Judith Bouman

Judith Bouman

Mathematical modeller of
infectious diseases

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publications

Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches

Published in PLOS Computational Biology, 2021

A systemic comparison of cutoff-based and cutoff-free (mixture model) methods to estimate cumulative incidence of infection using seroprevalence data.

Recommended citation: Bouman, JA, Riou, J, Bonhoeffer, S, Regoes, RR (2021). "Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches" PLOS Computational Biology. 17(2), e1008728. https://doi.org/10.1371/journal.pcbi.1008728

Diversity of vaccination-induced immune responses can prevent the spread of vaccine escape mutants

Published in bioRXiv, 2021

A theoretical exercise to study how the diversity in vaccination-induced immune responses can explain (in part) why vaccination escape is less often observed compared to resistance to treatment.

Recommended citation: Bouman, JA, Capelli, C, Regoes, RR (2021). "Diversity of vaccination-induced immune responses can prevent the spread of vaccine escape mutants" BioRXiv preprint https://doi.org/10.1101/2021.04.14.439790

Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva

Published in Epidemics, 2022

An application of mixture models to SARS-CoV-2 serosurvey data from the SEROCoV-POP study in Geneva. Additional to the cumulitive incidence, an indirect indicator of disease severity is estimated

Recommended citation: Bouman, JA, Kadelka, S, Stringhini, S, Pennacchio, F, Meyer, B, Yerly, S, Kaiser, L, Guessous, I, Azman, AS, Bonhoeffer, S, Regoes, RR (2022). "Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva" Epidemics. 39, 100572 https://doi.org/10.1016/j.epidem.2022.100572

Per-pathogen virulence of HIV-1 subtypes A, C and D

Published in Proceedings of the Royal Society B, 2023

Evolutionary framework for estimating the per-pathogen virulence of HIV-1 subtypes A, C and D using clinical data.

Recommended citation: Bouman, JA, Venner, CM, Walker, C, Arts, EJ, Regoes, RR (2023). "Per-pathogen virulence of HIV-1 subtypes A, C and D" Proceedings of the Royal Society B. 290 (1998), 20222572 https://doi.org/10.1098/rspb.2022.2572

Correcting for Antibody Waning in Cumulative Incidence Estimation from Sequential Serosurveys

Published in American journal of Epidemiology, 2023

Empirically-supported approach for sero-reversion correction in cumulative incidence estimation when sequential serosurveys are conducted in the context of a newly emerging infectious disease.

Recommended citation: Kadelka, S, Bouman, JA, Ashcroft, P, Regoes, RR (2023). "Correcting for Antibody Waning in Cumulative Incidence Estimation from Sequential Serosurveys" American journal of epidemiology https://doi.org/10.1093/aje/kwad226

Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models

Published in PLOS Computational Biology, 2023

A Bayesian workflow for including time-varying transmission in stratified SIR-like infectious disease transmission models. The workflow includes the comparison of three different methods for time-varying transmission: B-splines, Gaussian processes, and Brownian motion. Moreover, the models are applied to both simulated and real-world SARS-CoV-2 data.

Recommended citation: Bouman, JA, Hauser, A, Grimm, SL, Wohlfender, M, Bhatt, S, Semenova, E, Gelman, A, Althaus, CL, Riou, J (2023). "Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models" PLOS Computational Biology https://doi.org/10.1371/journal.pcbi.1011575

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