CV

For the full list of academic achievements, please download my CV.

Education and Training

• Postdoc Fellow in Regulatory Genomics of Kidney Disease @ Susztak Lab, University of Pennsylvania, 2018
• Postdoc Fellow in Epigenomics of Cancer @ Shen Lab, Van Andel Institute, 2016
• Ph.D in Biomedical Engineering (Developmental Biology) @ Wu Lab, Harbin Institute of Technology, 2015
• M.S. in Biomedical Engineering (Bioinformatics) @ Zhang Lab, Harbin Medical University, 2010
• B.S. in Information and Computing Science, School of Mathematical Sciences, Qufu Normal University, 2007

Work experience

• Mar 2024: Assistant Professor
  • University of Rochester Medical Center, University of Rochester
  • Duties included: Teaching and Mentoring
• Aug 2023: Research Associate
  • Department of Genetics and Medicine, University of Pennsylvania
  • Duties included: Research
• Oct 2015: Associate Professor
  • College of Bioinformatics Science and Technology, Harbin Medical University
  • Duties included: Teaching and Mentoring
• Sep 2010: Assistant Professor
  • College of Bioinformatics Science and Technology, Harbin Medical University
  • Duties included: Teaching and Mentoring

Research interests

• Population Genetics
• Epigenetic Regulation
• Single cell Omics
• Age-Related Chronic Diseases
• Developmental Origins of Diseases

Selected Publications

(#Contributed equally; ✉️Corresponding author)

• Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy H, Nadkarni G, Abedini A, Miao Z, Palmer M, Voight B, Li H, Brown C, Ritchie M, Shu Y and Susztak K✉️. (2022) Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Nature Genetics, 54(7):950–962. Full text
• Guan Y#, Liu H#, Ma Z, Li SY, Park J, Sheng X and Susztak K✉️. (2020) Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. Journal of the American Society of Nephrology, 31(4), 765-782. Full text
• Xu S#, Liu H#, Wan L#, Zhang W, Wang Q, Zhang S, Shang S, Zhang Y✉️ and Pang D✉️. (2019) The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA–RNA interactions in breast cancer. Cell Death & Disease, 10(12), 920. Full text
• Xiong Y#, Wei Y#, Gu Y#, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H✉️, Zhang Y✉️ (2017) DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Research, 45(D1):D888-895. Full text
• Liu H✉️#, Liu X#, Zhang S#, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, and Zhang Y✉️ (2016) Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell-type-specific hypomethylation in regulation of cell identify genes. Nucleic Acids Research, 44(1):75-94. Full text
• Wei Y#, Zhang S#, Shang S#, Zhang B, Wang X, Li S, Liu H✉️, Zhang Y✉️ (2016) SEA: a Super-Enhancer Archive. Nucleic Acids Research, 44(D1):D172-179. Full text
• Liu H#, Zhu R#, Lv J#, He H, Yang L, Huang Z, Su J, Zhang Y, Yu S and Wu Q✉️. (2014) DevMouse, the mouse developmental methylome database and analysis tools. Database, 2014:bat084. Full text
• Lv J#, Huang Z#, Liu H#, Liu H#, Cui W, Li B, He H, Guo J, Liu Q and Zhang Y and Wu Q✉️. (2014) Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Molecular Genetics and Genomics, 289(6), 1225-1235. Full text
• Liu H#, Chen Y#, Lv J#, Zhu R, Su J, Liu X, Zhang Y✉️, Wu Q✉️ (2013) Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. Scientific Reports, 3:2576. Full text
• Lv J#, Liu H#, Huang Z#, Su J, He H, Xiu Y, Zhang Y and Wu Q✉️ (2013) Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Research, 41, 10044-10061. Full text
• Lv J#, Cui W#, Liu H#, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y and Wu Q✉️. (2013) Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PloS One, 8, e71152.Full text
• Lv J#, Liu H#, Su J#, Wu X, Li B, Xiao X, Wang F, Wu Q✉️, Zhang Y✉️ (2012) DiseaseMeth: a human disease methylation database. Nucleic Acids Research, 40, D1030-1035. Full text
• Zhang Y✉️#, Liu H#, Lv J#, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F and Cui Y (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Research, 39(9):e58. Full text
• Zhang Y✉️#, Lv J#, Liu H#, Zhu J, Su J, Wu Q, Qi Y, Wang F and Li X✉️: (2010) HHMD: the human histone modification database. Nucleic Acids Research, 38, D149-154. Full text

For the full list of academic publications, check out my Google Scholar profile.

Talks

• 10/07/2022 MidAtlantic Bioinformatics Conference (2022), Philadelphia, PA
• 08/08/2022 International Conference on Intelligent Biology and Medicine (ICIBM), Philadelphia, PA
• 05/19/2022 Chinese Genomics Meet-up online, CGM online
• 04/25/2022 Penn Genetics 2022 Global Scientific Symposium, Philadelphia, PA
• 03/06/2019 Keystone symposia: Unraveling the Secrets of Kidney Disease, Whistler Conference Centre, BC Canada
• 07/10/2016 The International Symposium on the Frontier of Big Data in Science, Baotou, China

Teaching experience

• Computational Epigenetics, Instructor, Fall 2015, Spring 2016
• Biomolecular Network Analysis, Instructor, Spring 2011, Spring 2012, Spring 2016
• Combinatorics and Graph Theory, Instructor, Fall 2015
• Database Principles and Applications, Instructor, Fall 2011
• System Biology, Instructor, Fall 2010
• Advanced Mathematics, Instructor, Fall 2010

Mentoring experience

• Shanshan Zhang (undergraduate), 2015 - 2016 (Now: Graduate student at Case Western Reserve University Link)
• Shipeng Shang (undergraduate), 2014 - 2015 (Now: Assistant professor at Qingdao University Link)
• Yunzhen Wei (undergraduate), 2013 - 2014 (Now: Assistant professor at Guangdong Medical University)
• Rangfei Zhu (undergraduate), 2012 - 2014 (Now: CEO of Hangzhou Mugu Technology Co., Ltd Link)