An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. - Kevin J. Liu; Jingxuan Dai; Kathy Truong; Ying Song; Michael H. Kohn; Luay Nakhleh (PLoS Comput. Biol., 2014)

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. - Hussein A. Hejase; Kevin J. Liu (BMC Bioinform., 2016)

Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach. - Hussein A. Hejase; Kevin J. Liu (BMC Genom., 2016)

Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins. - Hussein A. Hejase; Natalie Vande Pol; Gregory M. Bonito; Patrick P. Edger; Kevin J. Liu (BCB, 2017)

FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data. - Hussein A. Hejase; Natalie Vande Pol; Gregory M. Bonito; Kevin J. Liu (RECOMB-CG, 2018)

Scalable Statistical Introgression Mapping Using Approximate Coalescent-Based Inference. - Qiqige Wuyun; Nicholas W. VanKuren; Marcus Kronforst; Sean P. Mullen; Kevin J. Liu (BCB, 2019)

An Application of Random Walk Resampling to Phylogenetic HMM Inference and Learning. - Wei Wang 337; Qiqige Wuyun; Kevin J. Liu (BIBM, 2019)

Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences. - Wei Wang 337; Jack Smith; Hussein A. Hejase; Kevin J. Liu (Algorithms Mol. Biol., 2020)

Statistical analysis of GC-biased gene conversion and recombination hotspots in eukaryotic genomes: a phylogenetic hidden Markov model-based approach. - Meijun Gao; Kevin J. Liu (BCB, 2021)

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited. - Wei Wang 337; Ahmad Hejasebazzi; Julia Zheng; Kevin J. Liu (Bioinform., 2021)

The impact of gene sequence alignment and gene tree estimation error on summary-based species network estimation. - Meijun Gao; Wei Wang 337; Kevin J. Liu (BCB, 2022)

Phylogenetic Placement of Aligned Genomes and Metagenomes with Non-tree-like Evolutionary Histories. - Md Alamin; Kevin J. Liu (BCB, 2023)

The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction. - Julia Zheng; Yuya Nishida; Alicja Okrasinska; Gregory M. Bonito; Elizabeth A. C. Heath-Heckman; Kevin J. Liu (BCB, 2023)

A Statistical Optimization Technique to Inform Statistical Resampling Assessments of Phylogenetic Reconstruction Reliability. - Byungho Lee; Kevin J. Liu (BIBM, 2024)

Estimating confidence intervals on reconstructed cophylogenies using bootstrap resampling. - Julia Zheng; Yuya Nishida; Elizabeth A. C. Heath-Heckman; Kevin J. Liu (BIBM, 2024)

Detecting and Mapping Local Model Violations During Biomolecular Sequence Analysis: a REsampling and Visual EvALuation Approach. - Meijun Gao; Kevin J. Liu (RECOMB-CG, 2025)