Quick Facts
Biography
Louxin Zhang is a Canadian computational biologist. He is currently a professor in the Department of Mathematics at the National University of Singapore. He is recognized for his contributions to combinatorial semigroup theory in mathematics. In addition, he is recognized for his work on the mathematical understanding of phylogenetic trees and networks, as well as the analysis of spaced seeds for sequence comparison in bioinformatics.
Early life
Louxin Zhang grew up in Luoyang, Henan, China. He graduated from Lanzhou University with an undergraduate degree in mathematics and a master's degree in mathematics. Then he proceeded to Canada to pursue a doctorate in computer science at the University of Waterloo, where he earned his Ph.D. in Computer Science with a thesis entitled "Emulations and Embeddings of Meshes of Trees and Hypercubes of Cliques.
Career
After postdoctoral research in the laboratory of Ming Li, Zhang began his independent research career in 1996 at the Institute of Systems Sciences (currently the Institute for Infocomm Research), where he was awarded a three-year Lee Kuan Yew Postdoctoral Fellowship in 1997. He introduced the string rewriting technique to investigate the word problem and the conjugacy problem in special monoids. He discovered an elegant relationship between gene loss, gene duplication, and incomplete lineage sorting costs. Along with his colleagues, he developed the tree component decomposition method for studying phylogenetic networks. The technique yields a solution to an open problem regarding tree containment, the exact and asymptotic counting of the so-called tree-child networks, and a scalable method for inferring the minimum phylogeny. He also contributed to the theoretical knowledge of spaced seeds for sequence comparison and reconstruction of ancestral genome sequences.
Publications
- Zhang L. 1991. Conjugacy in special monoids. Journal of Algebra 143: 487-497.
- Ma B, Li M, Zhang L. From gene trees to species trees. SIAM Journal on Computing 30:729-752.
- Choi KP, Zeng F, Zhang L. Good spaced seeds for homology search. Bioinformatics 20:1053-1059.
- Li, Guoliang; Steel, Mike; Zhang, Louxin (2008-08-01). "More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States". Systematic Biology. 57 (4): 647–653. arXiv:0803.0195. doi:10.1080/10635150802203898. ISSN 1063-5157. PMID 18709600. S2CID 1373201.
- Zhang, Louxin (November 2011). "From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8 (6): 1685–1691. doi:10.1109/TCBB.2011.83. ISSN 1557-9964. PMID 21576759. S2CID 226872.
- Tran, Ngoc Hieu; Choi, Kwok Pui; Zhang, Louxin (2013-08-06). "Counting motifs in the human interactome". Nature Communications. 4 (1): 2241. Bibcode:2013NatCo...4.2241T. doi:10.1038/ncomms3241. ISSN 2041-1723. PMC 3741638. PMID 23917172.
- Gambette, Philippe; Gunawan, Andreas D. M.; Labarre, Anthony; Vialette, Stéphane; Zhang, Louxin (2015). "Locating a Tree in a Phylogenetic Network in Quadratic Time". Research in Computational Molecular Biology. Lecture Notes in Computer Science. Vol. 9029. pp. 96–107. arXiv:1502.03379. doi:10.1007/978-3-319-16706-0_12. ISBN 978-3-319-16705-3. S2CID 8258359.
- Zheng, Yu; Zhang, Louxin (2017-08-17). "Reconciliation With Nonbinary Gene Trees Revisited". Journal of the ACM. 64 (4): 24:1–24:28. doi:10.1145/3088512. ISSN 0004-5411. S2CID 7715566.
- Gunawan, Andreas D. M.; DasGupta, Bhaskar; Zhang, Louxin (2017-02-01). "A decomposition theorem and two algorithms for reticulation-visible networks". Information and Computation. 252: 161–175. doi:10.1016/j.ic.2016.11.001. ISSN 0890-5401.
- Zhang, Louxin; Abhari, Niloufar; Colijn, Caroline; Wu, Yufeng (2023-01-03). "A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees by Aligning Lineage Taxon Strings". arXiv:2301.00992 [q-bio.PE].