Searching journal content for Y Zhang in author.

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  1. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    OPEN ACCESS ARTICLE
  2. Corrigendum: Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
    • Ran Li,
    • Mian Gong,
    • Xinmiao Zhang,
    • Fei Wang,
    • Zhenyu Liu,
    • Lei Zhang,
    • Qimeng Yang,
    • Yuan Xu,
    • Mengsi Xu,
    • Huanhuan Zhang,
    • Yunfeng Zhang,
    • Xuelei Dai,
    • Yuanpeng Gao,
    • Zhuangbiao Zhang,
    • Wenwen Fang,
    • Yuta Yang,
    • Weiwei Fu,
    • Chunna Cao,
    • Peng Yang,
    • Zeinab Amiri Ghanatsaman,
    • Niloufar Jafarpour Negari,
    • Hojjat Asadollahpour Nanaei,
    • Xiangpeng Yue,
    • Yuxuan Song,
    • Xianyong Lan,
    • Weidong Deng,
    • Xihong Wang,
    • Chuanying Pan,
    • Ruidong Xiang,
    • Eveline M. Ibeagha-Awemu,
    • Pat (J.S.) Heslop-Harrison,
    • Benjamin D. Rosen,
    • Johannes A. Lenstra,
    • Shangquan Gan,
    • and Yu Jiang
    Genome Res. October 2025 35: 2375; doi:10.1101/gr.281340.125
    OPEN ACCESS ARTICLE
  3. Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    OPEN ACCESS ARTICLE
  4. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
  5. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    OPEN ACCESS ARTICLE
  6. Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
    • Jian-Hai Chen,
    • Patrick Landback,
    • Deanna Arsala,
    • Alexander Guzzetta,
    • Shengqian Xia,
    • Jared Atlas,
    • Dylan Sosa,
    • Yong E. Zhang,
    • Jingqiu Cheng,
    • Bairong Shen,
    • and Manyuan Long
    Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
    OPEN ACCESS ARTICLE
  7. Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
    • Hang Zhang,
    • Yi Zhang,
    • Kai Ming Ting,
    • Jie Zhang,
    • and Qiuran Zhao
    Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
    OPEN ACCESS ARTICLE
  8. Research: 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
  9. Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
    • Song Zhang,
    • Chao Wang,
    • Shenghua Qin,
    • Choulin Chen,
    • Yongzhou Bao,
    • Yuanyuan Zhang,
    • Lingna Xu,
    • Qingyou Liu,
    • Yunxiang Zhao,
    • Kui Li,
    • Zhonglin Tang,
    • and Yuwen Liu
    Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
  10. Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
    • Niccoló Tesi,
    • Alex Salazar,
    • Yaran Zhang,
    • Sven van der Lee,
    • Marc Hulsman,
    • Lydian Knoop,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Anne-Fleur Schneider,
    • Maartje Pennings,
    • Kristel Sleegers,
    • Erik-Jan Kamsteeg,
    • Marcel Reinders,
    • and Henne Holstege
    Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
    OPEN ACCESS ARTICLE
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