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). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006930

Kamvar, Zhian N; Cai, Jun; Pulliam, Juliet RC; Schumacher, Jakob; Jombart, Thibaut; (2019) Epidemic curves made easy using the R package incidence. F1000Research, 8. p. 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). p. 20180276. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2018.0276

Beugin, Marie-Pauline; Gayet, Thibault; Pontier, Dominique; Devillard, Sebastien; 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). 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). ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1006885

Cori, Anne; Nouvellet, Pierre; Garske, Tini; Bourhy, Herve; Nakoune, Emmanuel; Jombart, Thibaut; (2018) A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies. PLOS COMPUTATIONAL BIOLOGY, 14 (12). 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

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, Aurelien; Devillard, Sebastien; 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). 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). 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). ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-017-1988-y

Agua-Agum, Junerlyn; Allegranzi, Benedetta; Ariyarajah, Archchun; Aylward, R Bruce; Blake, Isobel M; Barboza, Philippe; Bausch, Daniel; Brennan, Richard J; Clement, Peter; Coffey, Pasqualina; +39 more... 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, Celine; Gutierrez, Giovanna Jaramillo; Hamblion, Esther; Hinsley, Wes; Holden, Robert; Holmes, David; Hugonnet, Stephane; 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; Minh, Tang; 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

Agua-Agum, Junerlyn; Ariyarajah, Archchun; Aylward, Bruce; Bawo, Luke; Bilivogui, Pepe; Blake, Isobel M; Brennan, Richard J; Cawthorne, Amy; Cleary, Eilish; Clement, Peter; +52 more... 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). ISSN 1549-1676 DOI: https://doi.org/10.1371/journal.pmed.1002170

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). 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; da-Silva, Nathalie Jourdan; 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). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000070

Karkey, Abhilasha; Jombart, Thibaut; Walker, Alan W; Thompson, Corinne N; Torres, Andres; Dongol, Sabina; Nga, Tran Vu Thieu; Duy, Pham Thanh; Dung, Tran Thi Ngoc; Phat, Voong Vinh; +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). ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0004346

Agua-Agum, Junerlyn; Ariyarajah, Archchun; Blake, Isobel M; Cori, Anne; Donnelly, Christl A; Dorigatti, Ilaria; Dye, Christopher; Eckmanns, Tim; Ferguson, Neil M; Fowler, Robert A; +13 more... 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

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

Aylward, Bruce; Barboza, Philippe; Bawo, Luke; Bertherat, Eric; Bilivogui, Pepe; Blake, Isobel; Brennan, Rick; Briand, Sylvie; Chakauya, Jethro Magwati; Chitala, Kennedy; +51 more... 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; Kone, 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; Krishnan, Ravi Santhana Gopala; Senga, Mikiko; Shuaib, Faisal; Van Kerkhove, Maria D; Vaz, Rui; Kannangarage, Niluka Wijekoon; 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, 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). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1003457

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

Nuebel, Ulrich; Dordel, Janina; Kurt, Kevin; Strommenger, Birgit; Westh, Henrik; Shukla, Sanjay K; Zemlickova, Helena; Leblois, Raphael; Wirth, Thierry; Jombart, Thibaut; +2 more... Balloux, Francois; 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). ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1000855

Balloux, Francois; 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

Laloe, Denis; Jombart, Thibaut; Dufour, Anne-Beatrice; 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/10.1051/gse:2007021 Item availability may be restricted.