A genotype calling algorithm for the Illumina BeadArray platform. - Yik Y. Teo; Michael Inouye; Kerrin S. Small; Rhian Gwilliam; Panagiotis Deloukas; Dominic Kwiatkowski; Taane G. Clark (Bioinform., 2007)

SnoopCGH: software for visualizing comparative genomic hybridization data. - Jacob Almagro-Garcia; Magnus Manske; Celine Carret; Susana G. Campino; Sarah Auburn; Bronwyn L. MacInnis; Gareth Maslen; Arnab Pain; Christopher I. Newbold; Dominic Kwiatkowski; Taane G. Clark (Bioinform., 2009)

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals. - Taane G. Clark; Susana G. Campino; Elisa Anastasi; Sarah Auburn; Yik Y. Teo; Kerrin S. Small; Kirk A. Rockett; Dominic Kwiatkowski; Christopher C. Holmes (Bioinform., 2010)

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. - Francesc Coll; Kim Mallard; Mark D. Preston; Stephen D. Bentley; Julian Parkhill; Ruth McNerney; Nigel J. Martin 001; Taane G. Clark (Bioinform., 2012)

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. - Mark D. Preston; Magnus Manske; Neil R. Horner; Samuel A. Assefa; Susana G. Campino; Sarah Auburn; Issaka Zongo; Jean-Bosco Ouedraogo; Francois Nosten; Timothy J. C. Anderson; Taane G. Clark (Bioinform., 2012)

estMOI: estimating multiplicity of infection using parasite deep sequencing data. - Samuel A. Assefa; Mark D. Preston; Susana G. Campino; Harold Ocholla; Colin J. Sutherland; Taane G. Clark (Bioinform., 2014)

SVAMP: sequence variation analysis, maps and phylogeny. - Raeece Naeem; Lailatul Hidayah; Mark D. Preston; Taane G. Clark; Arnab Pain (Bioinform., 2014)

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. - Ernest D. Benavente; Francesc Coll; Nick Furnham; Ruth McNerney; Judith R. Glynn; Susana G. Campino; Arnab Pain; Fady R. Mohareb; Taane G. Clark (BMC Bioinform., 2015)

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)

SV-Pop: population-based structural variant analysis and visualization. - Matt Ravenhall; Susana G. Campino; Taane G. Clark (BMC 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)

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)