Year Item Type Full Text

2022

Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic. (2022) Evans, Beth; Jombart, Thibaut

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. (2022) 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; 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

2021

Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction. (2021) Abbas, M; Robalo Nunes, T; Cori, A; Cordey, S; Laubscher, F; Baggio, S; Jombart, T; Iten, A; Vieux, L; Teixeira, D; Perez, M; Pittet, D; Frangos, E; Graf, CE; Zingg, W; Harbarth, S

Modelling that shaped the early COVID-19 pandemic response in the UK. (2021) Brooks-Pollock, Ellen; Danon, Leon; Jombart, Thibaut; Pellis, Lorenzo

Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. (2021) Campbell, Finlay; Archer, Brett; Laurenson-Schafer, Henry; Jinnai, Yuka; Konings, Franck; Batra, Neale; Pavlin, Boris; Vandemaele, Katelijn; Van Kerkhove, Maria D; Jombart, Thibaut; Morgan, Oliver; le Polain de Waroux, Olivier

How to improve outbreak response: a case study of integrated outbreak analytics from Ebola in Eastern Democratic Republic of the Congo. (2021) 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; Bulemfu Nkakirande, Dorothée; Esmail, Marjam; Earle-Richardson, Giulia; Degail, Marie-Amelie; Umutoni, Chantal; Anoko, Julienne Ngoundoung; Gobat, Nina

Why development of outbreak analytics tools should be valued, supported, and funded. (2021) Jombart, Thibaut

Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection. (2021) Jombart, Thibaut; Ghozzi, Stéphane; Schumacher, Dirk; Taylor, Timothy J; Leclerc, Quentin J; Jit, Mark; Flasche, Stefan; Greaves, Felix; Ward, Tom; Eggo, Rosalind M; Nightingale, Emily; Meakin, Sophie; Brady, Oliver J; Centre for Mathematical Modelling of Infectious Diseases COVID-1; Medley, Graham F; Höhle, Michael; Edmunds, W John

Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England. (2021) Leclerc, Quentin J; Nightingale, Emily S; Abbott, Sam; CMMID COVID-19 Working Group; Jombart, Thibaut

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. (2020) 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

Estimating number of cases and spread of coronavirus disease (COVID-19) using critical care admissions, United Kingdom, February to March 2020. (2020) Jit, Mark; Jombart, Thibaut; Nightingale, Emily S; Endo, Akira; Abbott, Sam; LSHTM Centre for Mathematical Modelling of Infectious Diseases C; Edmunds, W John

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. (2020) 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; 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

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

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

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

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. (2020) Mobula, Linda Meta; Samaha, Hadia; Yao, Michel; Gueye, Abdou Salam; Diallo, Boubacar; Umutoni, Chantal; Anoko, Julienne; Lokonga, Jean-Pierre; Minikulu, Luigi; Mossoko, Mathias; Bruni, Emanuele; Carter, Simone; Jombart, Thibaut; Fall, Ibrahima Soce; Ahuka-Mundeke, Steve

Differential antimicrobial susceptibility profiles between symptomatic and asymptomatic non-typhoidal Salmonella infections in Vietnamese children. (2020) 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; Kirk, Martyn D; Baker, Stephen

The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam. (2020) 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; Glass, Kathryn; Kirk, Martyn D; Baker, Stephen

COVID-19 length of hospital stay: a systematic review and data synthesis. (2020) 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

2019

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data. (2019) Campbell, Finlay; Cori, Anne; Ferguson, Neil; Jombart, Thibaut

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination. (2019) Dighe, Amy; Jombart, Thibaut; Van Kerkhove, Maria D; Ferguson, Neil

Epidemic curves made easy using the R package incidence. (2019) Kamvar, Zhian N; Cai, Jun; Pulliam, Juliet RC; Schumacher, Jakob; Jombart, Thibaut

Outbreak analytics: a developing data science for informing the response to emerging pathogens. (2019) Polonsky, Jonathan A; Baidjoe, Amrish; Kamvar, Zhian N; Cori, Anne; Durski, Kara; Edmunds, W John; Eggo, Rosalind M; Funk, Sebastian; Kaiser, Laurent; Keating, Patrick; de Waroux, Olivier le Polain; Marks, Michael; Moraga, Paula; Morgan, Oliver; Nouvellet, Pierre; Ratnayake, Ruwan; Roberts, Chrissy H; Whitworth, Jimmy; Jombart, Thibaut picture_as_pdf

Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus. (2019) Sewell, Thomas R; Zhu, Jianing; Rhodes, Johanna; Hagen, Ferry; Meis, Jacques F; Fisher, Matthew C; Jombart, Thibaut

Improved inference of time-varying reproduction numbers during infectious disease outbreaks. (2019) Thompson, RN; Stockwin, JE; van Gaalen, RD; Polonsky, JA; Kamvar, ZN; Demarsh, PA; Dahlqwist, E; Li, S; Miguel, E; Jombart, T; Lessler, J; Cauchemez, S; Cori, A

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. (2019) Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; 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

2018

A fast likelihood solution to the genetic clustering problem. (2018) Beugin, Marie-Pauline; Gayet, Thibault; Pontier, Dominique; Devillard, Sébastien; Jombart, Thibaut

outbreaker2: a modular platform for outbreak reconstruction. (2018) Campbell, Finlay; Didelot, Xavier; Fitzjohn, Rich; Ferguson, Neil; Cori, Anne; Jombart, Thibaut

When are pathogen genome sequences informative of transmission events? (2018) Campbell, Finlay; Strang, Camilla; Ferguson, Neil; Cori, Anne; Jombart, Thibaut

