Table of Contents

February 2023; 33 (2)

Research

  • The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory

    • Varsha Poondi Krishnan,
    • Barbara Morone,
    • Shir Toubiana,
    • Monika Krzak,
    • Salvatore Fioriniello,
    • Floriana Della Ragione,
    • Maria Strazzullo,
    • Claudia Angelini,
    • Sara Selig,
    • and Maria R. Matarazzo
    Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122

  • Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation

    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122

  • Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells

    • Cui Du,
    • Jing Jiang,
    • Yuzhuo Li,
    • Miao Yu,
    • Jian Jin,
    • Shuai Chen,
    • Hairui Fan,
    • Todd S. Macfarlan,
    • Bin Cao,
    • and Ming-an Sun
    Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122

Methods

  • Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

    • Brendan L. O'Connell,
    • Ruth V. Nichols,
    • Dmitry Pokholok,
    • Jerushah Thomas,
    • Sonia N. Acharya,
    • Andrew Nishida,
    • Casey A. Thornton,
    • Marissa Co,
    • Andrew J. Fields,
    • Frank J. Steemers,
    • and Andrew C. Adey
    Genome Res. February 2023 33: 208-217; Published in Advance February 15, 2023, doi:10.1101/gr.276655.122
    OPEN ACCESS ARTICLE

  • Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis

    • Shreya Mishra,
    • Neetesh Pandey,
    • Smriti Chawla,
    • Madhu Sharma,
    • Omkar Chandra,
    • Indra Prakash Jha,
    • Debarka SenGupta,
    • Kedar Nath Natarajan,
    • and Vibhor Kumar
    Genome Res. February 2023 33: 218-231; Published in Advance January 18, 2023, doi:10.1101/gr.277015.122

  • Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning

    • Tian Tian,
    • Cheng Zhong,
    • Xiang Lin,
    • Zhi Wei,
    • and Hakon Hakonarson
    Genome Res. February 2023 33: 232-246; Published in Advance February 27, 2023, doi:10.1101/gr.277068.122

  • Characterization of network hierarchy reflects cell state specificity in genome organization

    • Jingyao Wang,
    • Yue Xue,
    • Yueying He,
    • Hui Quan,
    • Jun Zhang,
    • and Yi Qin Gao
    Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122

Resources

  • The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

    • Simon Bray,
    • John Chilton,
    • Matthias Bernt,
    • Nicola Soranzo,
    • Marius van den Beek,
    • Bérénice Batut,
    • Helena Rasche,
    • Martin Čech,
    • Peter J.A. Cock,
    • Björn Grüning,
    • and Anton Nekrutenko
    Genome Res. February 2023 33: 261-268; Published in Advance February 24, 2023, doi:10.1101/gr.276963.122
    OPEN ACCESS ARTICLE

  • A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements

    • Salam Idriss,
    • Mohammad Hallal,
    • Abdullah El-Kurdi,
    • Hasan Zalzali,
    • Inaam El-Rassi,
    • Erik A. Ehli,
    • Christel M. Davis,
    • Philip E.D. Chung,
    • Deena M.A. Gendoo,
    • Eldad Zacksenhaus,
    • Raya Saab,
    • and Pierre Khoueiry
    Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122

  • A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

    • Jack F. Cazet,
    • Stefan Siebert,
    • Hannah Morris Little,
    • Philip Bertemes,
    • Abby S. Primack,
    • Peter Ladurner,
    • Matthias Achrainer,
    • Mark T. Fredriksen,
    • R. Travis Moreland,
    • Sumeeta Singh,
    • Suiyuan Zhang,
    • Tyra G. Wolfsberg,
    • Christine E. Schnitzler,
    • Andreas D. Baxevanis,
    • Oleg Simakov,
    • Bert Hobmayer,
    • and Celina E. Juliano
    Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
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This Issue

February 2023; 33 (2)
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