Table of Contents

March 2024; 34 (3)

Review

  • A systematic review on the biochemical threshold of mitochondrial genetic variants

    • Karan K. Smith,
    • Jesse D. Moreira,
    • Callum R. Wilson,
    • June O. Padera,
    • Ashlee N. Lamason,
    • Liying Xue,
    • Deepa M. Gopal,
    • David B. Flynn,
    • and Jessica L. Fetterman
    Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
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Research

  • Inference of selective forces on house mouse genomes during secondary contact in East Asia

    • Kazumichi Fujiwara,
    • Shunpei Kubo,
    • Toshinori Endo,
    • Toyoyuki Takada,
    • Toshihiko Shiroishi,
    • Hitoshi Suzuki,
    • and Naoki Osada
    Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
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  • Systematic identification and characterization of exon–intron circRNAs

    • Yinchun Zhong,
    • Yan Yang,
    • Xiaolin Wang,
    • Bingbing Ren,
    • Xueren Wang,
    • Ge Shan,
    • and Liang Chen
    Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
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  • Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation

    • Blandine C. Mercier,
    • Emmanuel Labaronne,
    • David Cluet,
    • Laura Guiguettaz,
    • Nicolas Fontrodona,
    • Alicia Bicknell,
    • Antoine Corbin,
    • Mélanie Wencker,
    • Fabien Aube,
    • Laurent Modolo,
    • Karina Jouravleva,
    • Didier Auboeuf,
    • Melissa J. Moore,
    • and Emiliano P. Ricci
    Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
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  • Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements

    • Divya Selvaraju,
    • Filip Wierzbicki,
    • and Robert Kofler
    Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
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  • Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species

    • Charles Plessy,
    • Michael J. Mansfield,
    • Aleksandra Bliznina,
    • Aki Masunaga,
    • Charlotte West,
    • Yongkai Tan,
    • Andrew W. Liu,
    • Jan Grašič,
    • María Sara del Río Pisula,
    • Gaspar Sánchez-Serna,
    • Marc Fabrega-Torrus,
    • Alfonso Ferrández-Roldán,
    • Vittoria Roncalli,
    • Pavla Navratilova,
    • Eric M. Thompson,
    • Takeshi Onuma,
    • Hiroki Nishida,
    • Cristian Cañestro,
    • and Nicholas M. Luscombe
    Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
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  • Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

    • João L. Reis-Cunha,
    • Samuel A. Pimenta-Carvalho,
    • Laila V. Almeida,
    • Anderson Coqueiro-dos-Santos,
    • Catarina A. Marques,
    • Jennifer A. Black,
    • Jeziel Damasceno,
    • Richard McCulloch,
    • Daniella C. Bartholomeu,
    • and Daniel C. Jeffares
    Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
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Methods

  • Phased nanopore assembly with Shasta and modular graph phasing with GFAse

    • Ryan Lorig-Roach,
    • Melissa Meredith,
    • Jean Monlong,
    • Miten Jain,
    • Hugh E. Olsen,
    • Brandy McNulty,
    • David Porubsky,
    • Tessa G. Montague,
    • Julian K. Lucas,
    • Chris Condon,
    • Jordan M. Eizenga,
    • Sissel Juul,
    • Sean K. McKenzie,
    • Sara E. Simmonds,
    • Jimin Park,
    • Mobin Asri,
    • Sergey Koren,
    • Evan E. Eichler,
    • Richard Axel,
    • Bruce Martin,
    • Paolo Carnevali,
    • Karen H. Miga,
    • and Benedict Paten
    Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123

  • Robust chromatin state annotation

    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
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  • Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches

    • Muyoung Lee,
    • Qingqing Guo,
    • Mijeong Kim,
    • Joonhyuk Choi,
    • Alia Segura,
    • Alper Genceroglu,
    • Lucy LeBlanc,
    • Nereida Ramirez,
    • Yu Jin Jang,
    • Yeejin Jang,
    • Bum-Kyu Lee,
    • Edward M. Marcotte,
    • and Jonghwan Kim
    Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
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Resource

  • The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

    • Christine E. Schnitzler,
    • E. Sally Chang,
    • Justin Waletich,
    • Gonzalo Quiroga-Artigas,
    • Wai Yee Wong,
    • Anh-Dao Nguyen,
    • Sofia N. Barreira,
    • Liam B. Doonan,
    • Paul Gonzalez,
    • Sergey Koren,
    • James M. Gahan,
    • Steven M. Sanders,
    • Brian Bradshaw,
    • Timothy Q. DuBuc,
    • Febrimarsa,
    • Danielle de Jong,
    • Eric P. Nawrocki,
    • Alexandra Larson,
    • Samantha Klasfeld,
    • Sebastian G. Gornik,
    • R. Travis Moreland,
    • Tyra G. Wolfsberg,
    • Adam M. Phillippy,
    • James C. Mullikin,
    • Oleg Simakov,
    • Paulyn Cartwright,
    • Matthew Nicotra,
    • Uri Frank,
    • and Andreas D. Baxevanis
    Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
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Corrigendum

  • Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data

    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. March 2024 34: 514; doi:10.1101/gr.279293.124
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This Issue

March 2024; 34 (3)
Cover
  1. Review
  2. Research
  3. Methods
  4. Resource
  5. Corrigendum

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