spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex. - Chaka Tang; Josephine F. Reyes; Fabio Luciani; Andrew R. Francis; Mark M. Tanaka (Bioinform., 2008)

Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes. - Josephine F. Reyes; Andrew R. Francis; Mark M. Tanaka (BMC Bioinform., 2008)

Conditions for the Evolution of Gene Clusters in Bacterial Genomes. - Sara Ballouz; Andrew R. Francis; Ruiting Lan; Mark M. Tanaka (PLoS Comput. Biol., 2010)

Bacterial Genomics and Computational Group Theory: The BioGAP Package for GAP. - Attila Egri-Nagy; Andrew R. Francis; Volker Gebhardt (ICMS, 2014)

Which phylogenetic networks are merely trees with additional arcs? - Andrew R. Francis; Mike A. Steel (CoRR, 2015)

Tree-based unrooted phylogenetic networks. - Andrew R. Francis; Katharina T. Huber; Vincent Moulton (CoRR, 2017)

New characterisations of tree-based networks and proximity measures. - Andrew R. Francis; Charles Semple; Mike A. Steel (Adv. Appl. Math., 2018)

Bacterial phylogeny in the Cayley graph. - Chad Clark; Attila Egri-Nagy; Andrew R. Francis; Volker Gebhardt (Discret. Math. Algorithms Appl., 2019)

How tree-based is my network? Proximity measures for unrooted phylogenetic networks. - Mareike Fischer 001; Andrew R. Francis (Discret. Appl. Math., 2020)

Rooted NNI moves and distance-1 tail moves on tree-based phylogenetic networks. - Péter L. Erdös; Andrew R. Francis; Tamás Róbert Mezei (Discret. Appl. Math., 2021)

Encoding and ordering X-cactuses. - Andrew R. Francis; Katharina T. Huber; Vincent Moulton; Taoyang Wu (Adv. Appl. Math., 2023)

Factorizing the Brauer monoid in polynomial time. - Daniele Marchei; Emanuela Merelli; Andrew R. Francis (CoRR, 2024)