Jie Liu, PhD
Associate Professor of Computational Medicine and Bioinformatics
Associate Professor of Electrical Engineering and Computer Science
Department of Computational Medicine & Bioinformatics
100 Washtenaw Avenue, Room 2035D Palmer Commons
Ann Arbor, MI 48109
[email protected]

Available to mentor

Jie Liu, PhD
Associate Professor
  • Qualifications
  • Center Memberships
  • Research Overview
  • Links
  • Recent Publications
  • Qualifications
    • Senior Fellow
      University of Washington, Genome Sciences, 2018
    • PhD in Computer Science
      University of Wisconsin, Madison, 2014
    • Master in Statistics
      University of Wisconsin, Madison, 2011
    • Master in Computer Science
      University of Wisconsin, Madison, 2009
    • Master in Signal and Information Processing
      Peking University, Peking, 2007
    • Bachelor in Info. Management & Info. Systems
      Beijing University of Posts and Telecom, Beijing, 2004
    Center Memberships
    • Center Member
      Rogel Cancer Center
    Research Overview

    Dr. Liu’s research lab develops computational methods, tools, and resources for understanding the human genome and diseases such as diabetes. Recently, the methodology focuses are knowledge graphs and foundation models. We have developed a knowledge graph GenomicKB to accumulate human-readable knowledge about the human genome. We have extracted genomic knowledge from PubMed and developed another knowledge graph GLKB. We have also developed a genomic foundation model EPCOT which comprehensively predicts multiple genomic modalities. The lab currently participates in several NIH consortia, including 4DN, IGVF, HIRN, CFDE, and the recent PanKbase program. In particular, Dr. Liu co-leads the Machine Learning Focus Group at IGVF, co-leads the Data/Metadata Working Group at PanKbase, and leads the development of PanKgraph, the knowledge graph within the PanKbase system.

    Links
    • Liu Lab
    Recent Publications See All Publications
    • Report
      CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images.
      Tao Y, Feng F, Luo X, Reihsmann CV, Hopkirk AL, Cartailler J-P, Brissova M, Parker SCJ, Saunders DC, Liu J. 2024 Aug; e1012344 DOI:10.1371/journal.pcbi.1012344
      PMID: 39196899
    • Presentation
      A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome
      Liu J, Feng F. 2023 May 17;
    • Journal Article
      GenomicKB: a knowledge graph for the human genome.
      Feng F, Tang F, Gao Y, Zhu D, Li T, Yang S, Yao Y, Huang Y, Liu J. Nucleic Acids Res, 2023 Jan 6; 51 (D1): D950 - D956. DOI:10.1093/nar/gkac957
      PMID: 36318240
    • Journal Article
      NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.
      Huang Y, Wang B, Liu J. PLoS Comput Biol, 2022 Jul; 18 (7): e1010265 DOI:10.1371/journal.pcbi.1010265
      PMID: 35834552
    • Journal Article
      Multiple Testing under Dependence via Graphical Models.
      Liu J, Zhang C, Page D. Annals of Applied Statistics, 2016 Aug 1; 10 (3): 1699 - 1724.
    • Proceeding / Abstract / Poster
      New genetic variants improve personalized breast cancer diagnosis.
      Liu J, Page D, Peissig P, McCarty C, Onitilo AA, Trentham-Dietz A, Burnside E. AMIA Jt Summits Transl Sci Proc, 2014 2014: 83 - 89.
      PMID: 25717406
    • Proceeding / Abstract / Poster
      GenomicKB: a knowledge graph for the human genome
      Feng F, Tang F, Gao Y, Yang S, Li T, Zhu D, Yao Y, Huang Y, Liu J. 2023 May 15;
    • Proceeding / Abstract / Poster
      Unsupervised embedding of single-cell Hi-C data.
      Liu J, Lin D, Yardimci GG, Noble WS. Bioinformatics, 2018 Jul 1; 34 (13): i96 - i104. DOI:10.1093/bioinformatics/bty285
      PMID: 29950005
    Featured News & Stories EBS award trophees, engraved with professor Jie Liu and professor Weichen (Arthur) Zhou's names
    Department News
    Jie Liu, PhD, and Weichen (Arthur) Zhou, PhD, were recognized with a University of Michigan Endowment for Basic Sciences (EBS) award
    Jie Lui, PhD, was recognized with the EBS Research Award and Weichen (Arthur) Zhou, Ph.D., with the EBS Research Award
    Photos of DCMB promoted faculty: Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D.
    Department News
    Five DCMB faculty are promoted, congratulations!
    Five DCMB faculty were promoted. They are Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D. Congratulations!
    Department News
    Former DCMB PhD student Dr. Shuze Wang published in "Developmental Cell"
    Former DCMB PhD student Dr. Shuze Wang was published in Developmental Cell.