J
James Hadfield
Researcher at Fred Hutchinson Cancer Research Center
Publications - 61
Citations - 5246
James Hadfield is an academic researcher from Fred Hutchinson Cancer Research Center. The author has contributed to research in topics: Population & Outbreak. The author has an hindex of 22, co-authored 61 publications receiving 3327 citations. Previous affiliations of James Hadfield include University of Washington & University of Canterbury.
Papers
More filters
Journal ArticleDOI
Nextstrain: real-time tracking of pathogen evolution.
James Hadfield,Colin Megill,Sidney M Bell,Sidney M Bell,John Huddleston,John Huddleston,Barney Potter,Charlton Callender,Pavel Sagulenko,Trevor Bedford,Richard A. Neher,Richard A. Neher,Richard A. Neher +12 more
TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.
Journal ArticleDOI
Phandango: an interactive viewer for bacterial population genomics
James Hadfield,Nicholas J. Croucher,Richard Goater,Khalil Abudahab,David M. Aanensen,David M. Aanensen,Simon R. Harris +6 more
TL;DR: Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.
Journal ArticleDOI
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
Vanessa K. Wong,Vanessa K. Wong,Stephen Baker,Stephen Baker,Stephen Baker,Derek Pickard,Julian Parkhill,Andrew J. Page,Nicholas A. Feasey,Robert A. Kingsley,Robert A. Kingsley,Nicholas R. Thomson,Nicholas R. Thomson,Jacqueline A. Keane,François-Xavier Weill,David J. Edwards,Jane Hawkey,Simon R. Harris,Alison E. Mather,Amy K. Cain,James Hadfield,Peter J. Hart,Nga Tran Vu Thieu,Elizabeth J. Klemm,Dafni A. Glinos,Robert F. Breiman,Robert F. Breiman,Robert F. Breiman,Conall H. Watson,Samuel Kariuki,Samuel Kariuki,Melita A. Gordon,Robert S. Heyderman,Chinyere K. Okoro,Jan Jacobs,Jan Jacobs,Octavie Lunguya,W. John Edmunds,Chisomo L. Msefula,José A. Chabalgoity,Mike Kama,Kylie Jenkins,Shanta Dutta,Florian Marks,Josefina Campos,Corinne N. Thompson,Corinne N. Thompson,Stephen K. Obaro,Calman A. MacLennan,Calman A. MacLennan,Calman A. MacLennan,Christiane Dolecek,Karen H. Keddy,Anthony M. Smith,Christopher M. Parry,Christopher M. Parry,Abhilasha Karkey,E. Kim Mulholland,James Campbell,James Campbell,Sabina Dongol,Buddha Basnyat,Muriel Dufour,Don Bandaranayake,Take Toleafoa Naseri,Shalini Singh,Mochammad Hatta,Paul N. Newton,Paul N. Newton,Robert S. Onsare,Lupeoletalalei Isaia,David A. B. Dance,David A. B. Dance,Viengmon Davong,Guy E. Thwaites,Guy E. Thwaites,Lalith Wijedoru,John A. Crump,Elizabeth de Pinna,Satheesh Nair,Eric J. Nilles,Duy Pham Thanh,Paul Turner,Paul Turner,Paul Turner,Sona Soeng,Mary Valcanis,Joan Powling,Karolina Dimovski,Geoff Hogg,Jeremy Farrar,Jeremy Farrar,Kathryn E. Holt,Gordon Dougan +93 more
TL;DR: This whole-genome sequence analysis of Salmonella enterica serovar Typhi identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years, and identifies numerous transmissions of H58.
Journal ArticleDOI
Cryptic transmission of SARS-CoV-2 in Washington state.
Trevor Bedford,Trevor Bedford,Alexander L. Greninger,Alexander L. Greninger,Pavitra Roychoudhury,Pavitra Roychoudhury,Lea M. Starita,Michael Famulare,Meei-Li Huang,Meei-Li Huang,Arun K. Nalla,Gregory Pepper,Adam Reinhardt,Hong Xie,Lasata Shrestha,Truong N. Nguyen,Amanda Adler,Elisabeth Brandstetter,Shari Cho,Danielle Giroux,Peter D Han,Kairsten Fay,Chris D. Frazar,Misja Ilcisin,Kirsten Lacombe,Jover Lee,Anahita Kiavand,Matthew Richardson,Thomas R. Sibley,Melissa Truong,Caitlin R Wolf,Deborah A. Nickerson,Mark J. Rieder,Janet A. Englund,Janet A. Englund,James Hadfield,Emma B. Hodcroft,Emma B. Hodcroft,John Huddleston,John Huddleston,Louise H. Moncla,Nicola F. Müller,Richard A. Neher,Richard A. Neher,Xianding Deng,Wei Gu,Scot Federman,Charles Y. Chiu,Jeffrey S. Duchin,Jeffrey S. Duchin,Romesh Gautom,Geoff Melly,Brian Hiatt,Philip Dykema,Scott Lindquist,Krista Queen,Ying Tao,Anna Uehara,Suxiang Tong,Duncan MacCannell,Gregory L. Armstrong,Geoffrey S. Baird,Helen Y. Chu,Jay Shendure,Jay Shendure,Keith R. Jerome,Keith R. Jerome +66 more
TL;DR: It is found that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
Journal ArticleDOI
Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings
Nicholas A. Feasey,James Hadfield,Karen H. Keddy,Timothy J. Dallman,Jan Jacobs,Jan Jacobs,Xiangyu Deng,Xiangyu Deng,Paul Wigley,Lars Barquist,Gemma C. Langridge,Theresa Feltwell,Simon R. Harris,Alison E. Mather,Maria Fookes,Martin Aslett,Chisomo L. Msefula,Chisomo L. Msefula,Samuel Kariuki,Calman A. MacLennan,Calman A. MacLennan,Robert S. Onsare,François-Xavier Weill,Simon Le Hello,Anthony M. Smith,Michael McClelland,Prerak T. Desai,Christopher M. Parry,Christopher M. Parry,Christopher M. Parry,J.S. Cheesbrough,Neil French,Josefina Campos,José A. Chabalgoity,Laura Betancor,Katie L. Hopkins,Satheesh Nair,Tom J. Humphrey,Octavie Lunguya,Tristan A Cogan,Milagritos D. Tapia,Samba O. Sow,Sharon M. Tennant,Kristin Bornstein,Myron M. Levine,Lizeth Lacharme-Lora,Dean Everett,Robert A. Kingsley,Robert A. Kingsley,Julian Parkhill,Robert S. Heyderman,Robert S. Heyderman,Gordon Dougan,Melita A. Gordon,Melita A. Gordon,Nicholas R. Thomson,Nicholas R. Thomson +56 more
TL;DR: S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.