A photo of Yaping Liu.

Assistant Professor, UC Department of Pediatrics


Biography & Affiliation


Yaping Liu, PhD, worked on regulatory genomics and epigenomics for the last 10 years. His long-term research interest is to understand the interaction between genetics and epigenetics variations, and therefore bridge the gap between genotype and phenotype. His academic training and research experience has provided him with background in multiple disciplines including epigenomics, liquid biopsy, population genetics, and machine learning.

Dr. Liu built the first map-reduced probabilistic SNP and methylation caller, ‘Bis-SNP’, which overcomes the difficulties in accurate methylation and SNP calling at Bisulfite-seq. He developed nucleosome occupancy and methylome sequencing (NOMe-seq) technology together with the experimental biologists, which was recognized as one of the top 10 innovations in 2013 by The Scientist Magazine.

Together with experimental collaborators, Dr. Liu applied Bis-SNP and NOMe-seq together on a colon cancer cell line and its derived cell line with almost complete elimination of DNA methylation, which revealed the potential causal role of DNA methylation in colon cancer cells. He discovered the ‘recombination rate valley’ within regulatory domains through the data mining at a large number of public available functional links. Together with experimental collaborators, he also developed Methyl-HiC by adding an additional DNA methylation layer at in situ Hi-C assay and extended it to single-cell resolution.

Dr. Liu served as a joint-first author for DNA methylation part in an integrated analysis of NIH Epigenome Roadmap main consortium paper. He was also part of the GTEx integrative analysis consortium during the postdoc training.

Clinical Interests

Epigenomic and gene regulation mechanism in cancer and other common complex diseases

Research Interests

Epigenomics; liquid biopsy; computational biology/bioinformatics; gene-regulation; cell-free DNA; exosomal-DNA; single-cell -omics

Academic Affiliation

Assistant Professor, UC Department of Pediatrics


Human Genetics, Biomedical Informatics


Postdoc Training: Computer Science and Artificial Intelligence Lab (CSAIL), Massachusetts Institute of Technology, Broad Institute of MIT and Harvard, MA, 2014-2017.

PhD: USC Epigenome Center, University of Southern California, CA, 2009-2014.

BS: School of Life Sciences, Nanjing University, China, 2004-2008.


Joint profiling of DNA methylation and chromatin architecture in single cells. Li, G; Liu, Y; Zhang, Y; Kubo, N; Yu, M; Fang, R; Kellis, M; Ren, B. PLoS Medicine. 2019; 16:991-993.

Evidence of reduced recombination rate in human regulatory domains. Liu, Y; Sarkar, A; Kheradpour, P; Ernst, J; Kellis, M. Genome Biology: biology for the post-genomic era. 2017; 18.

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nature Genetics. 2017; 49:1664-1670.

Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Luo, H; Xi, Y; Li, W; Li, J; Li, Y; Dong, S; Peng, L; Liu, Y; Yu, W. Human Molecular Genetics. 2017; 26:4231-4243.