Searching journal content for X. Shirley Liu in author.

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  1. Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
    • Xiran Liu,
    • Lorin Crawford,
    • and Sohini Ramachandran
    Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
    OPEN ACCESS ARTICLE
  2. Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
    • Quanyou Cai,
    • Lihui Lin,
    • Xin Liu,
    • and Jiekai Chen
    Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
    OPEN ACCESS ARTICLE
  3. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    OPEN ACCESS ARTICLE
  4. Method: 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
  5. Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
    • Xudong Liu,
    • Ying Ni,
    • Lianwei Ye,
    • Zhihao Guo,
    • Lu Tan,
    • Jun Li,
    • Mengsu Yang,
    • Sheng Chen,
    • and Runsheng Li
    Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
  6. Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
    • Mengyuan Zhao,
    • Jiawei Li,
    • Xiaoyi Liu,
    • Ke Ma,
    • Jijun Tang,
    • and Fei Guo
    Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
  7. Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
    • Zhengcao Li,
    • Xiaohong Liu,
    • Chen Wang,
    • Zhenyang Li,
    • Bo Jiang,
    • Ruifeng Zhang,
    • Lu Tong,
    • Youping Qu,
    • Sheng He,
    • Haifan Chen,
    • Yafei Mao,
    • Qingnan Li,
    • Torsten Pook,
    • Yu Wu,
    • Yanjun Zan,
    • Hui Zhang,
    • Lu Li,
    • Keying Wen,
    • and Yaosheng Chen
    Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
    OPEN ACCESS ARTICLE
  8. Method: Partial alignment of multislice spatially resolved transcriptomics data
    • Xinhao Liu,
    • Ron Zeira,
    • and Benjamin J. Raphael
    Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123
  9. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ACCEPTED MANUSCRIPT
  10. Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
    • Xingyan Liu,
    • Qunlun Shen,
    • and Shihua Zhang
    Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
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