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Nicholas Thomson

Research Profile

Genes & Molecular Sequences

Procedures

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Evolution, Molecular

Chemicals & Drugs

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Bacterial Chromosomes

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Publications

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Helena M B Seth-Smith; Elena Shipitsyna; Rachel J Skilton; Magnus Unemo; Stephen Baker; Ian N Clarke; Lesley T Cutcliffe; Pham Thanh Duy; Daniel Golparian; Simon R Harris; Catherine A Ison; Hamid Jalal; David A Lewis; Peter Marsh; Colette O'Neill; Julian Parkhill; Surendra Parmar; Rachel Pitt; Frans M Radebe; Paul Scott; Nicholas R Thomson
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Helena M B Seth-Smith; Nicholas R Thomson
Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians.
Helena M B Seth-Smith; Wolfgang Gaede; David Longbottom; Konrad Sachse; Michelle Sait; Nicholas R Thomson
Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine.

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All Publications

2013: Helena M B Seth-Smith; Elena Shipitsyna; Rachel J Skilton; Magnus Unemo; Stephen Baker; Ian N Clarke; Lesley T Cutcliffe; Pham Thanh Duy; Daniel Golparian; Simon R Harris; Catherine A Ison; Hamid Jalal; David A Lewis; Peter Marsh; Colette O'Neill; Julian Parkhill; Surendra Parmar; Rachel Pitt; Frans M Radebe; Paul Scott; Nicholas R Thomson
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Genome research 2013;23(5):855-66.
2013: Helena M B Seth-Smith; Nicholas R Thomson
Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians.
Current opinion in infectious diseases 2013;26(1):90-8.
2013: Helena M B Seth-Smith; Wolfgang Gaede; David Longbottom; Konrad Sachse; Michelle Sait; Nicholas R Thomson
Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine.
Genome announcements 2013;1(1):.
2013: Vartul Sangal; Nicholas R Thomson; François-Xavier Weill; Derek Brown; Wanderley Dias da Silveira; Ingrid Filliol-Toutain; Kathryn E Holt; Dong-Wook Kim; Julian Parkhill; Derek Pickard; Jianfeng Yuan; Jun Yu
Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis.
Journal of clinical microbiology 2013;51(1):303-5.
2012: Kathryn E Holt; Dong Wook Kim; Su Hee Kim; Andrew Kitchen; Julian Parkhill; Derek J Pickard; Vartul Sangal; Stephen Baker; Derek Brown; Seon Young Choi; John E Coia; Wanderley D da Silveira; Gordon Dougan; Jeremy J Farrar; Edward C Holmes; François-Xavier Weill; Jun Yu; Nicholas R Thomson
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
Nature genetics 2012;44(9):1056-9.
2012: Simon R Harris; Martin J Holland; David A Lewis; David Mabey; Peter Marsh; Servaas A Morré; Julian Parkhill; Rosanna W Peeling; Kenneth Persson; Helena M B Seth-Smith; Rachel J Skilton; Anthony W Solomon; Arjen G C L Speksnijder; Brian G Spratt; Cécile M Bébéar; Carina Bjartling; Robert brunham; Ian N Clarke; Maïté Clerc; Lesley T Cutcliffe; Bertille De Barbeyrac; Henry J C de Vries; Magnus Unemo; Nicholas R Thomson
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.
Nature genetics 2012;44(4):413-9, S1.
2012: Sandra Reuter; Nicholas R Thomson; Alan McNally
Evolutionary dynamics of the Yersinia enterocolitica complex.
Advances in experimental medicine and biology 2012;954():15-22.
