Works matching AU Parkhill, Julian

Results: 278

What has high-throughput sequencing ever done for us?

Published in:

Nature Reviews Microbiology, 2013, v. 11, n. 10, p. 664, doi. 10.1038/nrmicro3112

By:

Parkhill, Julian

Publication type:

Article

Microbiology in the post-genomic era.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 6, p. 419, doi. 10.1038/nrmicro1901

By:

Medini, Duccio;
Serruto, Davide;
Parkhill, Julian;
Relman, David A.;
Donati, Claudio;
Moxon, Richard;
Falkow, Stanley;
Rappuoli, Rino

Publication type:

Article

Single-cell genomics.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 3, p. 176, doi. 10.1038/nrmicro1862

By:

Walker, Alan;
Parkhill, Julian

Publication type:

Article

Genome watch: Comparative Apicomplexan genomics.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 6, p. 454, doi. 10.1038/nrmicro1174

By:

Pain, Arnab;
Crossman, Lisa;
Parkhill, Julian

Publication type:

Article

Genome watch: Livelihood hazards.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 4, p. 278, doi. 10.1038/nrmicro1132

By:

Sebaihia, Mohammed;
Thomson, Nicholas R.;
Crossman, Lisa;
Parkhill, Julian

Publication type:

Article

Genome watch: Diversity at every level.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 3, p. 196, doi. 10.1038/nrmicro1479

By:

Crossman, Lisa;
Cerdeño-Tárraga, Ana;
Parkhill, Julian

Publication type:

Article

Genome watch: Brothers in arms.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 2, p. 100, doi. 10.1038/nrmicro1092

By:

Thomson, Nicholas;
Holden, Matthew;
Parkhill, Julian

Publication type:

Article

Genome watch: Genomic pot pourri.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 12, p. 928, doi. 10.1038/nrmicro1051

By:

Bentley, Stephen;
Crossman, Lisa;
Cerdeño-Tárraga, Ana;
Parkhill, Julian

Publication type:

Article

Genome watch: Eukaryotes: not beyond compare.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 11, p. 856, doi. 10.1038/nrmicro1028

By:

Pain, Arnab;
Bentley, Stephen;
Parkhill, Julian

Publication type:

Article

Genome watch: Pathogens in decay.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 10, p. 774, doi. 10.1038/nrmicro1009

By:

Cerdeño-Tárraga, Ana;
Thomson, Nicholas;
Parkhill, Julian

Publication type:

Article

Genome watch: Genomes beyond compare.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 8, p. 616, doi. 10.1038/nrmicro961

By:

Crossman, Lisa;
Holden, Matthew;
Pain, Arnab;
Parkhill, Julian

Publication type:

Article

Genome watch: New environments, versatile genomes.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 6, p. 446, doi. 10.1038/nrmicro910

By:

Cerdeño-Tárraga, Ana;
Crossman, Lisa;
Parkhill, Julian

Publication type:

Article

The Bordetellae: lessons from genomics.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 5, p. 379, doi. 10.1038/nrmicro886

By:

Preston, Andrew;
Parkhill, Julian;
Maskell, Duncan J.

Publication type:

Article

Genome watch: Strength in diversity.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 5, p. 358, doi. 10.1038/nrmicro889

By:

Pain, Arnab;
Crossman, Lisa;
Sebaihia, Mohammed;
Cerdeño-Tárraga, Ana;
Parkhill, Julian

Publication type:

Article

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1109, doi. 10.1093/bioinformatics/btw022

By:

Barquist, Lars;
Mayho, Matthew;
Cummins, Carla;
Cain, Amy K.;
Boinett, Christine J.;
Page, Andrew J.;
Langridge, Gemma C.;
Quail, Michael A.;
Keane, Jacqueline A.;
Parkhill, Julian

Publication type:

Article

Roary: rapid large-scale prokaryote pan genome analysis.

Published in:

Bioinformatics, 2015, v. 31, n. 22, p. 3691, doi. 10.1093/bioinformatics/btv421

By:

Page, Andrew J.;
Cummins, Carla A.;
Hunt, Martin;
Wong, Vanessa K.;
Reuter, Sandra;
Holden, Matthew T. G.;
Fookes, Maria;
Falush, Daniel;
Keane, Jacqueline A.;
Parkhill, Julian

Publication type:

Article

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.

