Evans, Beth; Jombart, Thibaut; (2022) Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic. Vaccine, 40 (26). pp. 3531-3535. ISSN 0264-410X DOI: https://doi.org/10.1016/j.vaccine.2022.01.044 Item availability may be restricted.

Jarvis, Christopher I; Gimma, Amy; Finger, Flavio; Morris, Tim P; Thompson, Jennifer A; le Polain de Waroux, Olivier; Edmunds, W John; Funk, Sebastian; Jombart, Thibaut; (2022) Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics. PLoS Computational Biology, 18 (5). e1008800. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008800

Lindsey, Benjamin B; Villabona-Arenas, Ch Julián; Campbell, Finlay; Keeley, Alexander J; Parker, Matthew D; Shah, Dhruv R; Parsons, Helena; Zhang, Peijun; Kakkar, Nishchay; Gallis, Marta; +18 more... Foulkes, Benjamin H; Wolverson, Paige; Louka, Stavroula F; Christou, Stella; State, Amy; Johnson, Katie; Raza, Mohammad; Hsu, Sharon; Jombart, Thibaut; Cori, Anne; Sheffield COVID-19 Genomics Group; COVID-19 Genomics UK (COG-UK) consortium; CMMID COVID-19 working group; Evans, Cariad M; Partridge, David G; Atkins, Katherine E; Hué, Stéphane; de Silva, Thushan I; (2022) Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature communications, 13 (1). 671-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-28291-y

Abbas, M; Robalo Nunes, T; Cori, A; Cordey, S; Laubscher, F; Baggio, S; Jombart, T; Iten, A; Vieux, L; Teixeira, D; +6 more... Perez, M; Pittet, D; Frangos, E; Graf, CE; Zingg, W; Harbarth, S; (2021) Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction. The Journal of hospital infection, 117. pp. 124-134. ISSN 0195-6701 DOI: https://doi.org/10.1016/j.jhin.2021.07.013

Brooks-Pollock, Ellen; Danon, Leon; Jombart, Thibaut; Pellis, Lorenzo; (2021) Modelling that shaped the early COVID-19 pandemic response in the UK. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 376 (1829). p. 20210001. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2021.0001

Campbell, Finlay; Archer, Brett; Laurenson-Schafer, Henry; Jinnai, Yuka; Konings, Franck; Batra, Neale; Pavlin, Boris; Vandemaele, Katelijn; Van Kerkhove, Maria D; Jombart, Thibaut; +2 more... Morgan, Oliver; le Polain de Waroux, Olivier; (2021) Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26 (24). pp. 1-6. ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2021.26.24.2100509

Carter, Simone E; Ahuka-Mundeke, Steve; Pfaffmann Zambruni, Jérôme; Navarro Colorado, Carlos; van Kleef, Esther; Lissouba, Pascale; Meakin, Sophie; le Polain de Waroux, Olivier; Jombart, Thibaut; Mossoko, Mathias; +7 more... Bulemfu Nkakirande, Dorothée; Esmail, Marjam; Earle-Richardson, Giulia; Degail, Marie-Amelie; Umutoni, Chantal; Anoko, Julienne Ngoundoung; Gobat, Nina; (2021) How to improve outbreak response: a case study of integrated outbreak analytics from Ebola in Eastern Democratic Republic of the Congo. BMJ global health, 6 (8). e006736-e006736. ISSN 2059-7908 DOI: https://doi.org/10.1136/bmjgh-2021-006736

Jombart, Thibaut; (2021) Why development of outbreak analytics tools should be valued, supported, and funded. The Lancet Infectious diseases, 21 (4). pp. 458-459. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(20)30996-8

Jombart, Thibaut; Ghozzi, Stéphane; Schumacher, Dirk; Taylor, Timothy J; Leclerc, Quentin J; Jit, Mark; Flasche, Stefan; Greaves, Felix; Ward, Tom; Eggo, Rosalind M; +7 more... Nightingale, Emily; Meakin, Sophie; Brady, Oliver J; Centre for Mathematical Modelling of Infectious Diseases COVID-1; Medley, Graham F; Höhle, Michael; Edmunds, W John; Centre for Mathematical Modelling; (2021) Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 376 (1829). 20200266-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2020.0266

