko,
    • Alex E. Harkess,
    • Bruce Kingham,
    • Brian D. Gregory,
    • James H. Leebens-Mack,
    • and Blake C. Meyers
    Genome Res. September 2018 28: 1333-1344; Published in Advance July 12, 2018, doi:10.1101/gr.228163.117

Methods

  • High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics

    • Maurizio Pellegrino,
    • Adam Sciambi,
    • Sebastian Treusch,
    • Robert Durruthy-Durruthy,
    • Kaustubh Gokhale,
    • Jose Jacob,
    • Tina X. Chen,
    • Jennifer A. Geis,
    • William Oldham,
    • Jairo Matthews,
    • Hagop Kantarjian,
    • P. Andrew Futreal,
    • Keyur Patel,
    • Keith W. Jones,
    • Koichi Takahashi,
    • and Dennis J. Eastburn
    Genome Res. September 2018 28: 1345-1352; Published in Advance August 7, 2018, doi:10.1101/gr.232272.117
    OPEN ACCESS ARTICLE

  • Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations

    • Yu-Jui Ho,
    • Naishitha Anaparthy,
    • David Molik,
    • Grinu Mathew,
    • Toby Aicher,
    • Ami Patel,
    • James Hicks,
    • and Molly Gale Hammell
    Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117

  • Whole-genome bisulfite sequencing with improved accuracy and cost

    • Masako Suzuki,
    • Will Liao,
    • Frank Wos,
    • Andrew D. Johnston,
    • Justin DeGrazia,
    • Jennifer Ishii,
    • Toby Bloom,
    • Michael C. Zody,
    • Soren Germer,
    • and John M. Greally
    Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117

  • Genome-scale identification of cellular pathways required for cell surface recognition

    • Sumana Sharma,
    • S. Josefin Bartholdson,
    • Amalie C.M. Couch,
    • Kosuke Yusa,
    • and Gavin J. Wright
    Genome Res. September 2018 28: 1372-1382; Published in Advance June 18, 2018, doi:10.1101/gr.231183.117
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  • Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs

    • Sara Silva Pereira,
    • Aitor Casas-Sánchez,
    • Lee R. Haines,
    • Moses Ogugo,
    • Kihara Absolomon,
    • Mandy Sanders,
    • Steve Kemp,
    • Álvaro Acosta-Serrano,
    • Harry Noyes,
    • Matthew Berriman,
    • and Andrew P. Jackson
    Genome Res. September 2018 28: 1383-1394; Published in Advance July 13, 2018, doi:10.1101/gr.234146.118
    OPEN ACCESS ARTICLE

  • GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Martin J. Sergeant,
    • Nina Luhmann,
    • Cátia Vaz,
    • Alexandre P. Francisco,
    • João André Carriço,
    • and Mark Achtman
    Genome Res. September 2018 28: 1395-1404; Published in Advance July 26, 2018, doi:10.1101/gr.232397.117
    OPEN ACCESS ARTICLE

Resources

  • Human proteins that interact with RNA/DNA hybrids

    • Isabel X. Wang,
    • Christopher Grunseich,
    • Jennifer Fox,
    • Joshua Burdick,
    • Zhengwei Zhu,
    • Niema Ravazian,
    • Markus Hafner,
    • and Vivian G. Cheung
    Genome Res. September 2018 28: 1405-1414; Published in Advance August 14, 2018, doi:10.1101/gr.237362.118
    OPEN ACCESS ARTICLE

  • High resolution annotation of zebrafish transcriptome using long-read sequencing

    • German Nudelman,
    • Antonio Frasca,
    • Brandon Kent,
    • Kirsten C. Sadler,
    • Stuart C. Sealfon,
    • Martin J. Walsh,
    • and Elena Zaslavsky
    Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117

Corrigendum

  • Corrigendum: Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

    • Endre Sebestyén,
    • Babita Singh,
    • Belén Miñana,
    • Amadís Pagès,
    • Francesca Mateo,
    • Miguel Angel Pujana,
    • Juan Valcárcel,
    • and Eduardo Eyras
    Genome Res. September 2018 28: 1426; doi:10.1101/gr.242214.118
    OPEN ACCESS ARTICLE
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This Issue

September 2018; 28 (9)
Cover
  1. Perspective
  2. Research
  3. Methods
  4. Resources
  5. Corrigendum

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