Judge, Ciara; Vaughan, Timothy; Russell, Timothy; Abbott, Sam; du Plessis, Louis; Stadler, Tanja; Brady, Oliver; Hill, Sarah; (2024) EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. PLoS computational biology, 20 (11). e1012528-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1012528

Kiniry, Stephen J; Judge, Ciara E; Michel, Audrey M; Baranov, Pavel V; (2021) Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data. Nucleic Acids Research, 49 (W1). W662-W670. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkab323

Lim, Ahyoung; Shearer, Freya M; Sewalk, Kara; Pigott, David M; Clarke, Joseph; Ghouse, Azhar; Judge, Ciara; Kang, Hyolim; Messina, Jane P; Kraemer, Moritz UG; +12 more... Gaythorpe, Katy AM; de Souza, William M; Nsoesie, Elaine O; Celone, Michael; Faria, Nuno; Ryan, Sadie J; Rabe, Ingrid B; Rojas, Diana P; Hay, Simon I; Brownstein, John S; Golding, Nick; Brady, Oliver J; (2025) The overlapping global distribution of dengue, chikungunya, Zika and yellow fever. Nature communications, 16. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-025-58609-5