2011: Ankur Mutreja; G Balakrish Nair; Swapan Kumar Niyogi; Julian Parkhill; T Ramamurthy; Nicholas R Thomson; James L N Wood; Seon Young Choi; Jongsik Chun; John D Clemens; Thomas R Connor; Nicholas J Croucher; Cecil Czerkinsky; Simon R Harris; Jan Holmgren; Samuel Kariuki; Dong Wook Kim; Eun Jin Kim; Michael Lebens; Je Hee Lee; Gordon Dougan
Evidence for several waves of global transmission in the seventh cholera pandemic.
Nature 2011;477(7365):462-5.
2011: Maria Fookes; Gad Frankel; Tom Humphrey; Robert Kingsley; Gemma C Langridge; Caterina Mammina; Duncan Maskell; Antonino Nastasi; Sean-Paul Nuccio; Julian Parkhill; Nicola K Petty; Mark Roberts; Keith Scott Robinson; Mandy Sanders; Carlos A Santiviago; Gunnar N Schroeder; Helena Seth-Smith; Paul Barrow; Andreas J Bäumler; Carlos Blondel; Thomas R Connor; Inés Contreras; Gordon Dougan; George S Vernikos; Nicholas R Thomson
Salmonella bongori provides insights into the evolution of the Salmonellae.
PLoS pathogens 2011;7(8):e1002191.
2011: Nicola K Petty; Theresa Feltwell; Derek Pickard; Simon Clare; Ana Toribio; Maria Fookes; Kevin Roberts; Rita Monson; Satheesh Nair; Robert Kingsley; Richard Bulgin; Siouxsie Wiles; David Goulding; Thomas Keane; Craig Corton; Nicola Lennard; David Harris; David Willey; Richard Rance; Lu Yu; Jyoti S Choudhary; Carol Churcher; Michael A Quail; Julian Parkhill; Gad Frankel; Gordon Dougan; George P C Salmond; Nicholas R Thomson
Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.
PLoS pathogens 2011;7(4):e1002018.
2011: Helena M B Seth-Smith; Simon R Harris; Richard Rance; Anthony P West; Juliette A Severin; Jacobus M Ossewaarde; Lesley T Cutcliffe; Rachel J Skilton; Pete Marsh; Julian Parkhill; Ian Clarke; Nicholas R Thomson
Genome sequence of the zoonotic pathogen Chlamydophila psittaci.
Journal of bacteriology 2011;193(5):1282-3.
2010: Giovanna Morelli; Yajun Song; Camila J Mazzoni; Mark Eppinger; Philippe Roumagnac; David M Wagner; Mirjam Feldkamp; Barica Kusecek; Amy J Vogler; Yanjun Li; Yujun Cui; Nicholas R Thomson; Thibaut Jombart; Raphael Leblois; Peter Lichtner; Lila Rahalison; Jeannine M Petersen; Francois Balloux; Paul Keim; Thierry Wirth; Jacques Ravel; Ruifu Yang; Elisabeth Carniel; Mark Achtman
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.
Nature genetics 2010;42(12):1140-3.
2010: Nicholas J Croucher; Nicholas R Thomson
Studying bacterial transcriptomes using RNA-seq.
Current opinion in microbiology 2010;13(5):619-24.
2010: Nicholas R Thomson; Ian N Clarke
Chlamydia trachomatis: small genome, big challenges.
Future microbiology 2010;5(4):555-61.
2010: Roy R Chaudhuri; Mohammed Sebaihia; Jon Hobman; Mark A Webber; Denisse Leyton; Martin D Goldberg; Adam F Cunningham; Anthony Scott-Tucker; Paul R Ferguson; Christopher M Thomas; Gad Frankel; Christoph M Tang; Edward G Dudley; Ian S Roberts; David Rasko; Mark J Pallen; Julian Parkhill; James P Nataro; Nicholas R Thomson; ian henderson
Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.
PloS one 2010;5(1):e8801.
2010: Nicola K Petty; Richard Bulgin; Valerie F Crepin; Ana Cerdeño-Tárraga; Gunnar N Schroeder; Michael A Quail; Nicola Lennard; Craig Corton; Andrew Barron; Louise Clark; Ana Toribio; Julian Parkhill; Gordon Dougan; Gad Frankel; Nicholas R Thomson
The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
Journal of bacteriology 2010;192(2):525-38.
