This page is brought to you by Brian Golding (Golding@McMaster.CA) and is copied locally here to speed your access. To go to the original page (should you find something interesting or should you wish to follow links) click on

Current Issue of Genome Research

Table of Contents — January 2025, 35 (1)

Table of Contents

January 2025; 35 (1)

Review

  • Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    OPEN ACCESS ARTICLE

Research

  • Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y

    • Shruthi Rengarajan,
    • Jason Derks,
    • Daniel W. Bellott,
    • Nikolai Slavov,
    • and David C. Page
    Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
    OPEN ACCESS ARTICLE

  • Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations

    • Yasine Malki,
    • Guannan Kang,
    • W.K. Jacky Lam,
    • Qing Zhou,
    • Suk Hang Cheng,
    • Peter P.H. Cheung,
    • Jinyue Bai,
    • Ming Lok Chan,
    • Chui Ting Lee,
    • Wenlei Peng,
    • Yiqiong Zhang,
    • Wanxia Gai,
    • Winsome W.S. Wong,
    • Mary-Jane L. Ma,
    • Wenshuo Li,
    • Xinzhou Xu,
    • Zhuoran Gao,
    • Irene O.L. Tse,
    • Huimin Shang,
    • L.Y. Lois Choy,
    • Peiyong Jiang,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
    OPEN ACCESS ARTICLE

  • The rate and spectrum of new mutations in mice inferred by long-read sequencing

    • Eugenio López-Cortegano,
    • Jobran Chebib,
    • Anika Jonas,
    • Anastasia Vock,
    • Sven Künzel,
    • Peter D. Keightley,
    • and Diethard Tautz
    Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
    OPEN ACCESS ARTICLE

  • Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging

    • Amy R. Vandiver,
    • Allen Herbst,
    • Paul Stothard,
    • and Jonathan Wanagat
    Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124

  • Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

    • Fangyuan Yang,
    • Li-Jun Cao,
    • Petr Nguyen,
    • Zhong-Zheng Ma,
    • Jin-Cui Chen,
    • Wei Song,
    • and Shu-Jun Wei
    Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124

  • Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

    • Thomas D. Lewin,
    • Isabel Jiah-Yih Liao,
    • Mu-En Chen,
    • John D.D. Bishop,
    • Peter W.H. Holland,
    • and Yi-Jyun Luo
    Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
    OPEN ACCESS ARTICLE

  • ISWI1 complex proteins facilitate developmental genome editing in Paramecium

    • Aditi Singh,
    • Lilia Häußermann,
    • Christiane Emmerich,
    • Emily Nischwitz,
    • Brandon K.B. Seah,
    • Falk Butter,
    • Mariusz Nowacki,
    • and Estienne C. Swart
    Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
    OPEN ACCESS ARTICLE

  • The chromatin landscape of the histone-possessing Bacteriovorax bacteria

    • Georgi K. Marinov,
    • Benjamin Doughty,
    • Anshul Kundaje,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124

Methods

  • KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome

    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124

  • Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach

    • Fabien Wehbe,
    • Levi Adams,
    • Jordan Babadoudou,
    • Samantha Yuen,
    • Yoon-Seong Kim,
    • and Yoshiaki Tanaka
    Genome Res. January 2025 35: 135-146; Published in Advance December 2, 2024, doi:10.1101/gr.278812.123
    OPEN ACCESS ARTICLE

  • A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

    • Shuai Guo,
    • Xiaoqian Liu,
    • Xuesen Cheng,
    • Yujie Jiang,
    • Shuangxi Ji,
    • Qingnan Liang,
    • Andrew Koval,
    • Yumei Li,
    • Leah A. Owen,
    • Ivana K. Kim,
    • Ana Aparicio,
    • Sanghoon Lee,
    • Anil K. Sood,
    • Scott Kopetz,
    • John Paul Shen,
    • John N. Weinstein,
    • Margaret M. DeAngelis,
    • Rui Chen,
    • and Wenyi Wang
    Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
    OPEN ACCESS ARTICLE

  • Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression

    • Howard J. Womersley,
    • Daniel Muliaditan,
    • Ramanuj DasGupta,
    • and Lih Feng Cheow
    Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
    OPEN ACCESS ARTICLE

  • Modeling gene interactions in polygenic prediction via geometric deep learning

    • Han Li,
    • Jianyang Zeng,
    • Michael P. Snyder,
    • and Sai Zhang
    Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
    OPEN ACCESS ARTICLE

Resources

  • High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration

    • Zihe Li,
    • Ziyu Xu,
    • Lei Zhu,
    • Tao Qin,
    • Jinrui Ma,
    • Zhanying Feng,
    • Huishan Yue,
    • Qing Guan,
    • Botong Zhou,
    • Ge Han,
    • Guokun Zhang,
    • Chunyi Li,
    • Shuaijun Jia,
    • Qiang Qiu,
    • Dingjun Hao,
    • Yong Wang,
    • and Wen Wang
    Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
    OPEN ACCESS ARTICLE

  • Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

    • Yujie Chen,
    • Yiran Hou,
    • Qinglin Zeng,
    • Irene Wang,
    • Meiru Shang,
    • Kwangdeok Shin,
    • Christopher Hemauer,
    • Xiaoyun Xing,
    • Junsu Kang,
    • Guoyan Zhao,
    • and Ting Wang
    Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
    OPEN ACCESS ARTICLE

This Issue

January 2025; 35 (1)
Cover
  1. Review
  2. Research
  3. Methods
  4. Resources

Find articles in this issue containing these words:

Preprint Server



Current Issue

  1. January 2025, 35 (1)
  1. Current Issue
  1. Alert me to new issues of Genome Research