Kevin J. Liu
National Library of Medicine Keck Postdoctoral Fellow
Department of Computer Science
Rice University
P.O. Box 1892
MS-132
Houston, TX 77251-1892
kevin.liu<at>rice<dot>edu

Postdoctoral adviser: Professor Luay K. Nakhleh
Postdoctoral co-adviser: Professor Michael H. Kohn

Graduate adviser: Professor Tandy Warnow
Graduate co-adviser: Professor C. Randal Linder

Research Interests

• Computational biology
• Phylogenetics, especially simultaneous estimation of alignments and trees
• Large-scale phylogenetic and alignment estimation at scales approaching the Tree of Life
  
• Multiple sequence alignment
• Population genetics
• Functional genomics
  
• Algorithmic design and empirical performance studies
  

Curriculum Vitae

Book Chapters

• K. Liu and T. Warnow, "Large-scale Multiple Sequence Alignment and Tree Estimation Using SATé," In Methods in Molecular Biology: Multiple Sequence Alignment, D. Russell (editor). Springer, to appear.

Refereed Journal and Conference Publications

• K. Liu, T. Warnow, M. T. Holder, S. Nelesen, J. Yu, A. Stamatakis, C. R. Linder, "SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees,'' Systematic Biology, vol. 61, no. 1, pp. 90-106, 2012, doi: 10.1093/sysbio/syr095.
• K. Liu and T. Warnow, "Treelength Optimization for Phylogeny Estimation," PLoS ONE, vol. 7, no. 3:e33104, 2012, doi: 10.1371/journal.pone.0033104.
• S. Nelesen, K. Liu, L. S. Wang, C. R. Linder, and T. Warnow, "DACTAL: divide-and-conquer trees (almost) without alignments,'' Proceedings of Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA, 2012. Acceptance rate of 13%.
• S. Nelesen, K. Liu, L. S. Wang, C. R. Linder, and T. Warnow, "DACTAL: divide-and-conquer trees (almost) without alignments,'' Bioinformatics, vol. 28, no. 12, pp. i274-i282, 2012, doi: 10.1093/bioinformatics/bts218.
  
• K. Liu, C. R. Linder, and T. Warnow, "RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation," PLoS ONE, vol. 6, no. 11:e27731, 2011, doi: 10.1371/journal.pone.0027731.
• K. Liu, C. R. Linder, and T. Warnow. "Multiple sequence alignment: a major challenge to large-scale phylogenetics,'' PLoS Currents: Tree of Life, 2010, doi: 10.1371/currents.RRN1198.
  
• C. R. Linder, R. Suri, K. Liu, and T. Warnow. "Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference,'' PLoS Currents: Tree of Life, 2010,  doi: 10.1371/currents.RRN1195.
  
• K. Liu, S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, "Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees," Science, vol. 324, no. 5934, pp. 1561-1564, 2009, doi: 10.1126/science.1171243. Selected by Faculty of 1000 Ecology.
  
• K. Liu, S. Nelesen, S. Raghavan, C. R. Linder, T. Warnow, "Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 7-21, 2009, doi: 10.1109/TCBB.2008.63.
• S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow, "The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analyses," Pacific Symposium on Biocomputing, vol. 13, pp. 15-24, 2008, doi: 10.1142/9789812776136_0004.
  

Working Manuscripts

• K. Liu et al., "The Functional and Adaptive Role of Hybridization in the House Mouse Genome," in preparation.
• M. J. Braun, K. Liu, E. L. Braun, C. R. Linder, and T. Warnow, "The Impact of Diverse Sequence Alignment Methods on Estimates of the Avian Tree of Life,'' in preparation.