Published in:

Bioinformatics, 2012, v. 28, n. 22, p. 2991, doi. 10.1093/bioinformatics/bts544

By:

Coll, Francesc;
Mallard, Kim;
Preston, Mark D.;
Bentley, Stephen;
Parkhill, Julian;
McNerney, Ruth;
Martin, Nigel;
Clark, Taane G.

Publication type:

Article

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

Published in:

Bioinformatics, 2012, v. 28, n. 4, p. 464, doi. 10.1093/bioinformatics/btr703

By:

Carver, Tim;
Harris, Simon R.;
Berriman, Matthew;
Parkhill, Julian;
McQuillan, Jacqueline A.

Publication type:

Article

BamView: viewing mapped read alignment data in the context of the reference sequence.

Published in:

Bioinformatics, 2010, v. 26, n. 5, p. 676, doi. 10.1093/bioinformatics/btq010

By:

Carver, Tim;
Böhme, Ulrike;
Otto, Thomas D.;
Parkhill, Julian;
Berriman, Matthew

Publication type:

Article

DNAPlotter: circular and linear interactive genome visualization.

Published in:

Bioinformatics, 2009, v. 25, n. 1, p. 119, doi. 10.1093/bioinformatics/btn578

By:

Carver, Tim;
Thomson, Nick;
Bleasby, Alan;
Berriman, Matthew;
Parkhill, Julian

Publication type:

Article

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

Published in:

Bioinformatics, 2008, v. 24, n. 23, p. 2672, doi. 10.1093/bioinformatics/btn529

By:

Tim Carver;
Matthew Berriman;
Adrian Tivey;
Chinmay Patel;
Ulrike Böhme;
Barclay G. Barrell;
Julian Parkhill;
Marie-Adèle Rajandream

Publication type:

Article

PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03194-2

By:

Coll, Francesc;
Gouliouris, Theodore;
Bruchmann, Sebastian;
Phelan, Jody;
Raven, Kathy E.;
Clark, Taane G.;
Parkhill, Julian;
Peacock, Sharon J.

Publication type:

Article

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology.

Published in:

JAMA Internal Medicine, 2013, v. 173, n. 15, p. 1397, doi. 10.1001/jamainternmed.2013.7734

By:

Reuter, Sandra;
Ellington, Matthew J.;
Cartwright, Edward J. P.;
Köser, Claudio U.;
Török, M. Estée;
Gouliouris, Theodore;
Harris, Simon R.;
Brown, Nicholas M.;
Holden, Matthew T. G.;
Quail, Mike;
Parkhill, Julian;
Smith, Geoffrey P.;
Bentley, Stephen D.;
Peacock, Sharon J.

Publication type:

Article

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-29986-3

By:

Palittapongarnpim, Prasit;
Ajawatanawong, Pravech;
Viratyosin, Wasna;
Smittipat, Nat;
Disratthakit, Areeya;
Mahasirimongkol, Surakameth;
Yanai, Hideki;
Yamada, Norio;
Nedsuwan, Supalert;
Imasanguan, Worarat;
Kantipong, Pacharee;
Chaiyasirinroje, Boonchai;
Wongyai, Jiraporn;
Toyo-oka, Licht;
Phelan, Jody;
Parkhill, Julian;
Clark, Taane G.;
Hibberd, Martin L.;
Ruengchai, Wuthiwat;
Palittapongarnpim, Panawun

Publication type:

Article

Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate.

Published in:

Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.960747

By:

Ijaz, Umer Zeeshan;
Gundogdu, Ozan;
Keating, Ciara;
Eekert, Miriam van;
Gibson, Walter;
Parkhill, Julian;
Abilahi, Faraji;
Liseki, Benard;
Nguyen, Viet-Anh;
Sudgen, Steven;
Quince, Christopher;
Ensink, Jeroen H. J.;
Torondel, Belen;
Walker, Alan W.

Publication type:

Article

Producing polished prokaryotic pangenomes with the Panaroo pipeline.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02090-4

By:

Tonkin-Hill, Gerry;
MacAlasdair, Neil;
Ruis, Christopher;
Weimann, Aaron;
Horesh, Gal;
Lees, John A.;
Gladstone, Rebecca A.;
Lo, Stephanie;
Beaudoin, Christopher;
Floto, R. Andres;
Frost, Simon D.W.;
Corander, Jukka;
Bentley, Stephen D.;
Parkhill, Julian

Publication type:

Article

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.