Leclerc, Quentin J; Nightingale, Emily S; Abbott, Sam; CMMID COVID-19 Working Group; Jombart, Thibaut; CMMID COVID-19 Working Group; (2021) Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England. Scientific reports, 11 (1). 7106-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-86266-3

Carter, Simone E; Gobat, Nina; Pfaffmann Zambruni, Jérôme; Bedford, Juliet; van Kleef, Esther; Jombart, Thibaut; Mossoko, Mathias; Bulemfu Nkakirande, Dorothée; Navarro Colorado, Carlos; Ahuka-Mundeke, Steve; (2020) What questions we should be asking about COVID-19 in humanitarian settings: perspectives from the Social Sciences Analysis Cell in the Democratic Republic of the Congo. BMJ GLOBAL HEALTH, 5 (9). e003607-e003607. ISSN 2059-7908 DOI: https://doi.org/10.1136/bmjgh-2020-003607

Jit, Mark; Jombart, Thibaut; Nightingale, Emily S; Endo, Akira; Abbott, Sam; LSHTM Centre for Mathematical Modelling of Infectious Diseases C; Edmunds, W John; (2020) Estimating number of cases and spread of coronavirus disease (COVID-19) using critical care admissions, United Kingdom, February to March 2020. EUROSURVEILLANCE, 25 (18). pp. 6-10. ISSN 1560-7917 DOI: https://doi.org/10.2807/1560-7917.ES.2020.25.18.2000632

Jombart, Thibaut; Jarvis, Christopher I; Mesfin, Samuel; Tabal, Nabil; Mossoko, Mathias; Mpia, Luigino Minikulu; Abedi, Aaron Aruna; Chene, Sonia; Forbin, Ekokobe Elias; Belizaire, Marie Roseline D; +13 more... de Radiguès, Xavier; Ngombo, Richy; Tutu, Yannick; Finger, Flavio; Crowe, Madeleine; Edmunds, W John; Nsio, Justus; Yam, Abdoulaye; Diallo, Boubacar; Gueye, Abdou Salam; Ahuka-Mundeke, Steve; Yao, Michel; Fall, Ibrahima Socé; (2020) The cost of insecurity: from flare-up to control of a major Ebola virus disease hotspot during the outbreak in the Democratic Republic of the Congo, 2019. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25 (2). pp. 19-22. ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2020.25.2.1900735 Item availability may be restricted.

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; Centre for the Mathematical Modelling of Infectious Diseases COV; (2020) Inferring the number of COVID-19 cases from recently reported deaths. Wellcome Open Res, 5. 78-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15786.1

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. medRxiv. DOI: https://doi.org/10.1101/2020.03.10.20033761

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. Wellcome open research, 5. 78-. DOI: https://doi.org/10.12688/wellcomeopenres.15786.1

Mobula, Linda Meta; Samaha, Hadia; Yao, Michel; Gueye, Abdou Salam; Diallo, Boubacar; Umutoni, Chantal; Anoko, Julienne; Lokonga, Jean-Pierre; Minikulu, Luigi; Mossoko, Mathias; +5 more... Bruni, Emanuele; Carter, Simone; Jombart, Thibaut; Fall, Ibrahima Soce; Ahuka-Mundeke, Steve; (2020) Recommendations for the COVID-19 Response at the National Level Based on Lessons Learned from the Ebola Virus Disease Outbreak in the Democratic Republic of the Congo. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 103 (1). pp. 12-17. ISSN 0002-9637 DOI: https://doi.org/10.4269/ajtmh.20-0256

