Google Scholar: https://scholar.google.com/citations?user=OghCU6kAAAAJ
A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.
Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA.Microb Genom. 2023 May;9(5):mgen001018. doi: 10.1099/mgen.0.001018.
A scalable analytical approach from bacterial genomes to epidemiology.
Didelot X, Parkhill J.Philos Trans R Soc Lond B Biol Sci. 2022 Oct 10;377(1861):20210246. doi: 10.1098/rstb.2021.0246.
Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial.
van Tonder AJ, Thornton MJ, Conlan AJK, Jolley KA, Goolding L, Mitchell AP, Dale J, Palkopoulou E, Hogarth PJ, Hewinson RG, Wood JLN, Parkhill J.PLoS Pathog. 2021 Nov 29;17(11):e1010075. doi: 10.1371/journal.ppat.1010075
Dissemination of Mycobacterium abscessus via global transmission networks.
Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, van Ingen J, Strong M, Floto RA, Parkhill J. Nat Microbiol. (2021) doi: 10.1038/s41564-021-00963-3
Stepwise pathogenic evolution of Mycobacterium abscessus.
Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, Grogono DM, Peterson CM, Verma D, Evans IE, Ruis C, Weimann A, Arora D, Malhotra S, Bannerman B, Passemar C, Templeton K, MacGregor G, Jiwa K, Fisher AJ, Blundell TL, Ordway DJ, Jackson M, Parkhill J, Floto RA. Science. (2021) 372(6541):eabb8699. doi: 10.1126/science.abb8699.
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.
Gouliouris T, Coll F, Ludden C, Blane B, Raven KE, Naydenova P, Crawley C, Török ME, Enoch DA, Brown NM, Harrison EM, Parkhill J, Peacock SJ. Nat Microbiol. (2021) 6:103-111. doi: 10.1038/s41564-020-00806-7
Producing polished prokaryotic pangenomes with the Panaroo pipeline.
Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. Genome Biol. (2020) 2:180. doi: 10.1186/s13059-020-02090-4.
Human placenta has no microbiome but can contain potential pathogens.
de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Nature. (2019) 572:329-334. doi: 10.1038/s41586-019-1451-5. Epub 2019 Jul 31.
The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort.
Dorman MJ, Feltwell T, Goulding DA, Parkhill J, Short FL. MBio. (2018) 9(6). pii: e01863-18
Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.
Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M, Holmes MA, de Goffau M, Brown NM, Parkhill J, Peacock SJ.
MBio. (2018) 9(6). pii: e01780-18
Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.
Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ. Sci Transl Med. (2017) 9(413). pii: eaak9745.
Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.
Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J. Genome Res. (2017) 27: 1437-1449
Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland.
Moradigaravand D, Martin V, Peacock SJ, Parkhill J. MBio. (2017) 8(1). pii: e01976-16
Global and regional dissemination and evolution of Burkholderia pseudomallei.
Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S, Bizet C, Mayo M, Wuthiekanun V, Limmathurotsakul D, Phetsouvanh R, Spratt BG, Corander J, Keim P, Dougan G, Dance DA, Currie BJ, Parkhill J, Peacock SJ. Nat Microbiol. (2017) 2:16263
Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA.
Science. (2016) 354(6313):751-757
Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.
David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C.
Genome Res. (2016) 26(11):1555-1564
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.
Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J.
Nat Commun. (2016) 7:12797
Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.
Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J.
PLoS Genet. (2014) 10(8):e1004547
