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

Kalimeri, Kyriaki; Delfino, Matteo; Cattuto, Ciro; Perrotta, Daniela; Colizza, Vittoria; Guerrisi, Caroline; Turbelin, Clement; Duggan, Jim; Edmunds, John; Obi, Chinelo; +8 more... Pebody, Richard; Franco, Ana O; Moreno, Yamir; Meloni, Sandro; Koppeschaar, Carl; Kjelso, Charlotte; Mexia, Ricardo; Paolotti, Daniela; (2019) Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms. PLOS COMPUTATIONAL BIOLOGY, 15 (4). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006173

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

Sumner, Tom; Orton, Richard J; Green, Darren M; Kao, Rowland R; Gubbins, Simon; (2017) Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock. PLOS COMPUTATIONAL BIOLOGY, 13 (4). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005470

Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E; (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS COMPUTATIONAL BIOLOGY, 13 (6). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005595

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

Lindgreen, Stinus; Umu, Sinan Ugur; Lai, Alicia Sook-Wei; Eldai, Hisham; Liu, Wenting; McGimpsey, Stephanie; Wheeler, Nicole E; Biggs, Patrick J; Thomson, Nick R; Barquist, Lars; +2 more... Poole, Anthony M; Gardner, Paul P; (2014) Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLOS COMPUTATIONAL BIOLOGY, 10 (10). ISSN 1553-7358 DOI: https://doi.org/10.1371/journal.pcbi.1003907