Artemis: sequence visualization and annotation. - Kim Rutherford; Julian Parkhill; James Crook; Terry Horsnell; Peter Rice; Marie-Adèle Rajandream; Bart Barrell (Bioinform., 2000)

GeneDB: a resource for prokaryotic and eukaryotic organisms. - Christiane Hertz-Fowler; Chris S. Peacock; Valerie Wood; Martin Aslett; Arnaud Kerhornou; Paul Mooney; Adrian Tivey; Matthew Berriman; Neil Hall; Kim Rutherford; Julian Parkhill; Alasdair C. Ivens; et al. (Nucleic Acids Res., 2004)

ACT: the Artemis comparison tool. - Tim J. Carver; Kim Rutherford; Matthew Berriman; Marie-Adèle Rajandream; Bart Barrell; Julian Parkhill (Bioinform., 2005)

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. - Georgios S. Vernikos; Julian Parkhill (Bioinform., 2006)

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. - Tim J. Carver; Matthew Berriman; Adrian Tivey; Chinmay Patel; Ulrike Böhme; Bart Barrell; Julian Parkhill; Marie-Adèle Rajandream (Bioinform., 2008)

DNAPlotter: circular and linear interactive genome visualization. - Tim J. Carver; Nick R. Thomson; Alan J. Bleasby; Matthew Berriman; Julian Parkhill (Bioinform., 2009)

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. - Kathryn E. Holt; Yik Y. Teo; Heng Li 002; Satheesh Nair; Gordon Dougan; John Wain; Julian Parkhill (Bioinform., 2009)

BamView: viewing mapped read alignment data in the context of the reference sequence. - Tim Carver; Ulrike Böhme; Thomas D. Otto; Julian Parkhill; Matthew Berriman (Bioinform., 2010)

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. - Tim Carver; Simon R. Harris; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Bioinform., 2012)

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)

GeneDB - an annotation database for pathogens. - Flora J. Logan-Klumpler; Nishadi De Silva; Ulrike Böhme; Matthew B. Rogers; Giles Velarde; Jacqueline A. McQuillan; Tim Carver; Martin Aslett; Christian Olsen; Sandhya Subramanian; Isabelle Phan; Carol Farris; et al. (Nucleic Acids Res., 2012)

BamView: visualizing and interpretation of next-generation sequencing read alignments. - Tim Carver; Simon R. Harris; Thomas D. Otto; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Briefings Bioinform., 2013)

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model. - Andries J. van Tonder; Shilan Mistry; James E. Bray; Dorothea M. C. Hill; Alison J. Cody; Chris L. Farmer; Keith P. Klugman; Anne von Gottberg; Stephen D. Bentley; Julian Parkhill; Keith A. Jolley; Martin C. J. Maiden; et al. (PLoS Comput. Biol., 2014)

Roary: rapid large-scale prokaryote pan genome analysis. - Andrew J. Page; Carla A. Cummins; Martin Hunt; Vanessa K. Wong; Sandra Reuter; Matthew T. G. Holden; Maria Fookes; Daniel Falush; Jacqueline A. Keane; Julian Parkhill (Bioinform., 2015)

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. - Lars Barquist; Matthew Mayho; Carla A. Cummins; Amy K. Cain; Christine J. Boinett; Andrew J. Page; Gemma C. Langridge; Michael A. Quail; Jacqueline A. Keane; Julian Parkhill (Bioinform., 2016)

Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage. - Yingbo Shen; Rong Zhang; Dongyan Shao; Lu Yang; Jiayue Lu; Congcong Liu; Xueyang Wang; Junyao Jiang; Boxuan Wang; Congming Wu; Julian Parkhill; Yang Wang; et al. (Genom. Proteom. Bioinform., 2022)