adegenet: a R package for the multivariate analysis of genetic markers von Jombart, Thibaut

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adegenet 1.3-1: new tools for the analysis of genome-wide SNP data von Jombart, Thibaut, Ahmed, Ismaïl

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COVID-19 length of hospital stay: a systematic review and data synthesis von 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

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Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data von Campbell, Finlay, Cori, Anne, Ferguson, Neil, Jombart, Thibaut

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Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021 von 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

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

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treespace: Statistical exploration of landscapes of phylogenetic trees von Jombart, Thibaut, Kendall, Michelle, Almagro‐Garcia, Jacob, Colijn, Caroline

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adephylo: new tools for investigating the phylogenetic signal in biological traits von Jombart, Thibaut, Balloux, François, Dray, Stéphane

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

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outbreaker2: a modular platform for outbreak reconstruction von Campbell, Finlay, Didelot, Xavier, Fitzjohn, Rich, Ferguson, Neil, Cori, Anne, Jombart, Thibaut

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How to measure and test phylogenetic signal von Münkemüller, Tamara, Lavergne, Sébastien, Bzeznik, Bruno, Dray, Stéphane, Jombart, Thibaut, Schiffers, Katja, Thuiller, Wilfried

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Sorting out assortativity: When can we assess the contributions of different population groups to epidemic transmission? von Geismar, Cyril, White, Peter J, Cori, Anne, Jombart, Thibaut

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Outbreak analytics: a developing data science for informing the response to emerging pathogens von 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

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Multivariate Analysis of Ecological Data with Ade4 von Thioulouse, Jean, Dray, Stéphane, Dufour, Anne-Béatrice, Siberchicot, Aurélie, Jombart, Thibaut, Pavoine, Sandrine

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

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Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections von Russell, Timothy W, Golding, Nick, Hellewell, Joel, Abbott, Sam, Wright, Lawrence, Pearson, Carl A B, van Zandvoort, Kevin, Jarvis, Christopher I, Gibbs, Hamish, Liu, Yang, Eggo, Rosalind M, Edmunds, W John, Kucharski, Adam J

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

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Key data for outbreak evaluation: building on the Ebola experience von 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.

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Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis von Cui, Yujun, Yu, Chang, Yan, Yanfeng, Li, Dongfang, Li, Yanjun, Jombart, Thibaut, Weinert, Lucy A., Wang, Zuyun, Guo, Zhaobiao, Xu, Lizhi, Zhang, Yujiang, Zheng, Hancheng, Qin, Nan, Xiao, Xiao, Wu, Mingshou, Wang, Xiaoyi, Zhou, Dongsheng, Qi, Zhizhen, Du, Zongmin, Wu, Honglong, Yang, Xianwei, Cao, Hongzhi, Wang, Hu, Wang, Jing, Yao, Shusen, Rakin, Alexander, Li, Yingrui, Falush, Daniel, Balloux, Francois, Achtman, Mark, Song, Yajun, Wang, Jun, Yang, Ruifu

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Discriminant analysis of principal components: a new method for the analysis of genetically structured populations von Jombart, Thibaut, Devillard, Sébastien, Balloux, François

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