Parisi, Andrea; Le Thi Phuong, Tu; Mather, Alison E; Jombart, Thibaut; Thanh Tuyen, Ha; Phu Huong Lan, Nguyen; Hoang Thu Trang, Nguyen; Carrique-Mas, Juan; Campbell, James I; Glass, Kathryn; +2 more... Kirk, Martyn D; Baker, Stephen; (2020) Differential antimicrobial susceptibility profiles between symptomatic and asymptomatic non-typhoidal Salmonella infections in Vietnamese children. EPIDEMIOLOGY AND INFECTION, 148. e144-. ISSN 0950-2688 DOI: https://doi.org/10.1017/S0950268820001168

Parisi, Andrea; Phuong, Tu Le Thi; Mather, Alison E; Jombart, Thibaut; Tuyen, Ha Thanh; Lan, Nguyen Phu Huong; Trang, Nguyen Hoang Thu; Carrique-Mas, Juan; Campbell, James I; Trung, Nguyen Vinh; +3 more... Glass, Kathryn; Kirk, Martyn D; Baker, Stephen; (2020) The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam. INFECTION GENETICS AND EVOLUTION, 85. 104534-. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2020.104534

Rees, Eleanor M; Nightingale, Emily S; Jafari, Yalda; Waterlow, Naomi R; Clifford, Samuel; B Pearson, Carl A; Group, Cmmid Working; Jombart, Thibaut; Procter, Simon R; Knight, Gwenan M; (2020) COVID-19 length of hospital stay: a systematic review and data synthesis. BMC MEDICINE, 18 (1). 270-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-020-01726-3

Campbell, Finlay; Cori, Anne; Ferguson, Neil; Jombart, Thibaut; (2019) Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data. PLOS COMPUTATIONAL BIOLOGY, 15 (3). e1006930-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006930

Dighe, Amy; Jombart, Thibaut; Van Kerkhove, Maria D; Ferguson, Neil; (2019) A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination. Epidemics, 29. 100350-. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2019.100350

Kamvar, Zhian N; Cai, Jun; Pulliam, Juliet RC; Schumacher, Jakob; Jombart, Thibaut; (2019) Epidemic curves made easy using the R package incidence. F1000Research, 8. 139-. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.18002.1

Polonsky, Jonathan A; Baidjoe, Amrish; Kamvar, Zhian N; Cori, Anne; Durski, Kara; Edmunds, W John; Eggo, Rosalind M; Funk, Sebastian; Kaiser, Laurent; Keating, Patrick; +9 more... de Waroux, Olivier le Polain; Marks, Michael; Moraga, Paula; Morgan, Oliver; Nouvellet, Pierre; Ratnayake, Ruwan; Roberts, Chrissy H; Whitworth, Jimmy; Jombart, Thibaut; (2019) Outbreak analytics: a developing data science for informing the response to emerging pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 374 (1776). 20180276-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2018.0276

Sewell, Thomas R; Zhu, Jianing; Rhodes, Johanna; Hagen, Ferry; Meis, Jacques F; Fisher, Matthew C; Jombart, Thibaut; (2019) Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus. mBio, 10 (3). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00392-19

Thompson, RN; Stockwin, JE; van Gaalen, RD; Polonsky, JA; Kamvar, ZN; Demarsh, PA; Dahlqwist, E; Li, S; Miguel, E; Jombart, T; +3 more... Lessler, J; Cauchemez, S; Cori, A; (2019) Improved inference of time-varying reproduction numbers during infectious disease outbreaks. Epidemics, 29. 100356-. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2019.100356

Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; +17 more... Harris, David; Chieu, Tran Thi Bich; Van Vinh Chau, Nguyen; Campbell, James; Schultsz, Constance; Parkhill, Julian; Bentley, Stephen D; Langford, Paul R; Rycroft, Andrew N; Wren, Brendan W; Farrar, Jeremy; Baker, Stephen; Hoa, Ngo Thi; Holden, Matthew TG; Tucker, Alexander W; Maskell, Duncan J; BRaDP1T Consortium; (2019) Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. NATURE COMMUNICATIONS, 10 (1). 5326-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-019-13138-w

