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)

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. - Kristi Gdanetz; Gian Maria Niccolò Benucci; Natalie Vande Pol; Gregory M. Bonito (BMC Bioinform., 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)

CONSTAX2: improved taxonomic classification of environmental DNA markers. - Julian A. Liber; Gregory M. Bonito; Gian Maria Niccolò Benucci (Bioinform., 2021)

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)