Research

RESEARCH TOPICS

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  • Statistical Phylogenetics  
  • Comparative genomics
  • Microarray data analysis                      
  • Survival analysis
  • Stochastic process
  • Bayesian statistics

PUBLICATIONS (Google Scholar)

2019

  • Cai, L., Xi, Z., Amorim, A.M., Sugumaran, M., Rest, J., Liu, L., Davis, C.C. Widespread ancient whole genome duplications in Malpighiales coincide with Eocene global climatic upheaval. New Phytologist 2019, 221:565-576

2018

  • Chen, Y., Liu, X., Jiang, C., Liu, L., Ordovas, J.M., Lai, C. Curcumin supplementation increases survival and lifespan in Drosophila under heat stress conditions. BioFactors 2018, 44:577-587

  • Yu, L., Liu, L., Chen, D.G. A homoscedasticity test for the accelerated failure time model. Computational Statistics 2018, 34:433-446

  • Wang, K., Lenstrab, J.A., Liu, L., Hu, Q., Ma, T., Liu, J. Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent. Communications Biology 2018, 1:169

  • Wu, S., Edwards, S.V., Liu, L. Genome-scale DNA sequence data and the evolutionary history of placental mammals. Data in Brief 2018, 18:1971-1975.

  • Liu, L., Anderson, C., Pearl, D.K., Edwards, S.V. Modern phylogenomics: building phylogenetic trees using the multispecies coalescent model. In: Evolutionary genomics: statistical and computational methods 2018.

  • Yohe, L.R., Liu, L., Dávalos, L.M., Liberles D.A. Protocols for the molecular evolutionary analysis of gene duplicates. In: Computational Methods in Protein Evolution 2018.

  • Han, Z., Liu, L., Zheng, Y. Chemical probes and chemical biology approaches for the investigation of enzymatic functions of lysine acetyltransferases (KATs). Angewandte Chemie 2018, 57:1162-1184

2017

  • Liu, L, Zhang, Jin, Rheindt, F.E., Lei, F., Qu, Y., Wang, Y., Sullivan, C., Ni, W., Wang, J., Yang, F., Chen, J., Edwards, S.V., Meng, J., and Wu, S. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proceedings of the National Academy of Sciences (USA) 2017. doi: 10.1073/pnas.1616744114. Download alignments

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  • Han, Z., Liu, L., Zheng, Y. Chemical probes and chemical biology approaches for the investigation of enzymatic functions of lysine acetyltransferases (KATs). Angewandte Chemie 2017, doi: 10.1002/ange.201704745.

2016

  • Xin, X., Chen, Y., Chen, D., Xiao, F., Parnell, L., Zhao, J., Liu, L., Ordovas, J., Lai, C., Shen, L. Supplementation with Major Royal Jelly Proteins Increases Lifespan, Feeding and Fecundity in Drosophila. Journal of Agricultural and Food Chemistry 2016, 64(29):5803-5812

  • Teufel, A., Liu, L., Liberles, L. Models for gene duplication when dosage balance works as a transition state to subsequent neo- or sub-functionalization. BMC Evol Biol 2016, 16:45

  • Edwards, S.V., Xi, Z., Janke, A., Faircloth, B.C., McCormack, J.E., Glenn, T.C., Zhong, B., Wu, S., Lemmon, E.M., Lemmon, A.R., Leaché, A.D., Liu, L., Davis, C.C. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol Phylogenet Evol 2016, 94:447-462

  • H. Lorenzi, A. Khan, M.S. Behnke,  S. Namasivayam, L.S. Swapna, M. Hadjithomas, S. Karamycheva1, D. Pinney, B. Brunk, J.W. Ajioka, D. Ajzenberg, J.C. Boothroyd, J.P. Boyle, M.L. Dardé, M.A. Diaz-Miranda, J.P. Dubey, H.M. Fritz, SM Gennari, B.D. Gregory, K. Kim, J. Saeij, C. Su, M.W. White, XQ Zhu, D.K. Howe, B M. Rosenthal, M.E. Grigg, J. Parkinson, L. Liu, J.C. Kissinger, D.S. Roos, L. D. Sibley. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nature Comm 2016, 7:10147.

  • Xi, Z., Liu, L., Davis, C.C. The impact of missing data on species tree estimation. Mol Biol Evol 2016, 33:838-860

2015

  • Zhao, J., Teufel, A.I., Liberles, D.A., Liu, L. A generalized birth and death process for modeling the fates of gene duplication. BMC Evol Biol 2015, 15:275.

  • Xi, Z., Liu, L., Davis, C.C. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol Phylogenet Evol 2015, 92:63-71.

  • Liu, L., Wu, S., Xi, Z., Davis, C.C., S V. Edwards, S.V. Estimating phylogenetic trees from genome-scale data. NY. Acad. Sci. 2015, 1360:36-53.

  • Liu, L., Edwards S.V. Comment on Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 2015, 350 (6257): 171.

  • Liu, L., Wu, S., Yu, L. Coalescent methods for estimating species trees from phylogenomic data. Journal of Systematic Evolution 2015, 53(5):380-390.

  • Su, D., Zhou, X., Chen, Q., Jiang, Y., Yang, X., Zheng, W., Tao, K., Wu, J., Yan, Z., Liu, L., Wu, S., Mao, W. Prognostic nomogram for thoracic esophageal squamous cell carcinoma after radical esophagectomy. PLoS One 2015, 10: e0124437.

  • Liu, L., Xi, Z., Davis, C.C. Coalescent methods are robust to long-branch artifacts in species tree estimation. Mol Biol Evol 2015, 32(3): 791-805.