2010: T J Evans; M A Crow; Neil R Williamson; W Orme; Nicholas R Thomson; E Komitopoulou; George P C Salmond
Characterization of a broad-host-range flagellum-dependent phage that mediates high-efficiency generalized transduction in, and between, Serratia and Pantoea.
Microbiology (Reading, England) 2010;156(Pt 1):240-7.
2009: Robert Kingsley; Chisomo L Msefula; Nicholas R Thomson; SAMUEL KARIUKI; Kathryn E Holt; Melita A Gordon; David Harris; Louise Clarke; Sally Whitehead; Vartul Sangal; Kevin Marsh; Mark Achtman; Malcolm E Molyneux; Martin Cormican; Julian Parkhill; Calman A MacLennan; Robert S Heyderman; Gordon Dougan
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype.
Genome research 2009;19(12):2279-87.
2009: Nicholas J Croucher; Maria C Fookes; Timothy T Perkins; Daniel J Turner; Samuel B Marguerat; Thomas Keane; Michael A Quail; Miao He; Sammey Assefa; Jürg Bähler; Robert Kingsley; Julian Parkhill; Stephen D Bentley; Gordon Dougan; Nicholas R Thomson
A simple method for directional transcriptome sequencing using Illumina technology.
Nucleic acids research 2009;37(22):e148.
2009: Timothy T Perkins; Robert Kingsley; Maria C Fookes; Paul P Gardner; Keith D James; Lu Yu; Samuel A Assefa; Miao He; Nicholas J Croucher; Derek Pickard; Duncan J Maskell; Julian Parkhill; Jyoti Choudhary; Nicholas R Thomson; Gordon Dougan
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
PLoS genetics 2009;5(7):e1000569.
2009: Minh Duy Phan; Claire Kidgell; Satheesh Nair; Kathryn E Holt; Arthur K Turner; Jason Hinds; Philip Butcher; Fiona J Cooke; Nicholas R Thomson; Richard Titball; Zulfiqar A Bhutta; Rumina Hasan; Gordon Dougan; John Wain
Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever.
Antimicrobial agents and chemotherapy 2009;53(2):716-27.
2009: Andrew Jackson; Gavin H Thomas; Julian Parkhill; Nicholas R Thomson
Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement.
BMC genomics 2009;10():584.
2009: Kathryn E Holt; Nicholas R Thomson; John Wain; Gemma C Langridge; Rumina Hasan; Zulfiqar A Bhutta; Michael A Quail; Halina Norbertczak; Danielle Walker; Mark Simmonds; Brian White; Nathalie Bason; Karen Mungall; Gordon Dougan; Julian Parkhill
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi.
BMC genomics 2009;10():36.
2008: Fiona J Cooke; Derek Brown; Maria Fookes; Derek Pickard; Alasdair Ivens; John Wain; Mark Roberts; Robert Kingsley; Nicholas R Thomson; Gordon Dougan
Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104.
Journal of bacteriology 2008;190(24):8155-62.
2008: Derek Pickard; Nicholas R Thomson; Stephen Baker; John Wain; Mercedes Pardo; David Goulding; Nancy Hamlin; Jyoti Choudhary; John Threfall; Gordon Dougan
Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.
Journal of bacteriology 2008;190(7):2580-7.
2008: Lisa Crossman; Virginia C Gould; J Maxwell Dow; George S Vernikos; Aki Okazaki; Mohammed Sebaihia; David Saunders; Claire Arrowsmith; Tim Carver; Nicholas Peters; Ellen Adlem; Arnaud Kerhornou; Angela Lord; Lee Murphy; kathy seeger; Robert Squares; Simon Rutter; Michael A Quail; Mari-Adele Rajandream; David Harris; Carol Churcher; Stephen D Bentley; Julian Parkhill; Nicholas R Thomson; Matthew B Avison
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.
Genome biology 2008;9(4):R74.
