Jie Liu, PhD
Assistant Professor of Computational Medicine and Bioinformatics
Assistant 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
Assistant 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

    My lab develops computational approaches for understanding the connections between different modalities of the functional genomic data, including the epigenome, transcriptome and 3D chromatin organization. A unique perspective that we bring to the field is that the connections among these modalities need to be investigated at a sufficiently high resolution. While Hi-C has been the most popular technology to profile 3D chromatin organization, the DNA fragments it profiles tend to cover a few nucleosomes, thus the resulting chromatin contact maps can only reach the resolution of thousands of nucleotides. A recent technology, Micro-C, improves the mapping to nucleosome resolution. As human epigenetic and transcriptomic activities take place at nucleosome or sub-nucleosome resolution, jointly analyzing nucleosome-resolution Micro-C data with epigenome and transcriptome data became the research focus of my lab.

    Links
    • Liu Lab
    Recent Publications See All Publications
    • Journal Article
      Positional cloning and characterization reveal the role of TaSRN-3D and TaBSR1 in the regulation of seminal root number in wheat.
      Chen Z, Li X, He F, Liu B, Xu W, Chai L, Cheng X, Song L, Guo W, Hu Z, Su Z, Liu J, Xin M, Peng H, Yao Y, Sun Q, Xing J, Ni Z. New Phytol, 2024 Jun; 242 (6): 2510 - 2523. DOI:10.1111/nph.19740
      PMID: 38629267
    • Journal Article
      Type I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat.
      Zhang J, Zhang Z, Zhang R, Yang C, Zhang X, Chang S, Chen Q, Rossi V, Zhao L, Xiao J, Xin M, Du J, Guo W, Hu Z, Liu J, Peng H, Ni Z, Sun Q, Yao Y. Plant Biotechnol J, 2024 Jan; 22 (1): 200 - 215. DOI:10.1111/pbi.14180
      PMID: 37752705
    • Journal Article
      Genetic risk converges on regulatory networks mediating early type 2 diabetes.
      Walker JT, Saunders DC, Rai V, Chen H-H, Orchard P, Dai C, Pettway YD, Hopkirk AL, Reihsmann CV, Tao Y, Fan S, Shrestha S, Varshney A, Petty LE, Wright JJ, Ventresca C, Agarwala S, Aramandla R, Poffenberger G, Jenkins R, Mei S, Hart NJ, Phillips S, Kang H, Greiner DL, Shultz LD, Bottino R, Liu J, Below JE, HPAP Consortium , Parker SCJ, Powers AC, Brissova M. Nature, 2023 Dec; 624 (7992): 621 - 629. DOI:10.1038/s41586-023-06693-2
      PMID: 38049589
    • Journal Article
      Mutation of a highly conserved amino acid in RPM1 causes leaf yellowing and premature senescence in wheat.
      Zhang W, Zhang Z, Chen Q, Wang Z, Song W, Yang K, Xin M, Hu Z, Liu J, Peng H, Lai J, Guo W, Ni Z, Sun Q, Du J, Yao Y. Theor Appl Genet, 2023 Nov 25; 136 (12): 254 DOI:10.1007/s00122-023-04499-4
      PMID: 38006406
    • Journal Article
      A highly conserved amino acid in high molecular weight glutenin subunit 1Dy12 contributes to gluten functionality and processing quality in wheat.
      Yang C, Chen Q, Xin M, Su Z, Du J, Guo W, Hu Z, Liu J, Peng H, Ni Z, Sun Q, Yao Y. J Genet Genomics, 2023 Nov; 50 (11): 909 - 912. DOI:10.1016/j.jgg.2022.11.002
      PMID: 36396014
    • Journal Article
      TaACTIN7-D regulates plant height and grain shape in bread wheat.
      Li X, Cao B, Du D, Song L, Tian L, Xie X, Chen Z, Ding Y, Cheng X, Yao Y, Guo W, Su Z, Sun Q, Ni Z, Chai L, Liu J. J Genet Genomics, 2023 Nov; 50 (11): 895 - 908. DOI:10.1016/j.jgg.2023.09.001
      PMID: 37709194
    • Journal Article
      Plant-specific BLISTER interacts with kinase BIN2 and BRASSINAZOLE RESISTANT1 during skotomorphogenesis.
      Yang R, Liu P, Zhang T, Dong H, Jing Y, Yang Z, Tang S, Zhang Y, Lv M, Liu J, Zhang Y, Qiao W, Liu J, Sun J. Plant Physiol, 2023 Sep 22; 193 (2): 1580 - 1596. DOI:10.1093/plphys/kiad353
      PMID: 37335918
    • Journal Article
      Thermosensitive SUMOylation of TaHsfA1 defines a dynamic ON/OFF molecular switch for the heat stress response in wheat.
      Wang H, Feng M, Jiang Y, Du D, Dong C, Zhang Z, Wang W, Liu J, Liu X, Li S, Chen Y, Guo W, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Liu J. Plant Cell, 2023 Sep 27; 35 (10): 3889 - 3910. DOI:10.1093/plcell/koad192
      PMID: 37399070
    Featured News & Stories 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.