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  1. Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
    • Sergey V. Ulianov,
    • Ekaterina E. Khrameeva,
    • Alexey A. Gavrilov,
    • Ilya M. Flyamer,
    • Pavel Kos,
    • Elena A. Mikhaleva,
    • Aleksey A. Penin,
    • Maria D. Logacheva,
    • Maxim V. Imakaev,
    • Alexander Chertovich,
    • Mikhail S. Gelfand,
    • Yuri Y. Shevelyov,
    • and Sergey V. Razin
    Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
  2. Research: 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
    • Alice Cortesi,
    • Matthieu Pesant,
    • Shruti Sinha,
    • Federica Marasca,
    • Eleonora Sala,
    • Francesco Gregoretti,
    • Laura Antonelli,
    • Gennaro Oliva,
    • Chiara Chiereghin,
    • Giulia Soldà,
    • and Beatrice Bodega
    Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
    OPEN ACCESS ARTICLE
  3. Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
    • Jacob C. Kimmel,
    • Lolita Penland,
    • Nimrod D. Rubinstein,
    • David G. Hendrickson,
    • David R. Kelley,
    • and Adam Z. Rosenthal
    Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
    OPEN ACCESS ARTICLE
  4. Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
    • Kimberly N. Griffin,
    • Benjamin William Walters,
    • Haixin Li,
    • Huafeng Wang,
    • Giulia Biancon,
    • Toma Tebaldi,
    • Carolyn B. Kaya,
    • Jean Kanyo,
    • TuKiet T. Lam,
    • Andy L. Cox,
    • Stephanie Halene,
    • Jean-Ju Chung,
    • and Bluma J. Lesch
    Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
  5. Research: Ultra-long-range interactions between active regulatory elements
    • Elias T. Friman,
    • Ilya M. Flyamer,
    • Davide Marenduzzo,
    • Shelagh Boyle,
    • and Wendy A. Bickmore
    Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
    OPEN ACCESS ARTICLE
  6. Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
    • Elise Parey,
    • Diego Fernandez-Aroca,
    • Stephanie Frost,
    • Ainhoa Uribarren,
    • Thomas J. Park,
    • Markus Zöttl,
    • Ewan St. John Smith,
    • Camille Berthelot,
    • and Diego Villar
    Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
    OPEN ACCESS ARTICLE
  7. Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
    • Wilfried M. Guiblet,
    • Michael DeGiorgio,
    • Xiaoheng Cheng,
    • Francesca Chiaromonte,
    • Kristin A. Eckert,
    • Yi-Fei Huang,
    • and Kateryna D. Makova
    Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
    OPEN ACCESS ARTICLE
  8. Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
    • Frédéric Chaux,
    • Nicolas Agier,
    • Clotilde Garrido,
    • Gilles Fischer,
    • Stephan Eberhard,
    • and Zhou Xu
    Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
    OPEN ACCESS ARTICLE
  9. Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
    • Mark E. Gill,
    • Alexia Rohmer,
    • Serap Erkek-Ozhan,
    • Ching-Yeu Liang,
    • Sunwoo Chun,
    • Evgeniy A. Ozonov,
    • and Antoine H.F.M. Peters
    Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
    OPEN ACCESS ARTICLE
  10. Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
    • Gregor Diensthuber,
    • Leszek P. Pryszcz,
    • Laia Llovera,
    • Morghan C. Lucas,
    • Anna Delgado-Tejedor,
    • Sonia Cruciani,
    • Jean-Yves Roignant,
    • Oguzhan Begik,
    • and Eva Maria Novoa
    Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
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