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

    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
      Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing.
      Niu J, Wang W, Wang Z, Chen Z, Zhang X, Qin Z, Miao L, Yang Z, Xie C, Xin M, Peng H, Yao Y, Liu J, Ni Z, Sun Q, Guo W. Genome Biol, 2024 Jul 1; 25 (1): 171 DOI:10.1186/s13059-024-03315-6
      PMID: 38951917
    • Journal Article
      The TaWAK2-TaNAL1-TaDST pathway regulates leaf width via cytokinin signaling in wheat.
      Du D, Li Z, Yuan J, He F, Li X, Wang N, Li R, Ke W, Zhang D, Chen Z, Jiang Z, Liu Y, Chai L, Liu J, Hu Z, Guo W, Peng H, Yao Y, Sun Q, Ni Z, Xin M. Sci Adv, 2024 Aug 30; 10 (35): eadp5541 DOI:10.1126/sciadv.adp5541
      PMID: 39196932
    • 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
    • Journal Article
      A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality.
      Zhang Z, Liu D, Li B, Wang W, Zhang J, Xin M, Hu Z, Liu J, Du J, Peng H, Hao C, Zhang X, Ni Z, Sun Q, Guo W, Yao Y. Mol Plant, 2024 Jul 1; 17 (7): 1038 - 1053. DOI:10.1016/j.molp.2024.05.006
      PMID: 38796709
    • Journal Article
      Genetic difference and genome association analysis of grain quality traits in Xinjiang winter wheat
      Ma YM, Lou HY, Wang W, Sun N, Yan GR, Zhang SJ, Liu J, Ni ZF, Xu L. Acta Agronomica Sinica(China), 2024 Jun 12; 50 (6): 1394 - 1405. DOI:10.3724/SP.J.1006.2024.31030
    • Journal Article
      Fine-mapping and validation of the major quantitative trait locus QFlANG-4B for flag leaf angle in wheat.
      Zhang W, Chen X, Yang K, Chang S, Zhang X, Liu M, Wu L, Xin M, Hu Z, Liu J, Peng H, Ni Z, Sun Q, Yao Y, Du J. Theor Appl Genet, 2024 May 6; 137 (6): 121 DOI:10.1007/s00122-024-04629-6
      PMID: 38709317
    • 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
    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.