Beugin, Marie-Pauline; Gayet, Thibault; Pontier, Dominique; Devillard, Sébastien; Jombart, Thibaut; (2018) A fast likelihood solution to the genetic clustering problem. METHODS IN ECOLOGY AND EVOLUTION, 9 (4). pp. 1006-1016. ISSN 2041-210X DOI: https://doi.org/10.1111/2041-210X.12968

Campbell, Finlay; Didelot, Xavier; Fitzjohn, Rich; Ferguson, Neil; Cori, Anne; Jombart, Thibaut; (2018) outbreaker2: a modular platform for outbreak reconstruction. BMC BIOINFORMATICS, 19 (Suppl). 363-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-018-2330-z

Campbell, Finlay; Strang, Camilla; Ferguson, Neil; Cori, Anne; Jombart, Thibaut; (2018) When are pathogen genome sequences informative of transmission events? PLOS PATHOGENS, 14 (2). e1006885-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1006885

Cori, Anne; Nouvellet, Pierre; Garske, Tini; Bourhy, Hervé; Nakouné, Emmanuel; Jombart, Thibaut; (2018) A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies. PLOS COMPUTATIONAL BIOLOGY, 14 (12). e1006554-. ISSN 1553-7358 DOI: https://doi.org/10.1371/journal.pcbi.1006554

Dupuis, Julian R; Bremer, Forest T; Jombart, Thibaut; Sim, Sheina B; Geib, Scott M; (2018) mvmapper: Interactive spatial mapping of genetic structures. Molecular Ecology Resources, 18 (2). pp. 362-367. ISSN 1755-098X DOI: https://doi.org/10.1111/1755-0998.12724

Moraga, Paula; Dorigatti, Ilaria; Kamvar, Zhian N; Piatkowski, Pawel; Toikkanen, Salla E; Nagraj, VP; Donnelly, Christl A; Jombart, Thibaut; (2018) epiflows: an R package for risk assessment of travel-related spread of disease. F1000Research, 7. 1374-. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.16032.3

Nagraj, VP; Randhawa, Nistara; Campbell, Finlay; Crellen, Thomas; Sudre, Bertrand; Jombart, Thibaut; (2018) epicontacts: Handling, visualisation and analysis of epidemiological contacts. F1000Research, 7. 566-. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.14492.2

Nouvellet, Pierre; Cori, Anne; Garske, Tini; Blake, Isobel M; Dorigatti, Ilaria; Hinsley, Wes; Jombart, Thibaut; Mills, Harriet L; Nedjati-Gilani, Gemma; Van Kerkhove, Maria D; +4 more... Fraser, Christophe; Donnelly, Christl A; Ferguson, Neil M; Riley, Steven; (2018) A simple approach to measure transmissibility and forecast incidence. EPIDEMICS, 22. pp. 29-35. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2017.02.012

Bertranpetit, Emilie; Jombart, Thibaut; Paradis, Emmanuel; Pena, Hilda; Dubey, Jitender; Su, Chunlei; Mercier, Aurélien; Devillard, Sébastien; Ajzenberg, Daniel; (2017) Phylogeography of Toxoplasma gondii points to a South American origin. INFECTION GENETICS AND EVOLUTION, 48. pp. 150-155. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2016.12.020

Cori, Anne; Donnelly, Christl A; Dorigatti, Ilaria; Ferguson, Neil M; Fraser, Christophe; Garske, Tini; Jombart, Thibaut; Nedjati-Gilani, Gemma; Nouvellet, Pierre; Riley, Steven; +3 more... Van Kerkhove, Maria D; Mills, Harriet L; Blake, Isobel M; (2017) Key data for outbreak evaluation: building on the Ebola experience. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 372 (1721). p. 20160371. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2016.0371