Published in:

PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0209395

By:

Otchere, Isaac Darko;
van Tonder, Andries J.;
Asante-Poku, Adwoa;
Sánchez-Busó, Leonor;
Coscollá, Mireia;
Osei-Wusu, Stephen;
Asare, Prince;
Aboagye, Samuel Yaw;
Ekuban, Samuel Acquah;
Yahayah, Abdallah Iddrisu;
Forson, Audrey;
Baddoo, Akosua;
Laryea, Clement;
Parkhill, Julian;
Harris, Simon R.;
Gagneux, Sebastien;
Yeboah-Manu, Dorothy

Publication type:

Article

Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.

Published in:

PLoS ONE, 2019, v. 14, n. 1, p. 1, doi. 10.1371/journal.pone.0208356

By:

Mohamed, Naglaa;
Timofeyeva, Yekaterina;
Jamrozy, Dorota;
Rojas, Eduardo;
Hao, Li;
Silmon de Monerri, Natalie C.;
Hawkins, Julio;
Singh, Guy;
Cai, Bing;
Liberator, Paul;
Sebastian, Shite;
Donald, Robert G. K.;
Scully, Ingrid L.;
Jones, C. Hal;
Creech, C. Buddy;
Thomsen, Isaac;
Parkhill, Julian;
Peacock, Sharon J.;
Jansen, Kathrin U.;
Holden, Matthew T. G.

Publication type:

Article

Evolution and transmission of drug-resistant tuberculosis in a Russian population.

Published in:

Nature Genetics, 2014, v. 46, n. 3, p. 279, doi. 10.1038/ng.2878

By:

Casali, Nicola;
Nikolayevskyy, Vladyslav;
Balabanova, Yanina;
Harris, Simon R;
Ignatyeva, Olga;
Kontsevaya, Irina;
Corander, Jukka;
Bryant, Josephine;
Parkhill, Julian;
Nejentsev, Sergey;
Horstmann, Rolf D;
Brown, Timothy;
Drobniewski, Francis

Publication type:

Article

Dense genomic sampling identifies highways of pneumococcal recombination.

Published in:

Nature Genetics, 2014, v. 46, n. 3, p. 305, doi. 10.1038/ng.2895

By:

Chewapreecha, Claire;
Harris, Simon R;
Croucher, Nicholas J;
Turner, Claudia;
Marttinen, Pekka;
Cheng, Lu;
Pessia, Alberto;
Aanensen, David M;
Mather, Alison E;
Page, Andrew J;
Salter, Susannah J;
Harris, David;
Nosten, Francois;
Goldblatt, David;
Corander, Jukka;
Parkhill, Julian;
Turner, Paul;
Bentley, Stephen D

Publication type:

Article

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

Published in:

Nature Genetics, 2013, v. 45, n. 10, p. 1176, doi. 10.1038/ng.2744

By:

Comas, Iñaki;
Coscolla, Mireia;
Luo, Tao;
Borrell, Sonia;
Holt, Kathryn E;
Kato-Maeda, Midori;
Parkhill, Julian;
Malla, Bijaya;
Berg, Stefan;
Thwaites, Guy;
Yeboah-Manu, Dorothy;
Bothamley, Graham;
Mei, Jian;
Wei, Lanhai;
Bentley, Stephen;
Harris, Simon R;
Niemann, Stefan;
Diel, Roland;
Aseffa, Abraham;
Gao, Qian

Publication type:

Article

Population genomics of post-vaccine changes in pneumococcal epidemiology.

Published in:

Nature Genetics, 2013, v. 45, n. 6, p. 656, doi. 10.1038/ng.2625

By:

Croucher, Nicholas J;
Finkelstein, Jonathan A;
Pelton, Stephen I;
Mitchell, Patrick K;
Lee, Grace M;
Parkhill, Julian;
Bentley, Stephen D;
Hanage, William P;
Lipsitch, Marc

Publication type:

Article

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.

