Chris

Chris

Associate Research Scientist at Columbia University Irving Medical Center.

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

Pages

Posts

Contributing code to Stan

less than 1 minute read

Published:

I wrote a blog post about how to contribute code to Stan. This was quite a long process for a noob like me, resulting in a long blog post. In this post, I will guide you through the process of implementing new native distributions in Stan, writing documentation and tests, modifying the Stan compiler, and creating pull requests on GitHub.

Generalized Profiling with Stan

less than 1 minute read

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This post is about implementing the generalized profiling method in Stan. Fitting ODE models to timeseries data can be hard, especially if the data shows signs of process noise that cannot be simply absorbed into the measurement noise. A good example is periodic dynamics, in which the phase drifts with time. The deterministic prediction will in this case get out of phase with the stochastic data.

Bayesian Multi-dimensional scaling (MDS)

less than 1 minute read

Published:

Antigenic cartography maps viruses and sera to a two-dimensional space to visualize their relation and the pace of antigenic drift. As antigens and antibodies are typically very high dimensional objects, special methods to embed them into lower dimensional spaces are required. MDS is one such method. In this post, I show how to implement a Bayesian version of MDS and apply this to influenza data.

How to calculate WBIC with Stan

less than 1 minute read

Published:

In Bayesian statistics, model comparison ideally is based on Bayes factors. However, these are not always easy to compute. For this reason, approximate measures have been developed. One of these measures is the WBIC, which has is similar to the BIC, but is not merely based on a point estimate and is valid for a larger class of models. In this post, I show how to compute WBIC with a Stan model.

portfolio

publications

Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution

Published in PLOS Computational Biology, 2014

We use a multi-level model of HIV evolution to investigate the effect of within-host selection and host-heterogeneity on virulence evolution.

Recommended citation: van Dorp, CH. et al (2014). "Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution." PLOS Computational Biology. 10(12): e1003899.
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Estimating Transmission Parameters for Respiratory Syncytial Virus and Predicting the Impact of Maternal and Pediatric Vaccination

Published in The Journal of Infectious Diseases, 2020

We fit age-structure transmission models to multiple RSV data streams and use the fitted models to investigate the impact of pediatric vaccination.

Recommended citation: van Boven, M et al (2020). "Estimating Transmission Parameters for Respiratory Syncytial Virus and Predicting the Impact of Maternal and Pediatric Vaccination." The Journal of Infectious Diseases. 222(Supplement_7): S688–S694.
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Models of SIV rebound after treatment interruption that involve multiple reactivation events

Published in PLOS Computational Biology, 2020

We derive a probability distribution for the time to SIV rebound after ART interruption that takes into account the possibility that multiple latently infected cells can reactivate and contribute to viral recrudescence.

Recommended citation: van Dorp, CH. et al (2020). "Models of SIV rebound after treatment interruption that involve multiple reactivation events." PLOS Computational Biology. 16(10): e1008241.
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A Participant-Derived Xenograft Model of HIV Enables Long-Term Evaluation of Autologous Immunotherapies

Published in Journal of Experimental Medicine, 2021

Using a humanized mouse model of an HIV infection, we explore immunotherapies that enhance the CD8+ T-cell response using an N-803 nanogen.

Recommended citation: McCann CD (2021). "A Participant-Derived Xenograft Model of HIV Enables Long-Term Evaluation of Autologous Immunotherapies." Journal of Experimental Medicine. 218(7): e20201908.
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Controlling the pandemic during the SARS-CoV-2 vaccination rollout

Published in Nature Communications, 2021

We make projections using a model fit to Portugese SARS-CoV-2 data to assess if and how non-pharmaceutical interventions can be lifted during planned mass-vaccination campaigns.

Recommended citation: Viana J et al (2021). "Controlling the pandemic during the SARS-CoV-2 vaccination rollout." Nature Communications 12, 3674.
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Estimating the strength of selection for new SARS-CoV-2 variants

Published in Nature Communications, 2021

We use isotonic regression, hierarchical logistic regression and stochastic modeling to estimate the fitness advantage of SARS-CoV-2 variants in different regions.

Recommended citation: van Dorp CH. et al (2021). "Estimating the strength of selection for new SARS-CoV-2 variants." Nature Communications 12, 7239.
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Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Published in Virus Evolution, 2022

We estimate region-specific selective advantages of the Omicron variant of SARS-CoV-2 using renewal equation models, genetic data and COVID-19 case counts.

Recommended citation: van Dorp CH. et al (2022). "Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron." Virus Evolution. 8(2): veac089.
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Numerical methods and hypoexponential approximations for gamma distributed delay differential equations

Published in IMA Journal of Applied Mathematics, 2022

Integration schemes for delay-differential equations, and a relaxation of the linear chain trick that is useful for estimating the shape parameter of the Gamma distribution.

Recommended citation: Cassidy T. et al (2022). "Numerical methods and hypoexponential approximations for gamma distributed delay differential equations." IMA Journal of Applied Mathematics. 87(6): 1043–1089.
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talks

teaching

SMB workshop: Stan for Immunobiology

Workshop, SMB, Immunobiology and Infection, 2021

For the Immunobiology and Infection subgroup of the Society for Mathematical Biology (SMB), I taught a workshop for attendees interested in learning to use Stan.

CIME Lecture Notes (work in progress)

Lecture notes, Springer, Lecture Notes in Mathematics, 2025

Together with Dr. Ganna Rozhnova (Utrecht University), I am currently working on a chapter for the upcoming "CIME Lecture Notes Mathematical modeling for epidemiology: analysis, simulation and forecasting"