A photo of Yaping Liu.

Assistant Professor, UC Department of Pediatrics

513-803-3207

Biography & Affiliation

Biography

Thanks to my diverse academic and industry experiences, I have a broad background in epigenomics, single-cell multi-omics, computational biology, gene regulation, population genetics and liquid biopsy. These skills and interests drive me to understand the interactions between genetic and epigenetic variations — and bridge the gaps between genotype and phenotype.

My PhD training included developing computational and experimental methods for the high throughput epigenomic assay, specifically in DNA methylation and DNA accessibility/nucleosome positioning. Following my postdoctoral training, where I focused on population epigenomics, I worked as a principal computational biologist at a liquid biopsy company.

Together with experimental biologists, I developed NOMe-seq, Methyl-HiC and single-cell Methyl-HiC to profile the multi-omics within the same assay and even in the same single cell. Our NOMe-seq technology was selected as one of the Top 10 Innovations in 2013 by Scientist Magazine. Our single-cell Methyl-HiC technology was highlighted by Nature Method as Method of the Year 2019 (single-cell multimodal omics).

Since joining Cincinnati Children’s in 2019, my lab has focused on developing and applying machine learning and high-throughput experimental methods to understand gene regulation and non-coding genetic variants.

I’ve received numerous honors and awards, including:

  • Trustee Award, Cincinnati Children’s Research Foundation (2019)
  • Stellar Abstract Award, 11th Annual Program in Quantitative Genomics (PQG) Conference, School of Public Health, Harvard University (2017)
  • Stellar Abstract Award, 7th Annual PQG conference (2013)
  • Charles Heidelberger Memorial Fellowship, University of Southern California (2013)
  • SABRETRAIN Fellowship, European Marie Curie Host Fellowships for Early Stage Research Training, FP6 program (2009)

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

Research Divisions

Human Genetics, Biomedical Informatics

Education

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.

Publications

FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Zheng, H; Zhu, MS; Liu, Y. Computer Applications in the Biosciences. 2020.

Expanded encyclopaedias of DNA elements in the human and mouse genomes. Abascal, F; Acosta, R; Addleman, NJ; Adrian, J; Afzal, V; Aken, B; Akiyama, JA; Jammal, OA; Amrhein, H; Anderson, SM; et al. Nature: New biology. 2020; 583:699-710.

Perspectives on ENCODE. ENCODE Project Consortium, ; Snyder, MP; Gingeras, TR; Moore, JE; Weng, Z; Gerstein, MB; Ren, B; Hardison, RC; Stamatoyannopoulos, JA; Graveley, BR; et al. Nature: New biology. 2020; 583:693-698.

Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA. Wan, N; Weinberg, D; Liu, TY; Niehaus, K; Ariazi, EA; Delubac, D; Kannan, A; White, B; Bailey, M; Bertin, M; et al. BMC Cancer. 2019; 19.

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. Nature Methods. 2019; 16:991-993.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Gamazon, ER; Segrè, AV; van de Bunt, M; Wen, X; Xi, HS; Hormozdiari, F; Ongen, H; Konkashbaev, A; Derks, EM; Aguet, F; et al. Nature Genetics. 2018; 50:956-967.

Evidence of reduced recombination rate in human regulatory domains. Liu, Y; Sarkar, A; Kheradpour, P; Ernst, J; Kellis, M. Genome Biology. 2017; 18.

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Stranger, BE; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; et al. Nature Genetics. 2017; 49:1664-1670.

Estimating the causal tissues for complex traits and diseases. Ongen, H; Brown, AA; Delaneau, O; Panousis, NI; Nica, AC; GTEx Consortium, ; Dermitzakis, ET. Nature Genetics. 2017; 49:1676-1683.

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.