Table of Contents

January 2021; 31 (1)

Review

  • Data structures based on k-mers for querying large collections of sequencing data sets

    • Camille Marchet,
    • Christina Boucher,
    • Simon J. Puglisi,
    • Paul Medvedev,
    • Mikaël Salson,
    • and Rayan Chikhi
    Genome Res. January 2021 31: 1-12; Published in Advance December 16, 2020, doi:10.1101/gr.260604.119

Research

  • Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis

    • Kai Li,
    • Jiayue Xu,
    • Yanyun Luo,
    • Dingfeng Zou,
    • Ruiqin Han,
    • Shunshun Zhong,
    • Qing Zhao,
    • Xinyu Mang,
    • Mengzhen Li,
    • Yanmin Si,
    • Yan Lu,
    • Pengyu Li,
    • Cheng Jin,
    • Zhipeng Wang,
    • Fang Wang,
    • Shiying Miao,
    • Bo Wen,
    • Linfang Wang,
    • Yanni Ma,
    • Jia Yu,
    • and Wei Song
    Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120

  • Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development

    • Suba Rajendren,
    • Alfa Dhakal,
    • Pranathi Vadlamani,
    • Jack Townsend,
    • Sarah N. Deffit,
    • and Heather A. Hundley
    Genome Res. January 2021 31: 27-39; Published in Advance December 18, 2020, doi:10.1101/gr.267575.120

  • Thermal stress accelerates Arabidopsis thaliana mutation rate

    • Eric J. Belfield,
    • Carly Brown,
    • Zhong Jie Ding,
    • Lottie Chapman,
    • Mengqian Luo,
    • Eleanor Hinde,
    • Sam W. van Es,
    • Sophie Johnson,
    • Youzheng Ning,
    • Shao Jian Zheng,
    • Aziz Mithani,
    • and Nicholas P. Harberd
    Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119

  • The origin and evolution of a distinct mechanism of transcription initiation in yeasts

    • Zhaolian Lu and
    • Zhenguo Lin
    Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120

  • Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

    • Jonathon L. Baker,
    • James T. Morton,
    • Márcia Dinis,
    • Ruth Alvarez,
    • Nini C. Tran,
    • Rob Knight,
    • and Anna Edlund
    Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120

Methods

  • DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution

    • Juniper J. Elacqua,
    • Navpreet Ranu,
    • Sarah E. DiIorio,
    • and Paul C. Blainey
    Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
    OPEN ACCESS ARTICLE

  • Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

    • Wanqing Shao and
    • Ting Wang
    Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120

  • Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data

    • Yasin Uzun,
    • Hao Wu,
    • and Kai Tan
    Genome Res. January 2021 31: 101-109; Published in Advance November 20, 2020, doi:10.1101/gr.267047.120
    OPEN ACCESS ARTICLE

  • Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster

    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119

  • Generation of mouse conditional knockout alleles in one step using the i-GONAD method

    • Renjie Shang,
    • Haifeng Zhang,
    • and Pengpeng Bi
    Genome Res. January 2021 31: 121-130; Published in Advance December 16, 2020, doi:10.1101/gr.265439.120

  • MAnorm2 for quantitatively comparing groups of ChIP-seq samples

    • Shiqi Tu,
    • Mushan Li,
    • Haojie Chen,
    • Fengxiang Tan,
    • Jian Xu,
    • David J. Waxman,
    • Yijing Zhang,
    • and Zhen Shao
    Genome Res. January 2021 31: 131-145; Published in Advance November 18, 2020, doi:10.1101/gr.262675.120

Resources

  • Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders

    • Guangsheng Pei,
    • Yin-Ying Wang,
    • Lukas M. Simon,
    • Yulin Dai,
    • Zhongming Zhao,
    • and Peilin Jia
    Genome Res. January 2021 31: 146-158; Published in Advance December 3, 2020, doi:10.1101/gr.265769.120

  • Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)

    • Sanjida H. Rangwala,
    • Anatoliy Kuznetsov,
    • Victor Ananiev,
    • Andrea Asztalos,
    • Evgeny Borodin,
    • Vladislav Evgeniev,
    • Victor Joukov,
    • Vadim Lotov,
    • Ravinder Pannu,
    • Dmitry Rudnev,
    • Andrew Shkeda,
    • Eric M. Weitz,
    • and Valerie A. Schneider
    Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
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This Issue

January 2021; 31 (1)
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  1. Review
  2. Research
  3. Methods
  4. Resources

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