pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. - Bui Quang Minh; Le Sy Vinh; Arndt von Haeseler; Heiko A. Schmidt (Bioinform., 2005)

Budgeted Phylogenetic Diversity on Circular Split Systems. - Bui Quang Minh; Fabio Pardi; Steffen Klaere; Arndt von Haeseler (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

ACOPHY: A Simple and General Ant Colony Optimization Approach for Phylogenetic Tree Reconstruction. - Huy Q. Dinh; Bui Quang Minh; Hoang Xuan Huan; Arndt von Haeseler (ANTS Conference, 2010)

Building Population-Specific Reference Genomes: A Case Study of Vietnamese Reference Genome. - Nguyen Dai Thanh; Pham Thi Minh Trang; Dang Thanh Hai; Nguyen Ha Anh Tuan; Si Quang Le; Bui Quang Minh; Quang Minh Dao; Pham Bao Son; Le Sy Vinh (KSE, 2015)

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. - Olga Chernomor; Bui Quang Minh; Arndt von Haeseler (J. Comput. Biol., 2015)

A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. - Diep Thi Hoang; Le Sy Vinh; Tomás Flouri; Alexandros Stamatakis; Arndt von Haeseler; Bui Quang Minh (KSE, 2016)

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. - Jana Trifinopoulos; Lam-Tung Nguyen; Arndt von Haeseler; Bui Quang Minh (Nucleic Acids Res., 2016)

pQMaker: empirically estimating amino acid substitution models in a parallel environment. - Nguyen Duc Canh; Cuong Cao Dang; Le Sy Vinh; Bui Quang Minh; Diep Thi Hoang (KSE, 2020)

Updated site concordance factors minimize effects of homoplasy and taxon sampling. - Yu K. Mo; Robert Lanfear; Matthew W. Hahn; Bui Quang Minh (Bioinform., 2023)

AliSim-HPC: parallel sequence simulator for phylogenetics. - Nhan Ly-Trong; Giuseppe M. J. Barca; Bui Quang Minh (Bioinform., 2023)

DecentTree: scalable Neighbour-Joining for the genomic era. - Weiwen Wang; James Barbetti; Thomas Wong; Bryan Thornlow; Russell Corbett-Detig; Yatish Turakhia; Robert Lanfear; Bui Quang Minh (Bioinform., 2023)