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
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.
Liu Lab
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Tao Y, Feng F, Luo X, Reihsmann CV, Hopkirk AL, Cartailler J-P, Brissova M, Parker SCJ, Saunders DC, Liu J. 2024 Aug; e1012344ReportCNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images.
DOI:10.1371/journal.pcbi.1012344 PMID: 39196899 -
Liu J, Feng F. 2023 May 17;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 -
Huang Y, Wang B, Liu J. PLoS Comput Biol, 2022 Jul; 18 (7): e1010265Journal ArticleNucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.
DOI:10.1371/journal.pcbi.1010265 PMID: 35834552 -
Liu J, Zhang C, Page D. Annals of Applied Statistics, 2016 Aug 1; 10 (3): 1699 - 1724.Journal ArticleMultiple Testing under Dependence via Graphical Models.
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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.Proceeding / Abstract / PosterNew genetic variants improve personalized breast cancer diagnosis.
PMID: 25717406 -
Feng F, Tang F, Gao Y, Yang S, Li T, Zhu D, Yao Y, Huang Y, Liu J. 2023 May 15;Proceeding / Abstract / PosterGenomicKB: a knowledge graph for the human genome
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Liu J, Lin D, Yardimci GG, Noble WS. Bioinformatics, 2018 Jul 1; 34 (13): i96 - i104.Proceeding / Abstract / PosterUnsupervised embedding of single-cell Hi-C data.
DOI:10.1093/bioinformatics/bty285 PMID: 29950005