Speaker:

Louxin Zhang （新加坡国立大学）

Time:

• July 3, 2023 (Monday) 10:30-11:30am

Venue:

电子科技大学清水河校区主楼B1-501

Abstract:

Phylogenetic networks are rooted, acyclic directed graph in which leaves are labelled with genes, genomes or species. They are used to model evolution with reticulate events. The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, then the smallest phylogenetic network that displays all the trees is computed. A tree-child network is a phylogenetic network satisfying the condition that every non-leaf node has at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees, where we reduce the tree-child network inference problem to the shortest common supersequence problem. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference. Our new program, named ALTS, is fast enough to infer a tree-child network with a large number of reticulations for a set of up to 100 phylogenetic trees with 50 taxa.

Speaker Bio:

Louxin Zhang is currently a Professor at the Department of Mathematics, the National University of Singapore and the Director of the Center for Data Science and Machine Learning. He obtained the BSc in mathematics from Lanzhou University, China, and the PhD degree in computer science from the University of Waterloo, Canada. His current research interests include algorithms in bioinformatics for genomics, complex networks and big data in biomedicine. He has published over 150 refereed journal and conference papers in mathematics, computer science and bioinformatics and is the co-author of a monograph on sequence comparison and a bioinformatics textbook. He is a member of the Editorial Board of Quantitative Biology, Bioinformatics Advances. He also served as the chair (or co-chair) of the program committee the 17th Annual Asia Pacific Bioinformatics Conference, the 18th RECOMB Comparative Genomics, the Evolution & Comparative Genomics track of the 2015 Annual Int’l Conference on Intelligent Systems for Molecular Biology (ISMB) and the European Conference on Computational Biology.