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

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; (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

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

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). p. 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. 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.