Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks. - Peng Du; Huw A. Ogilvie; Luay Nakhleh (ISBRA, 2019)

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. - Jiafan Zhu; Xinhao Liu 004; Huw A. Ogilvie; Luay Nakhleh (Bioinform., 2019)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account. - Berk A. Yakici; Huw A. Ogilvie; Luay Nakhleh (RECOMB-CG, 2022)

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data. - Mohammad Amin Edrisi; Monica V. Valecha; Sunkara B. V. Chowdary; Sergio Robledo; Huw A. Ogilvie; David Posada; Hamim Zafar; Luay Nakhleh (Bioinform., 2022)

Annotation-free delineation of prokaryotic homology groups. - Yongze Yin; Huw A. Ogilvie; Luay Nakhleh (PLoS Comput. Biol., 2022)

MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks. - Mohammad Amin Edrisi; Huw A. Ogilvie; Meng Li 002; Luay Nakhleh (RECOMB-CG, 2023)

NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. - Yushu Liu; Mohammad Amin Edrisi; Zhi Yan 008; Huw A. Ogilvie; Luay Nakhleh (Algorithms Mol. Biol., 2024)

tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial Genomes. - Yongze Yin; Bryce Kille; Huw A. Ogilvie; Todd J. Treangen; Luay Nakhleh (RECOMB-CG, 2025)