PrimedRPA: primer design for recombinase polymerase amplification assays. - Matthew Higgins; Matt Ravenhall; Daniel Ward; Jody Phelan; Amy Ibrahim; Matthew S. Forrest; Taane G. Clark; Susana G. Campino (Bioinform., 2019)

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers. - Julian Libiseller-Egger; Jody Phelan; Susana G. Campino; Fady R. Mohareb; Taane G. Clark (PLoS Comput. Biol., 2020)

Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. - Paula J. Gómez-González; Susana G. Campino; Jody Phelan; Taane G. Clark (Briefings Bioinform., 2022)

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data. - Jody Phelan; Wouter Deelder; Daniel Ward; Susana G. Campino; Martin L. Hibberd; Taane G. Clark (BMC Bioinform., 2022)

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing. - Romain Derelle; John Lees; Jody Phelan; Ajit Lalvani; Nimalan Arinaminpathy; Leonid Chindelevitch (Bioinform., 2023)

Bayesian compositional regression with microbiome features via variational inference. - Darren A. V. Scott; Ernest D. Benavente; Julian Libiseller-Egger; Dmitry V. Fedorov; Jody Phelan; Elena Ilina; Polina O. Tikhonova; Alexander Kudryavstev; Julia Galeeva; Taane G. Clark; Alex Lewin (BMC Bioinform., 2023)