2008: Nicholas R Thomson; Matthew T G Holden; Caroline Carder; Nicola Lennard; Sarah J Lockey; Pete Marsh; Paul Skipp; C David O'Connor; Ian Goodhead; Halina Norbertzcak; Barbara Harris; Doug Ormond; Richard Rance; Michael A Quail; Julian Parkhill; Richard S Stephens; Ian Clarke
Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates.
Genome research 2008;18(1):161-71.
2007: Kathryn E Holt; Nicholas R Thomson; John Wain; Minh Duy Phan; Satheesh Nair; Rumina Hasan; Zulfiqar A Bhutta; Michael A Quail; Halina Norbertczak; Danielle Walker; Gordon Dougan; Julian Parkhill
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.
Journal of bacteriology 2007;189(11):4257-64.
2007: Nicholas R Thomson; Sarah Howard; Brendan W Wren; Michael B Prentice
Comparative genome analyses of the pathogenic Yersiniae based on the genome sequence of Yersinia enterocolitica strain 8081.
Advances in experimental medicine and biology 2007;603():2-16.
2007: Thomas Walker; Lisa Klasson; Mohammed Sebaihia; Mandy J Sanders; Nicholas R Thomson; Julian Parkhill; Steven P Sinkins
Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group.
BMC biology 2007;5():39.
2007: George S Vernikos; Nicholas R Thomson; Julian Parkhill
Genetic flux over time in the Salmonella lineage.
Genome biology 2007;8(6):R100.
2007: Xavier Didelot; Mark Achtman; Julian Parkhill; Nicholas R Thomson; Daniel Falush
A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?
Genome research 2007;17(1):61-8.
2006: Nicholas R Thomson; Sarah Howard; Brendan W Wren; Matthew T G Holden; Lisa Crossman; Gregory L Challis; Carol Churcher; Karen Mungall; Karen Brooks; Tracey Chillingworth; Theresa Feltwell; Zahra Abdellah; Heidi Hauser; Kay Jagels; Mark Maddison; Sharon Moule; Mandy Sanders; Sally Whitehead; Michael A Quail; Gordon Dougan; Julian Parkhill; Michael B Prentice
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.
PLoS genetics 2006;2(12):e206.
2006: Mohammed Sebaihia; Nicholas R Thomson
Colonic irritation.
Nature reviews. Microbiology 2006;4(12):882-3.
2006: Mohammed Sebaihia; Andrew Preston; Duncan J Maskell; Holly Kuzmiak; Terry D Connell; Natalie D King; Paul E Orndorff; David M Miyamoto; Nicholas R Thomson; David Harris; Arlette Goble; Angela Lord; Lee Murphy; Michael A Quail; Simon Rutter; Robert Squares; Steven Squares; John Woodward; Julian Parkhill; Louise M Temple
Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.
Journal of bacteriology 2006;188(16):6002-15.
2005: Ana Cerdeño-Tárraga; Marcus J Claesson; Mohammed Sebaihia; Nicholas R Thomson
GI genomes.
Nature reviews. Microbiology 2005;3(5):368-9.
2005: Nicholas R Thomson; Corin Yeats; Kenneth Bell; Matthew T G Holden; Stephen Bentley; Morag Livingstone; Ana Cerdeño-Tárraga; Barbara Harris; Jon Doggett; Doug Ormond; Karen Mungall; Kay Clarke; Theresa Feltwell; Zahra Hance; Mandy Sanders; Michael A Quail; Claire Price; Bart Barrell; Julian Parkhill; David Longbottom
The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.
Genome research 2005;15(5):629-40.
2005: Mohammed Sebaihia; Nicholas R Thomson; Lisa Crossman; Julian Parkhill
Livelihood hazards.
Nature reviews. Microbiology 2005;3(4):278-9.
2005: Simon J McGowan; Anne M L Barnard; Gulgun Bosgelmez; Mohammed Sebaihia; Natalie J L Simpson; Nicholas R Thomson; Daniel E Todd; Martin Welch; Neil A Whitehead; George P C Salmond
Carbapenem antibiotic biosynthesis in Erwinia carotovora is regulated by physiological and genetic factors modulating the quorum sensing-dependent control pathway.
