| Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees K Liu, S Raghavan, S Nelesen, CR Linder, T Warnow Science 324 (5934), 1561-1564, 2009 | 349 | 2009 |
| SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees K Liu, TJ Warnow, MT Holder, SM Nelesen, J Yu, AP Stamatakis, ... Systematic biology 61 (1), 90, 2011 | 298 | 2011 |
| RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation K Liu, CR Linder, T Warnow PloS one 6 (11), e27731, 2011 | 142 | 2011 |
| Maximum likelihood inference of reticulate evolutionary histories Y Yu, J Dong, KJ Liu, L Nakhleh Proceedings of the National Academy of Sciences 111 (46), 16448-16453, 2014 | 140 | 2014 |
| Multiple sequence alignment: a major challenge to large-scale phylogenetics K Liu, CR Linder, T Warnow PLoS currents 2, 2010 | 65 | 2010 |
| Interspecific introgressive origin of genomic diversity in the house mouse KJ Liu, E Steinberg, A Yozzo, Y Song, MH Kohn, L Nakhleh Proceedings of the National Academy of Sciences 112 (1), 196-201, 2015 | 61 | 2015 |
| An HMM-based comparative genomic framework for detecting introgression in eukaryotes KJ Liu, J Dai, K Truong, Y Song, MH Kohn, L Nakhleh PLoS computational biology 10 (6), e1003649, 2014 | 40 | 2014 |
| DACTAL: divide-and-conquer trees (almost) without alignments S Nelesen, K Liu, LS Wang, CR Linder, T Warnow Bioinformatics 28 (12), i274-i282, 2012 | 40 | 2012 |
| The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses S Nelesen, K Liu, D Zhao, CR Linder, T Warnow Biocomputing 2008, 25-36, 2008 | 40 | 2008 |
| Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy K Liu, S Nelesen, S Raghavan, CR Linder, T Warnow IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 6 …, 2009 | 38 | 2009 |
| A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation HA Hejase, KJ Liu BMC bioinformatics 17 (1), 422, 2016 | 15 | 2016 |
| Large-scale multiple sequence alignment and tree estimation using SATé K Liu, T Warnow Multiple Sequence Alignment Methods, 219-244, 2014 | 14 | 2014 |
| Treelength optimization for phylogeny estimation K Liu, T Warnow PloS one 7 (3), e33104, 2012 | 9 | 2012 |
| Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference CR Linder, R Suri, K Liu, T Warnow PLoS currents 2, 2010 | 5 | 2010 |
| Fastnet: fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data HA Hejase, N VandePol, GM Bonito, KJ Liu RECOMB International conference on Comparative Genomics, 242-259, 2018 | 4 | 2018 |
| Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach HA Hejase, KJ Liu BMC genomics 17 (1), S8, 2016 | 4 | 2016 |
| A performance study of the impact of recombination on species tree analysis Z Wang, KJ Liu BMC genomics 17 (10), 785, 2016 | 3 | 2016 |
| Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences W Wang, J Smith, HA Hejase, KJ Liu RECOMB International conference on Comparative Genomics, 294-308, 2018 | 2 | 2018 |
| Coal-Miner: a statistical method for GWA studies of quantitative traits with complex evolutionary origins HA Hejase, NV Pol, GM Bonito, PP Edger, KJ Liu Proceedings of the 8th ACM International Conference on Bioinformatics …, 2017 | 2 | 2017 |
| FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data H Hejase, N VandePol, GM Bonito, KJ Liu bioRxiv, 132795, 2018 | 1 | 2018 |