2014

  • Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon YW Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabaldón, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C Warren, David Ray, Richard E Green, Michael W Bruford, Xiangjiang Zhan, Andrew Dixon, Shengbin Li, Ning Li, Yinhua Huang, Elizabeth P Derryberry, Mads Frost Bertelsen, Frederick H Sheldon, Robb T Brumfield, Claudio V Mello, Peter V Lovell, Morgan Wirthlin, Maria Paula Cruz Schneider, Francisco Prosdocimi, José Alfredo Samaniego, Amhed Missael Vargas Velazquez, Alonzo Alfaro-Núñez, Paula F Campos, Bent Petersen, Thomas Sicheritz-Ponten, An Pas, Tom Bailey, Paul Scofield, Michael Bunce, David M Lambert, Qi Zhou, Polina Perelman, Amy C Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Qiuemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnea Smeds, Frank E Rheindt, Michael Braun, Jon Fjeldsa, Ludovic Orlando, F Keith Barker, Knud Andreas Jønsson, Warren Johnson, Klaus-Peter Koepfli, Stephen O’Brien, David Haussler, Oliver A Ryder, Carsten Rahbek, Eske Willerslev, Gary R Graves, Travis C Glenn, John McCormack, Dave Burt, Hans Ellegren, Per Alström, Scott V Edwards, Alexandros Stamatakis, David P Mindell, Joel Cracraft, Edward L Braun, Tandy Warnow, Wang Jun, M Thomas P Gilbert, Guojie Zhang. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014 346 (6215), 1320-1331.

  • Xi, Z., Liu, L., Rest, J.S., Davis, C.C. Phylogenomics and Coalescent Analyses Resolve the Placement of Amborella as Sister to Water Lilies. Syst. Biol. 2014, 63 (6): 919-932.

  • Jhwueng, D., Huzurbazar, S., O'Meara, B.C., Liu, L.$. Investigating the performance of AIC in selecting phylogenetic models. Stat Appl. Genetic. Mole Biol 2014, doi: 10.1515/ samb-2013-0048.

​2013

  • Ma, Q., Reeves, J.H., Liberles, D.A., Yu, L., Chang, Z., Zhao, J., Cui, J., Xu, Y.$, Liu, L.$. A phylogenetic model for understanding the effect of gene duplication on cancer progression. Nuclear Acid Research. 2013, doi: 10.1093/nar/gkt1320

  • Liberles, D., Teufel, A., Liu, L., and Stadler, T. On the Need for Mechanistic Models in Computational Genomics and Metagenomics. Genome Biology and Evolution. 2013, 5(10):2008-18

  • Zhong, B.*, Liu, L.*, Yan, Z., and Penny, D. Origin of land plants using the multispecies coalescent model. Trends in Plant Science. 2013, 18:492-495 

  • Shaw, T., Z. Ruan, T. Glenn, and Liu, L$. STRAW: a web server for species tree analysis. Nucleic Acids Research. 2013, doi: 10.1093/nar/gkt377

  • Wu, S., Song, S., Liu, L., and S.V. Edwards. Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. PNAS. 2013, doi:10.1073/pnas.1300129110.

  • Yu, L., Liu, L. and Chen, D. Weighted least-squares method for right-censored data in accelerated failure time mode. Biometrics 2013, 69(2):358-65.

​2012

  • Song, S.*, Liu, L*., Edwards, S.V., Wu, S. Resolving Conflict in Placental Mammal Phylogeny Using Phylogenomics and the Multispecies Coalescent Model. PNAS. 2012, 109:14942-14947.

  • Yu, L., Liu, L. Extended Quasi-Likelihood with Fractional Polynomials in the Frame of the ATF model. Statistics in Medicine. 2012, 31:1369-1379.

  • Ronquist, F., M. Teslenko, P. Mark, D. L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M.A. Suchard and J.P. Huelsenbeck. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst Biol. 2012, 61:539-542

​2011

  • Liu, L., L. Yu, V. Kalavacharla, Z. Liu. A Bayesian model for gene family evolution. BMC Bioinformatics. 2011, 12:426.​

  • Liu, L., and L. Yu. Estimating species trees from unrooted gene trees. Syst. Biol. 2011, 60: 661-667.

​2010

  • Liu, L., L. Yu, S.V. Edwards. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.

  • Liu, L., and L. Yu. Phybase: an R package for species tree analysis. Bioinformatics. 2010 26(7):962-963.

​2009

  • Liu, L., L. Yu, D.K. Pearl, and S.V. Edwards. Estimating species phylogenies using coalescence times among sequences. Systematic Biology 2009, 58(5):468-477.

  • Liu, L., L. Yu, L. Kubatko, D.K. Pearl, and S.V. Edwards. Coalescent methods for estimating multilocus phylogenetic trees. Molecular Phylogenetics and Evolution 2009, 53(1): 320-328.

  • Liu, L., and S.V. Edwards. Phylogenetic Analysis in the Anomaly Zone. Systematic Biology 2009, 58(4):452-460.

  • Liu, L., L. Yu, and D.K. Pearl. Maximum tree: a consistent estimator of the species tree. Journal of Mathematical Biology 2009, 60(1):95-106.

  • Yu, L., R. Yu, L. Liu. Quasi-likelihood for Right-Censored Data in the Generalized Linear Model. Communications in Statistics - Theory and Methods 2009, 38:2187-2200.

​2008

  • Liu, L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 2008, 24(21):2542:2543.

  • Liu, L., D.K. Pearl, R.T. Brumfield, and S.V. Edwards. Estimating species trees using multiple-allele DNA sequence data. Evolution 2008, 62(8):2080-2091.

​2007

  • Liu, L. and D.K. Pearl. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 2007, 56:504-514.

  • Edwards*, S.V., L. Liu*, and D.K. Pearl. High resolution species trees without concatenation. Proceedings of the National Academy of Sciences (USA), 2007, 104:5936-5941.