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]
100 Washtenaw Avenue, Room 2035D Palmer Commons
Ann Arbor, MI 48109
Available to mentor
Jie Liu, PhD
Assistant Professor
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Senior FellowUniversity of Washington, Genome Sciences, 2018
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PhD in Computer ScienceUniversity of Wisconsin, Madison, 2014
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Master in StatisticsUniversity of Wisconsin, Madison, 2011
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Master in Computer ScienceUniversity of Wisconsin, Madison, 2009
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Master in Signal and Information ProcessingPeking University, Peking, 2007
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Bachelor in Info. Management & Info. SystemsBeijing University of Posts and Telecom, Beijing, 2004
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Center MemberRogel Cancer Center
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.
Liu Lab
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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 Apr 17;Journal ArticlePositional cloning and characterization reveal the role of TaSRN-3D and TaBSR1 in the regulation of seminal root number in wheat.
DOI:10.1111/nph.19740 PMID: 38629267 -
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.Journal ArticleType I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat.
DOI:10.1111/pbi.14180 PMID: 37752705 -
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.Journal ArticleGenetic risk converges on regulatory networks mediating early type 2 diabetes.
DOI:10.1038/s41586-023-06693-2 PMID: 38049589 -
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): 254Journal ArticleMutation of a highly conserved amino acid in RPM1 causes leaf yellowing and premature senescence in wheat.
DOI:10.1007/s00122-023-04499-4 PMID: 38006406 -
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.Journal ArticleA highly conserved amino acid in high molecular weight glutenin subunit 1Dy12 contributes to gluten functionality and processing quality in wheat.
DOI:10.1016/j.jgg.2022.11.002 PMID: 36396014 -
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.Journal ArticleTaACTIN7-D regulates plant height and grain shape in bread wheat.
DOI:10.1016/j.jgg.2023.09.001 PMID: 37709194 -
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.Journal ArticlePlant-specific BLISTER interacts with kinase BIN2 and BRASSINAZOLE RESISTANT1 during skotomorphogenesis.
DOI:10.1093/plphys/kiad353 PMID: 37335918 -
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.Journal ArticleThermosensitive SUMOylation of TaHsfA1 defines a dynamic ON/OFF molecular switch for the heat stress response in wheat.
DOI:10.1093/plcell/koad192 PMID: 37399070
Department News
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 was published in Developmental Cell.
