Table of Contents

October 2022; 32 (10)

Research

  • Mosaic loss of Chromosome Y in aged human microglia

    • Michael C. Vermeulen,
    • Richard Pearse,
    • Tracy Young-Pearse,
    • and Sara Mostafavi
    Genome Res. October 2022 32: 1795-1807; Published in Advance August 30, 2022, doi:10.1101/gr.276409.121
    OPEN ACCESS ARTICLE

  • Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis

    • Marija Petrić Howe,
    • Hamish Crerar,
    • Jacob Neeves,
    • Jasmine Harley,
    • Giulia E. Tyzack,
    • Pierre Klein,
    • Andres Ramos,
    • Rickie Patani,
    • and Raphaëlle Luisier
    Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
    OPEN ACCESS ARTICLE

  • Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels

    • Amanda J. Lea,
    • Julie Peng,
    • and Julien F. Ayroles
    Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
    OPEN ACCESS ARTICLE

  • Functional characterization of enhancer activity during a long terminal repeat's evolution

    • Alan Y. Du,
    • Xiaoyu Zhuo,
    • Vasavi Sundaram,
    • Nicholas O. Jensen,
    • Hemangi G. Chaudhari,
    • Nancy L. Saccone,
    • Barak A. Cohen,
    • and Ting Wang
    Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
    OPEN ACCESS ARTICLE

  • Natural variation in C. elegans short tandem repeats

    • Gaotian Zhang,
    • Ye Wang,
    • and Erik C. Andersen
    Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
    OPEN ACCESS ARTICLE

  • A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility

    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122

Methods

  • Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells

    • Keyi Geng,
    • Lara G. Merino,
    • Linda Wedemann,
    • Aniek Martens,
    • Małgorzata Sobota,
    • Yerma P. Sanchez,
    • Jonas Nørskov Søndergaard,
    • Robert J. White,
    • and Claudia Kutter
    Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122

  • Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

    • Stephanie M. Zimmerman,
    • Robin Fropf,
    • Bridget R. Kulasekara,
    • Maddy Griswold,
    • Oliver Appelbe,
    • Arya Bahrami,
    • Rich Boykin,
    • Derek L. Buhr,
    • Kit Fuhrman,
    • Margaret L. Hoang,
    • Quoc Huynh,
    • Lesley Isgur,
    • Andrew Klock,
    • Alecksandr Kutchma,
    • Alexa E. Lasley,
    • Yan Liang,
    • Jill McKay-Fleisch,
    • Jeffrey S. Nelson,
    • Karen Nguyen,
    • Erin Piazza,
    • Aric Rininger,
    • Daniel R. Zollinger,
    • Michael Rhodes,
    • and Joseph M. Beechem
    Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
    OPEN ACCESS ARTICLE

  • A model-based constrained deep learning clustering approach for spatially resolved single-cell data

    • Xiang Lin,
    • Le Gao,
    • Nathan Whitener,
    • Ashley Ahmed,
    • and Zhi Wei
    Genome Res. October 2022 32: 1906-1917; Published in Advance October 5, 2022, doi:10.1101/gr.276477.121

  • A statistical physics approach for disease module detection

    • Xu-Wen Wang,
    • Dandi Qiao,
    • Michael H. Cho,
    • Dawn L. DeMeo,
    • Edwin K. Silverman,
    • and Yang-Yu Liu
    Genome Res. October 2022 32: 1918-1929; Published in Advance October 11, 2022, doi:10.1101/gr.276690.122

  • Surveying mutation density patterns around specific genomic features

    • Hui Yu,
    • Scott Ness,
    • Chung-I Li,
    • Yongsheng Bai,
    • Peng Mao,
    • and Yan Guo
    Genome Res. October 2022 32: 1930-1940; Published in Advance September 13, 2022, doi:10.1101/gr.276770.122

Resources

  • A high-resolution map of small-scale inversions in the gibbon genome

    • Ludovica Mercuri,
    • Donato Palmisano,
    • Alberto L'Abbate,
    • Pietro D'Addabbo,
    • Francesco Montinaro,
    • Claudia Rita Catacchio,
    • Patrick Hasenfeld,
    • Mario Ventura,
    • Jan O. Korbel,
    • Ashley D. Sanders,
    • Flavia Angela Maria Maggiolini,
    • and Francesca Antonacci
    Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122

  • The western redcedar genome reveals low genetic diversity in a self-compatible conifer

    • Tal J. Shalev,
    • Omnia Gamal El-Dien,
    • Macaire M.S. Yuen,
    • Shu Shengqiang,
    • Shaun D. Jackman,
    • René L. Warren,
    • Lauren Coombe,
    • Lise van der Merwe,
    • Ada Stewart,
    • Lori B. Boston,
    • Christopher Plott,
    • Jerry Jenkins,
    • Guifen He,
    • Juying Yan,
    • Mi Yan,
    • Jie Guo,
    • Jesse W. Breinholt,
    • Leandro G. Neves,
    • Jane Grimwood,
    • Loren H. Rieseberg,
    • Jeremy Schmutz,
    • Inanc Birol,
    • Matias Kirst,
    • Alvin D. Yanchuk,
    • Carol Ritland,
    • John H. Russell,
    • and Joerg Bohlmann
    Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
    OPEN ACCESS ARTICLE

Corrigenda

  • Corrigendum: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells

    • Bingxiang Xu,
    • Xiaomeng Gao,
    • Xiaoli Li,
    • Yan Jia,
    • Feifei Li,
    • and Zhihua Zhang
    Genome Res. October 2022 32: 1965_1; doi:10.1101/gr.277270.122
    OPEN ACCESS ARTICLE

  • Corrigendum: Diversifying the genomic data science research community

    • The Genomic Data Science Community Network
    Genome Res. October 2022 32: 1965_2; doi:10.1101/gr.277322.122
    OPEN ACCESS ARTICLE
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This Issue

October 2022; 32 (10)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Corrigenda

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