getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data. - Sam Abbott (J. Open Source Softw., 2019)

Practical considerations for measuring the effective reproductive number, Rt. - Katelyn M. Gostic; Lauren McGough; Edward B. Baskerville; Sam Abbott; Keya Joshi; Christine Tedijanto; Rebecca Kahn; Rene Niehus; James A. Hay; Pablo M. De Salazar; Joel Hellewell; Sophie Meakin; et al. (PLoS Comput. Biol., 2020)

covidregionaldata: Subnational data for COVID-19 epidemiology. - Joseph Palmer; Katharine Sherratt; Richard Martin-Nielson; Jonnie Bevan; Hamish Gibbs; LSHTM CMMID COVID-19 Working Group; Sebastian Funk; Sam Abbott (J. Open Source Softw., 2021)

Correction: Practical considerations for measuring the effective reproductive number, Rt. - Katelyn M. Gostic; Lauren McGough; Edward B. Baskerville; Sam Abbott; Keya Joshi; Christine Tedijanto; Rebecca Kahn; Rene Niehus; James A. Hay; Pablo M. De Salazar; Joel Hellewell; Sophie Meakin; et al. (PLoS Comput. Biol., 2021)

Comparing human and model-based forecasts of COVID-19 in Germany and Poland. - Nikos I. Bosse; Sam Abbott; Johannes Bracher; Habakuk Hain; Billy J. Quilty; Mark Jit; Edwin van Leeuwen; Anne Cori; Sebastian Funk (PLoS Comput. Biol., 2022)

Scoring epidemiological forecasts on transformed scales. - Nikos I. Bosse; Sam Abbott; Anne Cori; Edwin van Leeuwen; Johannes Bracher; Sebastian Funk (PLoS Comput. Biol., 2023)

Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England. - James D. Munday; Sam Abbott; Sophie Meakin; Sebastian Funk (PLoS Comput. Biol., 2023)

Nowcasting the 2022 mpox outbreak in England. - Christopher E. Overton; Sam Abbott; Rachel Christie; Fergus Cumming; Julie Day; Owen Jones; Rob Paton; Charlie Turner; Thomas Ward (PLoS Comput. Biol., 2023)

Collaborative nowcasting of COVID-19 hospitalization incidences in Germany. - Daniel Wolffram; Sam Abbott; Matthias an der Heiden; Sebastian Funk; Felix Günther 003; Davide Hailer; Stefan Heyder; Thomas Hotz; Jan van de Kassteele; Helmut Küchenhoff; Sören Müller-Hansen; Diellë Syliqi; et al. (PLoS Comput. Biol., 2023)

Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany. - Elisabeth K. Brockhaus; Daniel Wolffram; Tanja Stadler; Michael Osthege; Tanmay Mitra; Jonas M. Littek; Ekaterina A. Krymova; Anna J. Klesen; Jana S. Huisman; Stefan Heyder; Laura Marie Helleckes; Matthias an der Heiden; et al. (PLoS Comput. Biol., 2023)

Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. - Kelly Charniga; Sang Woo Park; Andrei R. Akhmetzhanov; Anne Cori; Jonathan Dushoff; Sebastian Funk; Katelyn M. Gostic; Natalie M. Linton; Adrian Lison; Christopher E. Overton; Juliet R. C. Pulliam; Thomas Ward; et al. (PLoS Comput. Biol., 2024)

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. - Ciara E. Judge; Timothy G. Vaughan; Timothy Russell; Sam Abbott; Louis du Plessis; Tanja Stadler; Oliver Brady; Sarah Hill (PLoS Comput. Biol., 2024)

Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates. - Adrian Lison; Sam Abbott; Jana S. Huisman; Tanja Stadler (PLoS Comput. Biol., 2024)