Table of Contents

March 2020; 30 (3)

Review

  • Accurate and complete genomes from metagenomes

    • Lin-Xing Chen,
    • Karthik Anantharaman,
    • Alon Shaiber,
    • A. Murat Eren,
    • and Jillian F. Banfield
    Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
    OPEN ACCESS ARTICLE

Research

  • Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types

    • Akihiro Fujimoto,
    • Masashi Fujita,
    • Takanori Hasegawa,
    • Jing Hao Wong,
    • Kazuhiro Maejima,
    • Aya Oku-Sasaki,
    • Kaoru Nakano,
    • Yuichi Shiraishi,
    • Satoru Miyano,
    • Go Yamamoto,
    • Kiwamu Akagi,
    • Seiya Imoto,
    • and Hidewaki Nakagawa
    Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
    OPEN ACCESS ARTICLE

  • Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

    • Swati Venkat,
    • Arwen A. Tisdale,
    • Johann R. Schwarz,
    • Abdulrahman A. Alahmari,
    • H. Carlo Maurer,
    • Kenneth P. Olive,
    • Kevin H. Eng,
    • and Michael E. Feigin
    Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
    OPEN ACCESS ARTICLE

  • Identification of FMR1-regulated molecular networks in human neurodevelopment

    • Meng Li,
    • Junha Shin,
    • Ryan D. Risgaard,
    • Molly J. Parries,
    • Jianyi Wang,
    • Deborah Chasman,
    • Shuang Liu,
    • Sushmita Roy,
    • Anita Bhattacharyya,
    • and Xinyu Zhao
    Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119

  • Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism

    • Yen-Ju Chen,
    • Chia-Ying Chen,
    • Te-Lun Mai,
    • Chih-Fan Chuang,
    • Yu-Chen Chen,
    • Sachin Kumar Gupta,
    • Laising Yen,
    • Yi-Da Wang,
    • and Trees-Juen Chuang
    Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
    OPEN ACCESS ARTICLE

  • Systems genetics of the Drosophila metabolome

    • Shanshan Zhou,
    • Fabio Morgante,
    • Matthew S. Geisz,
    • Junwu Ma,
    • Robert R.H. Anholt,
    • and Trudy F.C. Mackay
    Genome Res. March 2020 30: 392-405; Published in Advance November 6, 2019, doi:10.1101/gr.243030.118
    OPEN ACCESS ARTICLE

  • Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila

    • Zhengyu Luo,
    • Tengfei Hu,
    • Hong Jiang,
    • Ruoyu Wang,
    • Qianlan Xu,
    • Simo Zhang,
    • Jun Cao,
    • and Xiaoyuan Song
    Genome Res. March 2020 30: 406-414; Published in Advance March 12, 2020, doi:10.1101/gr.241687.118

Methods

  • Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

    • Timothy M. Freeman,
    • Genomics England Research Consortium,
    • Dennis Wang,
    • and Jason Harris
    Genome Res. March 2020 30: 415-426; Published in Advance March 10, 2020, doi:10.1101/gr.255349.119

  • Human auditory ossicles as an alternative optimal source of ancient DNA

    • Kendra Sirak,
    • Daniel Fernandes,
    • Olivia Cheronet,
    • Eadaoin Harney,
    • Matthew Mah,
    • Swapan Mallick,
    • Nadin Rohland,
    • Nicole Adamski,
    • Nasreen Broomandkhoshbacht,
    • Kimberly Callan,
    • Francesca Candilio,
    • Ann Marie Lawson,
    • Kirsten Mandl,
    • Jonas Oppenheimer,
    • Kristin Stewardson,
    • Fatma Zalzala,
    • Alexandra Anders,
    • Juraj Bartík,
    • Alfredo Coppa,
    • Tumen Dashtseveg,
    • Sándor Évinger,
    • Zdeněk Farkaš,
    • Tamás Hajdu,
    • Jamsranjav Bayarsaikhan,
    • Lauren McIntyre,
    • Vyacheslav Moiseyev,
    • Mercedes Okumura,
    • Ildikó Pap,
    • Michael Pietrusewsky,
    • Pál Raczky,
    • Alena Šefčáková,
    • Andrei Soficaru,
    • Tamás Szeniczey,
    • Béla Miklós Szőke,
    • Dennis Van Gerven,
    • Sergey Vasilyev,
    • Lynne Bell,
    • David Reich,
    • and Ron Pinhasi
    Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119

  • Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

    • John Beaulaurier,
    • Elaine Luo,
    • John M. Eppley,
    • Paul Den Uyl,
    • Xiaoguang Dai,
    • Andrew Burger,
    • Daniel J. Turner,
    • Matthew Pendelton,
    • Sissel Juul,
    • Eoghan Harrington,
    • and Edward F. DeLong
    Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
    OPEN ACCESS ARTICLE

  • Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals

    • M. Jordan Rowley,
    • Axel Poulet,
    • Michael H. Nichols,
    • Brianna J. Bixler,
    • Adrian L. Sanborn,
    • Elizabeth A. Brouhard,
    • Karen Hermetz,
    • Hannah Linsenbaum,
    • Gyorgyi Csankovszki,
    • Erez Lieberman Aiden,
    • and Victor G. Corces
    Genome Res. March 2020 30: 447-458; Published in Advance March 3, 2020, doi:10.1101/gr.257832.119

  • Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses

    • Yiming Kang,
    • Nikhil R. Patel,
    • Christian Shively,
    • Pamela Samantha Recio,
    • Xuhua Chen,
    • Bernd J. Wranik,
    • Griffin Kim,
    • R. Scott McIsaac,
    • Robi Mitra,
    • and Michael R. Brent
    Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
    OPEN ACCESS ARTICLE

Resources

  • An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

    • Guanjue Xiang,
    • Cheryl A. Keller,
    • Elisabeth Heuston,
    • Belinda M. Giardine,
    • Lin An,
    • Alexander Q. Wixom,
    • Amber Miller,
    • April Cockburn,
    • Michael E.G. Sauria,
    • Kathryn Weaver,
    • Jens Lichtenberg,
    • Berthold Göttgens,
    • Qunhua Li,
    • David Bodine,
    • Shaun Mahony,
    • James Taylor,
    • Gerd A. Blobel,
    • Mitchell J. Weiss,
    • Yong Cheng,
    • Feng Yue,
    • Jim Hughes,
    • Douglas R. Higgs,
    • Yu Zhang,
    • and Ross C. Hardison
    Genome Res. March 2020 30: 472-484; Published in Advance March 4, 2020, doi:10.1101/gr.255760.119
    OPEN ACCESS ARTICLE

  • Gene expression networks in the Drosophila Genetic Reference Panel

    • Logan J. Everett,
    • Wen Huang,
    • Shanshan Zhou,
    • Mary Anna Carbone,
    • Richard F. Lyman,
    • Gunjan H. Arya,
    • Matthew S. Geisz,
    • Junwu Ma,
    • Fabio Morgante,
    • Genevieve St. Armour,
    • Lavanya Turlapati,
    • Robert R.H. Anholt,
    • and Trudy F.C. Mackay
    Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
    OPEN ACCESS ARTICLE

  • Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants

    • Alice Lunardon,
    • Nathan R. Johnson,
    • Emily Hagerott,
    • Tamia Phifer,
    • Seth Polydore,
    • Ceyda Coruh,
    • and Michael J. Axtell
    Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119

Corrigendum

  • Corrigendum: Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

    • Fantin Carpentier,
    • Ricardo C. Rodríguez de la Vega,
    • Sara Branco,
    • Alodie Snirc,
    • Marco A. Coelho,
    • Michael E. Hood,
    • and Tatiana Giraud
    Genome Res. March 2020 30: 514; doi:10.1101/gr.262188.120
    OPEN ACCESS ARTICLE
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This Issue

March 2020; 30 (3)
Cover
  1. Review
  2. Research
  3. Methods
  4. Resources
  5. Corrigendum

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