A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies. (2018) Cori, Anne; Nouvellet, Pierre; Garske, Tini; Bourhy, Hervé; Nakouné, Emmanuel; Jombart, Thibaut

mvmapper: Interactive spatial mapping of genetic structures. (2018) Dupuis, Julian R; Bremer, Forest T; Jombart, Thibaut; Sim, Sheina B; Geib, Scott M

epiflows: an R package for risk assessment of travel-related spread of disease. (2018) Moraga, Paula; Dorigatti, Ilaria; Kamvar, Zhian N; Piatkowski, Pawel; Toikkanen, Salla E; Nagraj, VP; Donnelly, Christl A; Jombart, Thibaut

epicontacts: Handling, visualisation and analysis of epidemiological contacts. (2018) Nagraj, VP; Randhawa, Nistara; Campbell, Finlay; Crellen, Thomas; Sudre, Bertrand; Jombart, Thibaut

A simple approach to measure transmissibility and forecast incidence. (2018) 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; Fraser, Christophe; Donnelly, Christl A; Ferguson, Neil M; Riley, Steven

2017

Phylogeography of Toxoplasma gondii points to a South American origin. (2017) Bertranpetit, Emilie; Jombart, Thibaut; Paradis, Emmanuel; Pena, Hilda; Dubey, Jitender; Su, Chunlei; Mercier, Aurélien; Devillard, Sébastien; Ajzenberg, Daniel

Key data for outbreak evaluation: building on the Ebola experience. (2017) Cori, Anne; Donnelly, Christl A; Dorigatti, Ilaria; Ferguson, Neil M; Fraser, Christophe; Garske, Tini; Jombart, Thibaut; Nedjati-Gilani, Gemma; Nouvellet, Pierre; Riley, Steven; Van Kerkhove, Maria D; Mills, Harriet L; Blake, Isobel M

Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016. (2017) Garske, Tini; Cori, Anne; Ariyarajah, Archchun; Blake, Isobel M; Dorigatti, Ilaria; Eckmanns, Tim; Fraser, Christophe; Hinsley, Wes; Jombart, Thibaut; Mills, Harriet L; 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

apex: phylogenetics with multiple genes. (2017) Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; Goudet, Jerome; Lapp, Hilmar

treespace: Statistical exploration of landscapes of phylogenetic trees. (2017) Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

An Eigenvalue test for spatial principal component analysis. (2017) Montano, V; Jombart, T

2016

Climate forcing of an emerging pathogenic fungus across a montane multi-host community. (2016) 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; Garner, Trenton WJ; Bosch, Jaime; Fisher, Matthew C

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network. (2016) Dallman, Tim; Inns, Thomas; Jombart, Thibaut; Ashton, Philip; Loman, Nicolas; Chatt, Carol; Messelhaeusser, Ute; Rabsch, Wolfgang; Simon, Sandra; Nikisins, Sergejs; Bernard, Helen; le Hello, Simon; Jourdan da-Silva, Nathalie; Kornschober, Christian; Mossong, Joel; Hawkey, Peter; de Pinna, Elizabeth; Grant, Kathie; Cleary, Paul

Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. (2016) 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; 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

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. (2016) 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; Singer, Andrew C; Parkhill, Julian; Thwaites, Guy; Basnyat, Buddha; Ferguson, Neil; Baker, Stephen

After Ebola in West Africa--Unpredictable Risks, Preventable Epidemics. (2016) 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; 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

2015

A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. (2015) 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; 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

The role of rapid diagnostics in managing Ebola epidemics. (2015) 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; Riley, Steven; Fraser, Christophe; Donnelly, Christl A; Ferguson, Neil M

Ebola virus disease among children in West Africa. (2015) 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; 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

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. (2015) Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; 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

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. (2015) Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; 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

2014

OutbreakTools: a new platform for disease outbreak analysis using the R software. (2014) Jombart, Thibaut; Aanensen, David M; Baguelin, Marc; Birrell, Paul; Cauchemez, Simon; Camacho, Anton; Colijn, Caroline; Collins, Caitlin; Cori, Anne; Didelot, Xavier; 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

Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. (2014) Jombart, Thibaut; Cori, Anne; Didelot, Xavier; Cauchemez, Simon; Fraser, Christophe; Ferguson, Neil

Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. (2014) WHO Ebola Response Team; Aylward, Bruce; Barboza, Philippe; Bawo, Luke; Bertherat, Eric; Bilivogui, Pepe; Blake, Isobel; Brennan, Rick; Briand, Sylvie; Chakauya, Jethro Magwati; 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

2010

Reconstructing disease outbreaks from genetic data: a graph approach. (2010) Jombart, T; Eggo, RM; Dodd, PJ; Balloux, F

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. (2010) Jombart, Thibaut; Devillard, Sébastien; Balloux, François

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. (2010) Morelli, Giovanna; Song, Yajun; Mazzoni, Camila J; Eppinger, Mark; Roumagnac, Philippe; Wagner, David M; Feldkamp, Mirjam; Kusecek, Barica; Vogler, Amy J; Li, Yanjun; 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

A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. (2010) Nübel, Ulrich; Dordel, Janina; Kurt, Kevin; Strommenger, Birgit; Westh, Henrik; Shukla, Sanjay K; Zemlicková, Helena; Leblois, Raphaël; Wirth, Thierry; Jombart, Thibaut; Balloux, François; Witte, Wolfgang

2009

Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. (2009) Balloux, François; Handley, Lori-Jayne Lawson; Jombart, Thibaut; Liu, Hua; Manica, Andrea

Pandemic potential of a strain of influenza A (H1N1): early findings. (2009) 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; 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

Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic. (2009) Jombart, Thibaut; Eggo, Rosalind M; Dodd, Pete; Balloux, Francois