- Assistant Professor
- Phone: 401.874.5994
- Email: pengyu.liu@uri.edu
- Office Location: Lippitt 202B
Biography
Dr. Pengyu (Peter) Liu is an Assistant Professor in the Department of Cell and Molecular Biology and the Department of Mathematics and Applied Mathematical Sciences. Dr. Liu’s work is at the interface of mathematics, life sciences and public health. His research group develops novel theories and methods rooted in discrete mathematics and topology for analyzing extensive genomic and structural data in molecular biology and systems biology, including phylogenies, nucleic acid and protein structures. Dr. Liu’s research group integrates and applies these mathematical and computational methods to understand pathogen evolution, host-pathogen interactions, formation and functions of disease-related molecular structures, as well as infectious disease transmission, aiming to solve pressing problems in public health and medicine.
Research
Structure encoding and structural data analytics
The advancements in sequencing technologies and artificial intelligence have led to the production of myriad structural data. Dr. Liu’s research group develops innovative theories and methods for analyzing extensive structural data to understand the formation, interaction, function and evolution of biomolecules.
Pathogen interaction, evolution and transmission
Infectious diseases pose major public health concerns, with pathogen evolution at the core of these challenges. Dr. Liu’s research group develops novel mathematical models and computational methods that take advantage of genomic and structural data for understanding pathogen interaction, evolution and transmission, to address pressing public health problems.
Education
Postdoctoral Fellow, University of California, Davis, 2022-2024
Postdoctoral Fellow, Simon Fraser University, 2018-2022
Ph.D., University of North Carolina at Charlotte, 2018
Selected Publications
Liu P, Lusk J, Jonoska N, Vázquez M. Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding. PLOS Computational Biology 20(12): e1012669 (2024).
Gonzalez-Isunza G, Jawaid MZ, Liu P, Cox DL, Vázquez M, Arsuaga J. Using machine learning to detect coronaviruses potentially infectious to humans. Scientific Reports 13: 9319 (2023).
Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nature Microbiology 7: 1736-1743 (2022).
Liu P, Biller P, Gould M, Colijn C. Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial. Systematic Biology 71(6): 1378-1390 (2022).
Liu P, Song Y, Colijn C, MacPherson A. The impact of sampling bias on viral phylogeographic reconstruction. PLOS Global Public Health 2(9): e0000577 (2022).
Liu P, McQuarrie L, Song Y, Colijn C. Modelling the impact of household size distribution on the transmission dynamics of COVID-19. Journal of Royal Society Interface:1820210036 (2021).