Garske, Tini; Cori, Anne; Ariyarajah, Archchun; Blake, Isobel M; Dorigatti, Ilaria; Eckmanns, Tim; Fraser, Christophe; Hinsley, Wes; Jombart, Thibaut; Mills, Harriet L; +11 more... Nedjati-Gilani, Gemma; Newton, Emily; Nouvellet, Pierre; Perkins, Devin; Riley, Steven; Schumacher, Dirk; Shah, Anita; Van Kerkhove, Maria D; Dye, Christopher; Ferguson, Neil M; Donnelly, Christl A; (2017) Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 372 (1721). p. 20160308. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2016.0308

Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; Goudet, Jerome; Lapp, Hilmar; (2017) apex: phylogenetics with multiple genes. [Conference or Workshop Item] https://doi.org/10.1111/1755-0998.12567

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline; (2017) treespace: Statistical exploration of landscapes of phylogenetic trees. MOLECULAR ECOLOGY RESOURCES, 17 (6). pp. 1385-1392. ISSN 1755-098X DOI: https://doi.org/10.1111/1755-0998.12676

Montano, V; Jombart, T; (2017) An Eigenvalue test for spatial principal component analysis. BMC BIOINFORMATICS, 18 (1). 562-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-017-1988-y

Clare, Frances C; Halder, Julia B; Daniel, Olivia; Bielby, Jon; Semenov, Mikhail A; Jombart, Thibaut; Loyau, Adeline; Schmeller, Dirk S; Cunningham, Andrew A; Rowcliffe, Marcus; +3 more... Garner, Trenton WJ; Bosch, Jaime; Fisher, Matthew C; (2016) Climate forcing of an emerging pathogenic fungus across a montane multi-host community. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 371 (1709). p. 20150454. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2015.0454

Dallman, Tim; Inns, Thomas; Jombart, Thibaut; Ashton, Philip; Loman, Nicolas; Chatt, Carol; Messelhaeusser, Ute; Rabsch, Wolfgang; Simon, Sandra; Nikisins, Sergejs; +9 more... Bernard, Helen; le Hello, Simon; Jourdan da-Silva, Nathalie; Kornschober, Christian; Mossong, Joel; Hawkey, Peter; de Pinna, Elizabeth; Grant, Kathie; Cleary, Paul; (2016) Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network. MICROBIAL GENOMICS, 2 (8). e000070-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000070

International Ebola Response Team; Agua-Agum, Junerlyn; Ariyarajah, Archchun; Aylward, Bruce; Bawo, Luke; Bilivogui, Pepe; Blake, Isobel M; Brennan, Richard J; Cawthorne, Amy; Cleary, Eilish; +53 more... Clement, Peter; Conteh, Roland; Cori, Anne; Dafae, Foday; Dahl, Benjamin; Dangou, Jean-Marie; Diallo, Boubacar; Donnelly, Christl A; Dorigatti, Ilaria; Dye, Christopher; Eckmanns, Tim; Fallah, Mosoka; Ferguson, Neil M; Fiebig, Lena; Fraser, Christophe; Garske, Tini; Gonzalez, Lice; Hamblion, Esther; Hamid, Nuha; Hersey, Sara; Hinsley, Wes; Jambei, Amara; Jombart, Thibaut; Kargbo, David; Keita, Sakoba; Kinzer, Michael; George, Fred Kuti; Godefroy, Beatrice; Gutierrez, Giovanna; Kannangarage, Niluka; Mills, Harriet L; Moller, Thomas; Meijers, Sascha; Mohamed, Yasmine; Morgan, Oliver; Nedjati-Gilani, Gemma; Newton, Emily; Nouvellet, Pierre; Nyenswah, Tolbert; Perea, William; Perkins, Devin; Riley, Steven; Rodier, Guenael; Rondy, Marc; Sagrado, Maria; Savulescu, Camelia; Schafer, Ilana J; Schumacher, Dirk; Seyler, Thomas; Shah, Anita; Van Kerkhove, Maria D; Wesseh, C Samford; Yoti, Zabulon; (2016) Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. PLOS MEDICINE, 13 (11). e1002170-. ISSN 1549-1676 DOI: https://doi.org/10.1371/journal.pmed.1002170