Molecular microbiology 2005;55(2):526-45.
2004: Mark Achtman; Giovanna Morelli; Peixuan Zhu; Thierry Wirth; Ines Diehl; Barica Kusecek; Amy J Vogler; David M Wagner; Christopher J Allender; W Ryan Easterday; Viviane Chenal-Francisque; Patricia Worsham; Nicholas R Thomson; Julian Parkhill; Luther E Lindler; Elisabeth Carniel; Paul Keim
Microevolution and history of the plague bacillus, Yersinia pestis.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(51):17837-42.
2004: Lisa Crossman; Ana Cerdeño-Tárraga; Nicholas R Thomson
Chalk and cheese.
Nature reviews. Microbiology 2004;2(7):528-9.
2004: Nicholas R Thomson; Mohammed Sebaihia; Ana Cerdeño-Tárraga; Matthew T G Holden; Julian Parkhill
Shrinking genomics.
Nature reviews. Microbiology 2004;2(1):11.
2003: Ana Cerdeño-Tárraga; Androulla Efstratiou; Lynn Dover; Matthew T G Holden; Mark J Pallen; Stephen Bentley; Gurdyal S Besra; Carol Churcher; Keith D James; Aruni De Zoysa; Tracey Chillingworth; Ann Cronin; L Dowd; Theresa Feltwell; Nancy Hamlin; Simon Holroyd; Kay Jagels; Sharon Moule; Michael A Quail; Ester Rabbinowitsch; Kim Rutherford; Nicholas R Thomson; L Unwin; Sally Whitehead; Bart Barrell; Julian Parkhill
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
Nucleic acids research 2003;31(22):6516-23.
2003: Stephen Bentley; Nicholas R Thomson; Mohammed Sebaihia; Lisa Crossman; Julian Parkhill
The devil is in the detail.
Trends in microbiology 2003;11(6):256-8.
2003: Nicholas R Thomson; Ana Cerdeño-Tárraga; Lisa Crossman; Mohammed Sebaihia; Julian Parkhill
All walks of life.
Trends in microbiology 2003;11(4):159-60.
2003: Nicholas R Thomson; Julian Parkhill
The building blocks of pathogenicity.
Trends in microbiology 2003;11(2):66-7.
2002: Nicholas R Thomson; Mohammed Sebaihia; Julian Parkhill
Microbial genomics: spot the difference. . .
Trends in microbiology 2002;10(11):489-90.
2001: Karin Eiglmeier; Julian Parkhill; Nadine Honoré; Thierry Garnier; Fredj Tekaia; A Telenti; P Klatser; Keith D James; Nicholas R Thomson; Paul R Wheeler; Carol Churcher; D Harris; Karen Mungall; Bart Barrell; Stewart T Cole
The decaying genome of Mycobacterium leprae.
Leprosy review 2001;72(4):387-98.
2000: Nicholas R Thomson; M A Crow; Simon J McGowan; Anthony Cox; George P C Salmond
Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control.
Molecular microbiology 2000;36(3):539-56.
1999: Nicholas R Thomson; W Nasser; Simon J McGowan; Mohammed Sebaihia; George P C Salmond
Erwinia carotovora has two KdgR-like proteins belonging to the IciR family of transcriptional regulators: identification and characterization of the RexZ activator and the KdgR repressor of pathogenesis.
Microbiology (Reading, England) 1999;145 ( Pt 7)():1531-45.
1998: A R Cox; Nicholas R Thomson; Barrie W Bycroft; GS Stewart; Paul Williams; George P C Salmond
A pheromone-independent CarR protein controls carbapenem antibiotic synthesis in the opportunistic human pathogen Serratia marcescens.
Microbiology (Reading, England) 1998;144 ( Pt 1)():201-9.
1997: Nicholas R Thomson; Anthony Cox; Barrie W Bycroft; GS Stewart; Paul Williams; George P C Salmond
The rap and hor proteins of Erwinia, Serratia and Yersinia: a novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens.
Molecular microbiology 1997;26(3):531-44.