100 Washtenaw Avenue, Room 2035D Palmer Commons
Ann Arbor, MI 48109
Available to mentor
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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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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 -
Liu J. 2023 Jun 7;PresentationGenomicKB: a knowledge graph for the human genome
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2023 Jun 6;PresentationAllele-specific analysis of human epigenome, transcriptome and high-resolution chromatin organization
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Liu J. 2023 May 22;PresentationComputational infrastructures for consolidating our knowledge regarding the human genome
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Liu J, Feng F. 2023 May 17;PresentationA generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome
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Liu J. 2023 May 16;PresentationA generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome
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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.Journal ArticleGenomicKB: a knowledge graph for the human genome.
DOI:10.1093/nar/gkac957 PMID: 36318240 -
Liu J. 2022 Dec 6;PresentationGenomicKB: a knowledge graph for the human genome