Karkey, Abhilasha; Jombart, Thibaut; Walker, Alan W; Thompson, Corinne N; Torres, Andres; Dongol, Sabina; Tran Vu Thieu, Nga; Pham Thanh, Duy; Tran Thi Ngoc, Dung; Voong Vinh, Phat; +6 more... Singer, Andrew C; Parkhill, Julian; Thwaites, Guy; Basnyat, Buddha; Ferguson, Neil; Baker, Stephen; (2016) The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. PLOS NEGLECTED TROPICAL DISEASES, 10 (1). e0004346-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0004346

WHO Ebola Response Team; Agua-Agum, Junerlyn; Allegranzi, Benedetta; Ariyarajah, Archchun; Aylward, R Bruce; Blake, Isobel M; Barboza, Philippe; Bausch, Daniel; Brennan, Richard J; Clement, Peter; +40 more... Coffey, Pasqualina; Cori, Anne; Donnelly, Christl A; Dorigatti, Ilaria; Drury, Patrick; Durski, Kara; Dye, Christopher; Eckmanns, Tim; Ferguson, Neil M; Fraser, Christophe; Garcia, Erika; Garske, Tini; Gasasira, Alex; Gurry, Céline; Hamblion, Esther; Hinsley, Wes; Holden, Robert; Holmes, David; Hugonnet, Stéphane; Jaramillo Gutierrez, Giovanna; Jombart, Thibaut; Kelley, Edward; Santhana, Ravi; Mahmoud, Nuha; Mills, Harriet L; Mohamed, Yasmine; Musa, Emmanuel; Naidoo, Dhamari; Nedjati-Gilani, Gemma; Newton, Emily; Norton, Ian; Nouvellet, Pierre; Perkins, Devin; Perkins, Mark; Riley, Steven; Schumacher, Dirk; Shah, Anita; Tang, Minh; Varsaneux, Olivia; Van Kerkhove, Maria D; (2016) After Ebola in West Africa--Unpredictable Risks, Preventable Epidemics. NEW ENGLAND JOURNAL OF MEDICINE, 375 (6). pp. 587-596. ISSN 0028-4793 DOI: https://doi.org/10.1056/NEJMsr1513109

Chung The, Hao; Karkey, Abhilasha; Pham Thanh, Duy; Boinett, Christine J; Cain, Amy K; Ellington, Matthew; Baker, Kate S; Dongol, Sabina; Thompson, Corinne; Harris, Simon R; +11 more... Jombart, Thibaut; Le Thi Phuong, Tu; Tran Do Hoang, Nhu; Ha Thanh, Tuyen; Shretha, Shrijana; Joshi, Suchita; Basnyat, Buddha; Thwaites, Guy; Thomson, Nicholas R; Rabaa, Maia A; Baker, Stephen; (2015) A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO molecular medicine, 7 (3). pp. 227-239. ISSN 1757-4676 DOI: https://doi.org/10.15252/emmm.201404767

Nouvellet, Pierre; Garske, Tini; Mills, Harriet L; Nedjati-Gilani, Gemma; Hinsley, Wes; Blake, Isobel M; Van Kerkhove, Maria D; Cori, Anne; Dorigatti, Ilaria; Jombart, Thibaut; +4 more... Riley, Steven; Fraser, Christophe; Donnelly, Christl A; Ferguson, Neil M; (2015) The role of rapid diagnostics in managing Ebola epidemics. NATURE, 528 (7580). S109-S116. ISSN 0028-0836 DOI: https://doi.org/10.1038/nature16041

