Table of Contents

May 2023; 33 (5)

Research

  • Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock

    • Akanksha Bafna,
    • Gareth Banks,
    • Michael H. Hastings,
    • and Patrick M. Nolan
    Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
    OPEN ACCESS ARTICLE

  • A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    OPEN ACCESS ARTICLE

  • Genomic insights into metabolic flux in hummingbirds

    • Ariel Gershman,
    • Quinn Hauck,
    • Morag Dick,
    • Jerrica M. Jamison,
    • Michael Tassia,
    • Xabier Agirrezabala,
    • Saad Muhammad,
    • Raafay Ali,
    • Rachael E. Workman,
    • Mikel Valle,
    • G. William Wong,
    • Kenneth C. Welch, Jr.,
    • and Winston Timp
    Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122

  • Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

    • Vivek Hari Sundar G,
    • Chenna Swetha,
    • Debjani Basu,
    • Kannan Pachamuthu,
    • Steffi Raju,
    • Tania Chakraborty,
    • Rebecca A. Mosher,
    • and P.V. Shivaprasad
    Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
    OPEN ACCESS ARTICLE

  • Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity

    • Cory A. Weller,
    • Ilya Andreev,
    • Michael J. Chambers,
    • Morgan Park,
    • NISC Comparative Sequencing Program,
    • Joshua S. Bloom,
    • and Meru J. Sadhu
    Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122

Methods

  • Multiplexed long-read plasmid validation and analysis using OnRamp

    • Camille Mumm,
    • Melissa L. Drexel,
    • Torrin L. McDonald,
    • Adam G. Diehl,
    • Jessica A. Switzenberg,
    • and Alan P. Boyle
    Genome Res. May 2023 33: 741-749; Published in Advance May 8, 2023, doi:10.1101/gr.277369.122
    OPEN ACCESS ARTICLE

  • Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation

    • Yang Zhou,
    • Qiongyu Sheng,
    • Jing Qi,
    • Jiao Hua,
    • Bo Yang,
    • Lei Wan,
    • and Shuilin Jin
    Genome Res. May 2023 33: 750-762; Published in Advance June 12, 2023, doi:10.1101/gr.277522.122

  • Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets

    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122

  • Targeted, programmable, and precise tandem duplication in the mammalian genome

    • Yaoge Jiao,
    • Min Li,
    • Xingyu He,
    • Yanhong Wang,
    • Junwei Song,
    • Yun Hu,
    • Li Li,
    • Lifang Zhou,
    • Lurong Jiang,
    • Junyan Qu,
    • Lifang Xie,
    • Qiang Chen,
    • and Shaohua Yao
    Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122

  • CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes

    • Marzia Rossato,
    • Luca Marcolungo,
    • Luca De Antoni,
    • Giulia Lopatriello,
    • Elisa Bellucci,
    • Gaia Cortinovis,
    • Giulia Frascarelli,
    • Laura Nanni,
    • Elena Bitocchi,
    • Valerio Di Vittori,
    • Leonardo Vincenzi,
    • Filippo Lucchini,
    • Kirstin E. Bett,
    • Larissa Ramsay,
    • David James Konkin,
    • Massimo Delledonne,
    • and Roberto Papa
    Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
    OPEN ACCESS ARTICLE

Resources

  • Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library

    • Jianjie He,
    • Kai Zhang,
    • Shuxiang Yan,
    • Mi Tang,
    • Weixian Zhou,
    • Yongtai Yin,
    • Kang Chen,
    • Chunyu Zhang,
    • and Maoteng Li
    Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123

  • The fine-scale recombination rate variation and associations with genomic features in a butterfly

    • Aleix Palahí i Torres,
    • Lars Höök,
    • Karin Näsvall,
    • Daria Shipilina,
    • Christer Wiklund,
    • Roger Vila,
    • Peter Pruisscher,
    • and Niclas Backström
    Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
    OPEN ACCESS ARTICLE

  • Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

    • Xiaoyu Zhuo,
    • Silas Hsu,
    • Deepak Purushotham,
    • Prashant Kumar Kuntala,
    • Jessica K. Harrison,
    • Alan Y. Du,
    • Samuel Chen,
    • Daofeng Li,
    • and Ting Wang
    Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
    OPEN ACCESS ARTICLE

Corrigendum

  • Corrigendum: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa

    • Mariana Villalba de la Peña,
    • Pauliina A.M. Summanen,
    • Martta Liukkonen,
    • and Ilkka Kronholm
    Genome Res. May 2023 33: 836-837; doi:10.1101/gr.278126.123
    OPEN ACCESS ARTICLE
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This Issue

May 2023; 33 (5)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Corrigendum

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