A vector representation of phylogenetic trees and its applications

讲座名称: A vector representation of phylogenetic trees and its applications
讲座时间: 2024-06-06
讲座人: Louxin Zhang, Department of Mathematics, National
形式: 线下
校区: 兴庆校区

报告题目:A vector representation of phylogenetic trees and its applications

报告人:Louxin Zhang, Department of Mathematics, National University of Singapore




报告摘要:Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on n taxa as a vector of length 2n in which each taxon appears exactly twice. Using this new tree representation, we introduce a novel tree rearrangement operator, termed a HOP, that results in a tree space of diameter n and a quadratic neighbourhood size. We also introduce a novel metric, the HOP distance, which is the minimum number of HOPs to transform a tree into another tree. The HOP distance can be computed in near-linear time, a rare instance of tree rearrangement distance that is intractable. In this talk, we will also discuss the application of the vector representation in inference of phylogenetic networks from multiple phylogenetic trees.


报告人简介:Louxin Zhang obtained his BSc in mathematics from Lanzhou University, China and a PhD in computer science from University of Waterloo, Canada, and now is a Professor of bioinformatics at the National University of Singapore. His current research is on bioinformatics in comparative genomics, protein networks, cancer biology and data applications in healthcare and biomedicine. He has made significant contributions to the study of phylogenetic networks and sequence comparison. He has actively published in top-notch computer science and biology journals, including Journal of the ACM, SIAM J. Computing, Genome Research and Nature Communications, and conferences such as Annual European Conference on Computational Biology (ECCB) and Annual International Conference on Research in Computational Molecular Biology (RECOMB). He also published a monograph on sequence comparison (published by Springer) and a bioinformatics textbook (in Chinese, published by High Education Press, Beijing). He served as the Area CoChair for the Evolution and Comparative Genomics track of the 23rd Annual Conference on Intelligent and Systems for Molecular Biology (ISMB) and 14th Annual European Conference on Computational Biology ECCB), jointly held in Dublin in 2015. He is a member of the editorial board for several bioinformatics journals.