WHO Ebola Response Team; Agua-Agum, Junerlyn; Ariyarajah, Archchun; Blake, Isobel M; Cori, Anne; Donnelly, Christl A; Dorigatti, Ilaria; Dye, Christopher; Eckmanns, Tim; Ferguson, Neil M; +14 more... Fowler, Robert A; Fraser, Christophe; Garske, Tini; Hinsley, Wes; Jombart, Thibaut; Mills, Harriet L; Murthy, Srinivas; Nedjati Gilani, Gemma; Nouvellet, Pierre; Pelletier, Louise; Riley, Steven; Schumacher, Dirk; Shah, Anita; Van Kerkhove, Maria D; (2015) Ebola virus disease among children in West Africa. NEW ENGLAND JOURNAL OF MEDICINE, 372 (13). pp. 1274-1277. ISSN 0028-4793 DOI: https://doi.org/10.1056/NEJMc1415318

Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; +17 more... Harris, David; Chieu, Tran Thi Bich; Chau, Nguyen Van Vinh; Campbell, James; Schultsz, Constance; Parkhill, Julian; Bentley, Stephen D; Langford, Paul R; Rycroft, Andrew N; Wren, Brendan W; Farrar, Jeremy; Baker, Stephen; Hoa, Ngo Thi; Holden, Matthew TG; Tucker, Alexander W; Maskell, Duncan J; BRaDP1T Consortium; (2015) Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature communications, 6 (1). 7272-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms8272

Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; +17 more... Harris, David; Chieu, Tran Thi Bich; Van Vinh Chau, Nguyen; Campbell, James; Schultsz, Constance; Parkhill, Julian; Bentley, Stephen D; Langford, Paul R; Rycroft, Andrew N; Wren, Brendan W; Farrar, Jeremy; Baker, Stephen; Hoa, Ngo Thi; Holden, Matthew TG; Tucker, Alexander W; Maskell, Duncan J; BRaDP1T Consortium; (2015) Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature communications, 6 (1). 6740-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms7740

Jombart, Thibaut; Aanensen, David M; Baguelin, Marc; Birrell, Paul; Cauchemez, Simon; Camacho, Anton; Colijn, Caroline; Collins, Caitlin; Cori, Anne; Didelot, Xavier; +13 more... Fraser, Christophe; Frost, Simon; Hens, Niel; Hugues, Joseph; Höhle, Michael; Opatowski, Lulla; Rambaut, Andrew; Ratmann, Oliver; Soubeyrand, Samuel; Suchard, Marc A; Wallinga, Jacco; Ypma, Rolf; Ferguson, Neil; (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7 (100). pp. 28-34. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.04.003

Jombart, Thibaut; Cori, Anne; Didelot, Xavier; Cauchemez, Simon; Fraser, Christophe; Ferguson, Neil; (2014) Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLOS COMPUTATIONAL BIOLOGY, 10 (1). e1003457-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1003457

WHO Ebola Response Team; Aylward, Bruce; Barboza, Philippe; Bawo, Luke; Bertherat, Eric; Bilivogui, Pepe; Blake, Isobel; Brennan, Rick; Briand, Sylvie; Chakauya, Jethro Magwati; +52 more... Chitala, Kennedy; Conteh, Roland M; Cori, Anne; Croisier, Alice; Dangou, Jean-Marie; Diallo, Boubacar; Donnelly, Christl A; Dye, Christopher; Eckmanns, Tim; Ferguson, Neil M; Formenty, Pierre; Fuhrer, Caroline; Fukuda, Keiji; Garske, Tini; Gasasira, Alex; Gbanyan, Stephen; Graaff, Peter; Heleze, Emmanuel; Jambai, Amara; Jombart, Thibaut; Kasolo, Francis; Kadiobo, Albert Mbule; Keita, Sakoba; Kertesz, Daniel; Koné, Moussa; Lane, Chris; Markoff, Jered; Massaquoi, Moses; Mills, Harriet; Mulba, John Mike; Musa, Emmanuel; Myhre, Joel; Nasidi, Abdusalam; Nilles, Eric; Nouvellet, Pierre; Nshimirimana, Deo; Nuttall, Isabelle; Nyenswah, Tolbert; Olu, Olushayo; Pendergast, Scott; Perea, William; Polonsky, Jonathan; Riley, Steven; Ronveaux, Olivier; Sakoba, Keita; Santhana Gopala Krishnan, Ravi; Senga, Mikiko; Shuaib, Faisal; Van Kerkhove, Maria D; Vaz, Rui; Wijekoon Kannangarage, Niluka; Yoti, Zabulon; (2014) Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. NEW ENGLAND JOURNAL OF MEDICINE, 371 (16). pp. 1481-1495. ISSN 0028-4793 DOI: https://doi.org/10.1056/NEJMoa1411100

