Yao-Ban Chan

Unravelling var complexity: Relationship between DBLα types and var genes in Plasmodium falciparum

Mun Hua Tan, Heejung Shim, Yao-ban Chan, Karen P Day

Journal article  |  2023  |  Frontiers in Parasitology

The enormous diversity and complexity of var genes that diversify rapidly by recombination has led to the exclusion of assembly of..

The large-sample asymptotic behaviour of quartet-based summary methods for species tree inference

Yao-ban Chan, Qiuyi Li, Celine Scornavacca

Journal article  |  2022  |  JOURNAL OF MATHEMATICAL BIOLOGY

methods seek to infer a species tree from a set of gene trees. A desirable property of such methods is that of statistical consist..

An accurate method for identifying recent recombinants from unaligned sequences

Qian Feng, Kathryn E Tiedje, Shazia Ruybal-Pesantez, Gerry Tonkin-Hill, Michael F Duffy, Karen P Day, Heejung Shim, Yao-Ban Chan

Journal article  |  2022  |  BIOINFORMATICS

MOTIVATION: Recombination is a fundamental process in molecular evolution, and the identification of recombinant sequences is thus..

Bayesian inference of ancestral recombination graphs

Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan, David Balding

Journal article  |  2022  |  PLOS COMPUTATIONAL BIOLOGY

We present a novel algorithm, implemented in the software ARGinfer, for probabilistic inference of the Ancestral Recombination Gra..

The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

Qiuyi Li, Celine Scornavacca, Nicolas Galtier, Yao-Ban Chan

Journal article  |  2021  |  SYSTEMATIC BIOLOGY

Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees..

Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents

Gerry Tonkin-Hill, Shazia Ruybal-Pesantez, Kathryn E Tiedje, Virginie Rougeron, Michael F Duffy, Sedigheh Zakeri, Tepanata Pumpaibool, Pongchai Harnyuttanakorn, OraLee H Branch, Lastenia Ruiz-Mesia, Thomas S Rask, Franck Prugnolle, Anthony T Papenfuss, Yao-ban Chan, Karen P Day

Journal article  |  2021  |  PLOS GENETICS

Malaria remains a major public health problem in many countries. Unlike influenza and HIV, where diversity in immunodominant surfa..

Reconciliation of a gene network and species tree

Yao-ban Chan, Charles Robin

Journal article  |  2019  |  JOURNAL OF THEORETICAL BIOLOGY

The phylogenetic trees of genes and the species which they belong to are similar, but distinct due to various evolutionary process..

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M Hogan, Stefan R Maetschke, Mark A Ragan

Journal article  |  2019  |  BRIEFINGS IN BIOINFORMATICS

We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fu..

Upper bounds on the growth rates of independent sets in two dimensions via corner transfer matrices

Yao-ban Chan, Andrew Rechnitzer

Journal article  |  2018  |  LINEAR ALGEBRA AND ITS APPLICATIONS

We devise an algorithm to calculate upper bounds on the growth rates of the number of independent sets on a variety of regular two..

Accurate Costing of Mining Equipment

Christina N Burt, Yao-ban Chan

Book Chapter  |  2018  |  Studies in Systems, Decision and Control

When performing equipment selection, we can best account for the operating cost by considering the number of hours that the equipm..