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. M. Gao and K. J. Liu, "Statistical analysis of GC-biased gene conversion and recombination hotspots in eukaryotic genomes: a phylogenetic hidden Markov model-based approach", submitted to ACM BCB 2021.
  2. W. Wang, A. Hejasebazzi, J. Zheng, and K. J. Liu, "Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited", accepted by ISMB/ECCB 2021 and to appear in Bioinformatics. Provisional acceptance rate of 18.6\%. Final acceptance rate TBA.
  3. W. Wang, J. Smith, H. A. Hejase, and K. J. Liu, "Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences", Algorithms for Molecular Biology, vol. 15, no. 1, p. 7, 2020, DOI: 10.1186/s13015-020-00167-0.
  4. S. P. Mullen, N. W. VanKuren, W. Zhang, S. Nallu, E. B. Kristiansen, Q. Wuyun, K. J. Liu, R. I. Hill, A. Briscoe, M. R. Kronforst, "Disentangling population history and character evolution among hybridizing lineages," Molecular Biology and Evolution, vol. 37, issue 5, 2020, DOI: 10.1093/molbev/msaa004.
  5. W. Wang, Q. Wuyun, and K. J. Liu, "An application of random walk resampling to phylogenetic HMM inference and learning," IEEE Transactions on NanoBioscience, vol. 19, no. 3, pp. 506-517, 2020, DOI: 10.1109/TNB.2020.2991302.
  6. W. Wang, Q. Wuyun, and K. J. Liu, "An application of random walk resampling to phylogenetic HMM inference and learning," Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 44-51, 2019, DOI: 10.1109/BIBM47256.2019.8983223.
  7. Q. Wuyun, N. W. VanKuren, M. Kronforst, S. P. Mullen, and K. J. Liu, "Scalable statistical introgression mapping using approximate coalescent-based inference," Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19), ACM, New York, NY, USA, pp. 535, 2019, DOI: 10.1145/3307339.3342165.
  8. H. A. Hejase, N. VandePol, G. M. Bonito, and K. J. Liu, "FastNet: fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data", Proceedings of the Sixteenth RECOMB Comparative Genomics Satellite Conference (RECOMB-CG), Magog-Orford, Québec, Canada, 2018. Conference paper published in Springer LNCS, vol. 11183, pp. 242-259, 2018, DOI: 10.1007/978-3-030-00834-5_14.
  9. W. Wang, J. Smith, H. A. Hejase, and K. J. Liu, "Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences", Proceedings of the Sixteenth RECOMB Comparative Genomics Satellite Conference (RECOMB-CG), Magog-Orford, Québec, Canada, 2018. Conference paper published in Springer LNCS, vol. 11183, pp. 294-308, 2018, DOI: 10.1007/978-3-030-00834-5_17.
  10. 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.
  11. 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.
  12. 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, Québec, Canada, 2016. Journal version published in BMC Genomics, vol. 17, no. 10, pp. 165-174, 2016, DOI: 10.1186/s12864-016-3104-5.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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

  • "New techniques for phylogenetic multiple sequence alignment", in preparation.
  • "A performance study of co-phylogenetic inference methods," in preparation.
  • "New statistical methods for detecting local evolutionary rate heterogeneity," in preparation.
  • "Scalable statistical inference of species phylogenies from large-scale resequenced genomic datasets," in preparation.
  • "A phylogenomic study of adaptive co-evolution between early diverging fungi and obligate bacterial endosymbionts in the Burkholderiaceae," in preparation.