Jombart, T; Eggo, RM; Dodd, PJ; Balloux, F; (2010) Reconstructing disease outbreaks from genetic data: a graph approach. Heredity, 106 (2). pp. 383-390. ISSN 0018-067X DOI: https://doi.org/10.1038/hdy.2010.78 Full text not available from this repository.

Jombart, Thibaut; Devillard, Sébastien; Balloux, François; (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC GENETICS, 11 (1). 94-. ISSN 1471-2156 DOI: https://doi.org/10.1186/1471-2156-11-94

Morelli, Giovanna; Song, Yajun; Mazzoni, Camila J; Eppinger, Mark; Roumagnac, Philippe; Wagner, David M; Feldkamp, Mirjam; Kusecek, Barica; Vogler, Amy J; Li, Yanjun; +14 more... Cui, Yujun; Thomson, Nicholas R; Jombart, Thibaut; Leblois, Raphael; Lichtner, Peter; Rahalison, Lila; Petersen, Jeannine M; Balloux, Francois; Keim, Paul; Wirth, Thierry; Ravel, Jacques; Yang, Ruifu; Carniel, Elisabeth; Achtman, Mark; (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics, 42 (12). pp. 1140-1143. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.705

Nübel, Ulrich; Dordel, Janina; Kurt, Kevin; Strommenger, Birgit; Westh, Henrik; Shukla, Sanjay K; Zemlicková, Helena; Leblois, Raphaël; Wirth, Thierry; Jombart, Thibaut; +2 more... Balloux, François; Witte, Wolfgang; (2010) A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLOS PATHOGENS, 6 (4). e1000855-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1000855

Balloux, François; Handley, Lori-Jayne Lawson; Jombart, Thibaut; Liu, Hua; Manica, Andrea; (2009) Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 276 (1672). pp. 3447-3455. ISSN 0962-8452 DOI: https://doi.org/10.1098/rspb.2009.0752

Fraser, Christophe; Donnelly, Christl A; Cauchemez, Simon; Hanage, William P; Van Kerkhove, Maria D; Hollingsworth, T Déirdre; Griffin, Jamie; Baggaley, Rebecca F; Jenkins, Helen E; Lyons, Emily J; +18 more... Jombart, Thibaut; Hinsley, Wes R; Grassly, Nicholas C; Balloux, Francois; Ghani, Azra C; Ferguson, Neil M; Rambaut, Andrew; Pybus, Oliver G; Lopez-Gatell, Hugo; Alpuche-Aranda, Celia M; Chapela, Ietza Bojorquez; Zavala, Ethel Palacios; Guevara, Dulce Ma Espejo; Checchi, Francesco; Garcia, Erika; Hugonnet, Stephane; Roth, Cathy; WHO Rapid Pandemic Assessment Collaboration; (2009) Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, NY), 324 (5934). pp. 1557-1561. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.1176062 Full text not available from this repository.

Jombart, Thibaut; Eggo, Rosalind M; Dodd, Pete; Balloux, Francois; (2009) Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic. PLoS currents, 1 (AUG). RRN1026-. ISSN 2157-3999 DOI: https://doi.org/10.1371/currents.rrn1026

Laloë, Denis; Jombart, Thibaut; Dufour, Anne-Béatrice; Moazami-Goudarzi, Katayoun; (2007) Consensus genetic structuring and typological value of markers using multiple co-inertia analysis. GENETICS SELECTION EVOLUTION, 39 (5). pp. 545-567. ISSN 0999-193X DOI: https://doi.org/10.1186/1297-9686-39-5-545 Item availability may be restricted.