Pengyu Liu

Research

My research projects lie in the fields of mathematics, biology and data science. I am interested in introducing and developing new mathematical methods for biology and medicine. Specifically, my current projects include developing methods based on discrete mathematics, topology and geometry for phylogenetics, genomics and molecular biology, aiming to help solve problems in epidemiology, public health and medicine.

Infectious disease modelling

Throughout the COVID-19 pandemic, as stay-at-home orders have been implemented to limit community transmission, transmission within household units has posed a challenge. Using an epidemiological model, we compare two health regions, one with more larger, multi-generational households and the other with more single-person households. We determine that the differences in the size of households between the two regions can cause significant differences in COVID-19 incidence. Our results also suggest that offering individuals a place to isolate outside their households can reduce transmission effectively in regions with larger households. This study is based on data from British Columbia, Canada.

Publication

• Modelling the impact of household size distribution on the transmission dynamics of COVID-19
  With Lisa McQuarrie, Yexuan Song and Caroline Colijn
  To appear in Journal of the Royal Society Interface
  Preprint, DOI: 10.1101/2021.01.12.21249707

Polynomial phylogenetic analysis

In this project, we introduce graph polynomials for phylogenetic analysis. We define a polynomial that uniquely represents trees and use the polynomial with statistical and machine learning tools to solve problems in phylogenetics and evolutionary biology, which shows that graph polynomials are promising methods for phylogenetic analysis and for other related tasks.

Publications

• A tree distinguishing polynomial
  Discrete Applied Mathematics
  DOI: 10.1016/j.dam.2020.08.019
• Polynomial phylogenetic analysis of tree shapes
  With Priscila Biller, Matthew Gould and Caroline Colijn
  Preprint, DOI: 10.1101/2020.02.10.942367

Invited Conference Talks

• A tree distinguishing polynomial - an introduction to polynomial tree metrics
  SMB Annual Meeting, Université de Montréal, Montréal, QC.
  July 2019
• A tree distinguishing polynomial - an introduction to polynomial tree metrics
  CAIMS Annual Meeting, Whistler, BC.
  June 2019
• A tree distinguishing polynomial - an introduction to polynomial tree metrics
  CanaDAM 2019, Simon Fraser University, Vancouver, BC.
  May 2019

Monte-Carlo kDNA Model

Kinetoplast DNA or kDNA is a network of circular DNA in a mitochondrion of the organisms kinetoplastids, which include parasites that cause serious diseases like African sleeping sickness and Chagas disease. We develop a Monte-Carlo based model for the kDNA network using tools based on topology and discrete mathematics, aiming to study the structures and the mechanisms of the mitochondrial DNA.

Publications

• Estimating properties of kinetoplast DNA by fragmentation reactions
  With Lara Ibrahim, Yuanan Diao, Michele Klingbeil and Javier Arsuaga
  Journal of Physics A: Mathematical and Theoretical
  DOI: 10.1088/1751-8121/aaf15f
• Characterizing the topology of kinetoplast DNA using random knotting
  With Ryan Polischuk, Yuanan Diao and Javier Arsuaga
  Topology and Geometry of Biopolymers, Contemporary Mathematics
  DOI: 10.1090/conm/746

Invited Conference Talks

• Estimating properties of kinetoplast DNA by fragmentation reactions
  Workshop on Knotted Fields, Beijing University of Technology, Beijing, China.
  September 2019

Braid indices of alternating links

In this project, we solved a long-standing problem in knot theory. We fully characterized the alternating links whose braid indices equal the number of Seifert circles in their reduced diagrams. We also conjectured that for any alternating link, its braid index equals the difference of the number of Seifert circles in its reduced diagram and its reduction number. We proved the conjecture is true for a large class of alternating links including Montesinos links.

Publications

• The braid index of reduced alternating links
  With Yuanan Diao and Gábor Hetyei
  Mathematical Proceedings of the Cambridge Philosophical Society
  DOI: 10.1017/S0305004118000907
• The HOMFLY polynomial of links in closed braid form
  With Yuanan Diao and Gábor Hetyei
  Discrete Mathematics
  DOI: 10.1016/j.disc.2018.09.027
• A diagrammatic approach for determining the braid index of alternating links
  With Yuanan Diao, Claus Ernst and Gábor Hetyei
  To appear in Journal of Knot Theory and Its Ramifications
  Preprint, arXiv:1901.09778

Invited Conference Talks

• A diagrammatic approach for determining the braid index of alternating links
  The Geometry and Topology of Knotting and Entanglement in Proteins, CMO-BIRS Workshop, Oaxaca, Mexico.
  November 2017
• The braid index of reduced alternating links
  AMS Sectional Meeting, University of Saint Thomas, Minneapolis, MN.
  October 2016
• The HOMFLY polynomial of links in closed braid form
  Workshop on Graphs and Knots, Xiamen University, Xiamen, China.
  June 2016

Events

5/25-5/28, 2021 Online

CanaDAM 2021

Canadian Discrete and Algorithmic Mathematics Conference

6/15-6/24, 2020 SFU, Vancouver, BC

FoCM 2020

Foundations of Computational Mathematics Conference

9/7-9/8, 2019 Beijing, China

Workshop on Knotted Fields

Knotted Field Theory with Applications in Physical and Biological Sciences

7/22-7/26, 2019 Montréal, QC

SMB Annual Meeting 2019

The Annual Meeting and Conference of the Society for Mathematical Biology

6/17-6/28, 2019 IMA, Minneapolis, MN

BAGEL 2019

Biology, Analysis, Geometry, Energies, Links:
A Program on Low-dimensional Topology, Geometry, and Applications

6/9-6/13, 2019 Whsitler, BC

CAIMS Annual Meeting 2019

The Annual Meeting of the Canadian Society of Applied and Industrial Mathematics

5/28-5/31, 2019 SFU, Vancouver, BC

CanaDAM 2019

Canadian Discrete and Algorithmic Mathematics Conference

About

I am a postdoctoral fellow in the Department of Mathematics at Simon Fraser University. See the research page for information about my projects. I also produce music and take photographs. To know more, read one of my random stories.

Contact

Pengyu Liu
Simon Fraser University
Department of Mathematics
8888 University Dr.
Burnaby, BC V5A 1S6.

Email
pengyuliu.math@gmail.com

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Elements

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