Published in:

Nature Genetics, 2013, v. 45, n. 4, p. 450, doi. 10.1038/ng.2536

By:

Adler, Christina J;
Dobney, Keith;
Weyrich, Laura S;
Haak, Wolfgang;
Cooper, Alan;
Kaidonis, John;
Townsend, Grant;
Walker, Alan W;
Parkhill, Julian;
Bradshaw, Corey J A;
Sołtysiak, Arkadiusz;
Alt, Kurt W

Publication type:

Article

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

Published in:

Nature Genetics, 2012, v. 44, n. 11, p. 1215, doi. 10.1038/ng.2423

By:

Okoro, Chinyere K;
Kingsley, Robert A;
Connor, Thomas R;
Harris, Simon R;
Parry, Christopher M;
Al-Mashhadani, Manar N;
Kariuki, Samuel;
Msefula, Chisomo L;
Gordon, Melita A;
de Pinna, Elizabeth;
Wain, John;
Heyderman, Robert S;
Obaro, Stephen;
Alonso, Pedro L;
Mandomando, Inacio;
MacLennan, Calman A;
Tapia, Milagritos D;
Levine, Myron M;
Tennant, Sharon M;
Parkhill, Julian

Publication type:

Article

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.

Published in:

Nature Genetics, 2012, v. 44, n. 9, p. 1056, doi. 10.1038/ng.2369

By:

Holt, Kathryn E;
Baker, Stephen;
Weill, François-Xavier;
Holmes, Edward C;
Kitchen, Andrew;
Yu, Jun;
Sangal, Vartul;
Brown, Derek J;
Coia, John E;
Kim, Dong Wook;
Choi, Seon Young;
Kim, Su Hee;
da Silveira, Wanderley D;
Pickard, Derek J;
Farrar, Jeremy J;
Parkhill, Julian;
Dougan, Gordon;
Thomson, Nicholas R

Publication type:

Article

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Published in:

Nature Genetics, 2008, v. 40, n. 8, p. 987, doi. 10.1038/ng.195

By:

Holt, Kathryn E.;
Parkhill, Julian;
Mazzoni, Camila J.;
Roumagnac, Philippe;
Weill, François-Xavier;
Goodhead, Ian;
Rance, Richard;
Baker, Stephen;
Maskell, Duncan J.;
Wain, John;
Dolecek, Christiane;
Achtman, Mark;
Dougan, Gordon

Publication type:

Article

The use of genome annotation data and its impact on biological conclusions.

Published in:

2004

By:

Tettelin, Hervé;
Parkhill, Julian

Publication type:

Letter

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

Published in:

Nature Genetics, 2003, v. 35, n. 1, p. 32, doi. 10.1038/ng1227

By:

Parkhill, Julian;
Sebaihia, Mohammed;
Preston, Andrew;
Murphy, Lee D.;
Thomson, Nicholas;
Harris, David E.;
Holden, Matthew T. G.;
Churcher, Carol M.;
Bentley, Stephen D.;
Mungall, Karen L.;
Cerdeño-Tárraga, Ana M.;
Temple, Louise;
James, Keith;
Harris, Barbara;
Quail, Michael A.;
Achtman, Mark;
Atkin, Rebecca;
Baker, Steven;
Basham, David;
Bason, Nathalie

Publication type:

Article

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 545, doi. 10.1186/1471-2164-13-545

By:

Jihye Park;
Ying Zhang;
Buboltz, Anne M.;
Xuqing Zhang;
Schuster, Stephan C.;
Umesh Ahuja;
Minghsun Liu;
Miller, Jeff F.;
Sebaihia, Mohammed;
Bentley, Stephen D.;
Parkhill, Julian;
Harvill, Eric T.

Publication type:

Article

Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 454, doi. 10.1186/1471-2164-13-454

By:

Mappley, Luke J.;
Black, Michael L.;
AbuOun, Manal;
Darby, Alistair C.;
Woodward, Martin J.;
Parkhill, Julian;
Turner, A. Keith;
Bellgard, Matthew I.;
La, Tom;
Phillips, Nyree D.;
La Ragione, Roberto M.;
Hampson, David J.

Publication type:

Article

Identification, variation and transcription of pneumococcal repeat sequences.

Published in:

BMC Genomics, 2011, v. 12, p. 1, doi. 10.1186/1471-2164-12-120

By:

Croucher, Nicholas J;
Vernikos, Georgios S;
Parkhill, Julian;
Bentley, Stephen D

Publication type:

Article

Identification, variation and transcription of pneumococcal repeat sequences.

