Highlights

Recent research highlights include new computational methods for gene flow detection, which were used to uncover genome-wide patterns of adaptive introgression in M. musculus, and new methods enabling fast and accurate estimation of phylogenies and/or multiple sequence alignments with unprecedented scale.

Refereed Journal and Conference Publications

  1. H. A. Hejase, N. VandePol, G. A. Bonito, P. P. Edger, and K. J. Liu, "Coal-Miner: a coalescent-based method for GWA studies of quantitative traits with complex evolutionary origins," Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 107-114, 2017. DOI: 10.1145/3107411.3107490.
  2. H. A. Hejase and K. J. Liu, "A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation," BMC Bioinformatics, vol. 17, no. 1, p. 422, 2016, DOI: 10.1186/s12859-016-1277-1.
  3. Z. Wang and K. J. Liu, "A performance study of the impact of recombination on species tree analysis," Proceedings of the Fourteenth RECOMB Comparative Genomics Satellite Conference (RECOMB-CG), Montréal, Quebec, Canada, 2016. Journal version published in BMC Genomics, vol. 17, no. 10, pp. 165-174, 2016, DOI: 10.1186/s12864-016-3104-5.
  4. H. A. Hejase and K. J. Liu, "Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach," Proceedings of the Fourteenth Asia Pacific Bioinformatics Conference (APBC), San Francisco, CA, USA, 2016. Journal version published in BMC Genomics, vol. 17(Suppl 1), no. 8, pp. 41-57, 2016, DOI: 10.1186/s12864-015-2298-2.
  5. K. J. Liu, E. Steinberg, A. Yozzo, Y. Song, M. H. Kohn, and L. K. Nakhleh, "Interspecific introgressive origin of genomic diversity in the house mouse," Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 1, pp. 196-201, 2015, DOI: 10.1073/pnas.1406298111.
  6. K. J. Liu, J. Dai, K. Truong, Y. Song, M. H. Kohn, and L. K. Nakhleh, "An HMM-based comparative genomic framework for detecting introgression in eukaryotes," PLoS Computational Biology, vol. 10, no. 6, p. e1003649, 2014, DOI: 10.1371/journal.pcbi.1003649.
  7. Y. Yu, J. Dong, K. J. Liu, and L. K. Nakhleh, "Maximum likelihood inference of reticulate evolutionary histories," Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 46, pp. 16448-16453, 2014, DOI: 10.1073/pnas.1407950111.
  8. K. J. Liu, T. J. 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.
  9. K. J. Liu and T. J. Warnow, "Treelength optimization for phylogeny estimation," PLoS ONE, vol. 7, no. 3:e33104, 2012, DOI: 10.1371/journal.pone.0033104.
  10. S. Nelesen, K. J. Liu, L. S. Wang, C. R. Linder, and T. J. 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%. Journal version published in Bioinformatics, vol. 28, no. 12, pp. i274-i282, 2012, DOI: 10.1093/bioinformatics/bts218.
  11. K. J. Liu, C. R. Linder, and T. J. 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.
  12. K. J. Liu, C. R. Linder, and T. J. Warnow. "Multiple sequence alignment: a major challenge to large-scale phylogenetics,'' PLoS Currents: Tree of Life, 2010, DOI: 10.1371/currents.RRN1198.
  13. C. R. Linder, R. Suri, K. J. Liu, and T. J. 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.
  14. K. J. Liu, S. Raghavan, S. Nelesen, C. R. Linder, T. J. 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.
  15. K. J. Liu, S. Nelesen, S. Raghavan, C. R. Linder, T. J. 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.
  16. S. Nelesen, K. J. Liu, D. Zhao, C. R. Linder, T. J. Warnow, "The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses," Proceedings of the Pacific Symposium on Biocomputing, Kohala Coast, Hawaii, USA, 2008. Journal version published in Biocomputing, vol. 13, pp. 15-24, 2008, DOI: 10.1142/9789812776136\_0004.

Book Chapters

  1. K. J. Liu and T. J. Warnow, Large-scale multiple sequence alignment and tree estimation using SATé, In Methods in Molecular Biology: Multiple Sequence Alignment, D. Russell (editor). New York: Springer; 2014. p. 219-244, DOI: 10.1007/978-1-62703-646-7_15.

Working Manuscripts

  • "Fast and accurate statistical inference of phylogenetic networks using hundreds of genomic sequences", in preparation.
  • "New support estimation techniques for biomolecular sequence analysis", in preparation.
  • "Revisiting Felstenstein's question: new phylogenetic comparative methods using heterogeneous biological data," in preparation.
  • "A phylogenomic study of adaptive co-evolution between early diverging fungi and obligate bacterial endosymbionts in the Burkholderiaceae," in preparation.
  • "Microbial communities in global groundwaters: an evolutionary and ecological perspective," in preparation.