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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Posts

Future Blog Post

less than 1 minute read

Published: January 01, 2199

This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.

Blog Post number 4

less than 1 minute read

Published: August 14, 2015

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 3

less than 1 minute read

Published: August 14, 2014

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 2

less than 1 minute read

Published: August 14, 2013

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 1

less than 1 minute read

Published: August 14, 2012

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

portfolio

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publications

COVID-19 infectivity profile correction

Published in arXiv, 2020

Correction to the COVID-19 infectivity profil published in Nature Medicine by He et al. in April 2020.

Recommended citation: Ashcroft, P, Huisman, JS, Lehtinen, S, Bouman, JA, Althaus, CL, Regoes, RR, Bonhoeffer, S (2020). "COVID-19 infectivity profile correction" arXiv preprint https://doi.org/10.48550/arXiv.2007.06602

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