Published in:

BMC Genomics, 2011, v. 12, n. 1, p. 120, doi. 10.1186/1471-2164-12-120

By:

Croucher, Nicholas J.;
Vernikos, Georgios S.;
Parkhill, Julian;
Bentley, Stephen D.

Publication type:

Article

Comparative genomics of prevaccination and modern Bordetella pertussis strains.

Published in:

BMC Genomics, 2010, v. 11, n. 1, p. 1, doi. 10.1186/1471-2164-11-627

By:

Bart, Marieke J;
van Gent, Marjolein;
van der Heide, Han GJ;
Boekhorst, Jos;
Hermans, Peter;
Parkhill, Julian;
Mooi, Frits R

Publication type:

Article

Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06.

Published in:

BMC Genomics, 2010, v. 11, n. 1, p. 1, doi. 10.1186/1471-2164-11-652

By:

Bennett, Julia S;
Bentley, Stephen D;
Vernikos, Georgios S;
Quail, Michael A;
Cherevach, Inna;
White, Brian;
Parkhill, Julian;
Maiden, Martin CJ

Publication type:

Article

Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisserialactamica isolate 020-06.

Published in:

BMC Genomics, 2010, v. 11, p. 652, doi. 10.1186/1471-2164-11-652

By:

Bennett, Julia S.;
Bentley, Stephen D.;
Vernikos, Georgios S.;
Quail, Michael A.;
Cherevach, Inna;
White, Brian;
Parkhill, Julian;
Maiden, Martin C. J.

Publication type:

Article

Comparative genomics of prevaccination and modern Bordetella pertussis strains.

Published in:

BMC Genomics, 2010, v. 11, p. 627, doi. 10.1186/1471-2164-11-627

By:

Bart, Marieke J.;
van Gent, Marjolein;
van der Heide, Han G. J.;
Boekhorst, Jos;
Hermans, Peter;
Parkhill, Julian;
Mooi, Frits R.

Publication type:

Article

Comparative genomics and proteomics ofHelicobacter mustelae, an ulcerogenic andcarcinogenic gastric pathogen.

Published in:

BMC Genomics, 2010, v. 11, p. 164, doi. 10.1186/1471-2164-11-164

By:

O'Toole, Paul W.;
Snelling, William J.;
Canchaya, Carlos;
Forde, Brian M.;
Hardie, Kim R.;
Josenhans, Christine;
Graham, Robert L. J.;
McMullan, Geoff;
Parkhill, Julian;
Belda, Eugenio;
Bentley, Stephen D.

Publication type:

Article

Evolutionary diversification of an ancient gene family (rhs) throughC-terminal displacement.

Published in:

BMC Genomics, 2009, v. 10, p. 584, doi. 10.1186/1471-2164-10-584

By:

Jackson, Andrew P.;
Thomas, Gavin H.;
Parkhill, Julian;
Thomson, Nicholas R.

Publication type:

Article

Comparative genomics of the emerging human pathogenPhotorhabdus asymbiotica with the insect pathogen Photorhabdusluminescens.

Published in:

BMC Genomics, 2009, v. 10, p. 302, doi. 10.1186/1471-2164-10-302

By:

Wilkinson, Paul;
Waterfield, Nicholas R.;
Crossman, Lisa;
Corton, Craig;
Sanchez-Contreras, Maria;
Vlisidou, Isabella;
Barron, Andrew;
Bignell, Alexandra;
Clark, Louise;
Ormond, Douglas;
Mayho, Matthew;
Bason, Nathalie;
Smith, Frances;
Simmonds, Mark;
Churcher, Carol;
Harris, David;
Thompson, Nicholas R.;
Quail, Michael;
Parkhill, Julian;
ffrench-Constant, Richard H.

Publication type:

Article

Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis.

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-54

By:

Ward, Philip N.;
Holden, Matthew T. G.;
Leigh, James A.;
Lennard, Nicola;
Bignell, Alexandra;
Barron, Andy;
Clark, Louise;
Quail, Michael A.;
Woodward, John;
Barrell, Bart G.;
Egan, Sharon A.;
Field, Terence R.;
Maskell, Duncan;
Kehoe, Michael;
Dowson, Christopher G.;
Chanter, Neil;
Whatmore, Adrian M.;
Bentley, Stephen D.;
Parkhill, Julian

Publication type:

Article