Chris van Dorp
@chvandorp.bsky.social
Associate Research Scientist at Columbia University Irving Medical Center, dept of Pathology and Cell Biology.
Reposted by Chris van Dorp
Our TRM modeling paper is now published in PLOS Computational Biology! In this paper, we fit dynamical (ODE) models to single-cell flow cytometry data using a variational autoencoder that has a GMM with time-dependent weights as prior. journals.plos.org/ploscompbiol...
A variational deep-learning approach to modeling memory T cell dynamics
Author summary After an influenza infection, antibodies provide strong protection—but only against the same strain. Because influenza rapidly mutates its surface proteins, this protection soon becomes...
journals.plos.org
August 24, 2025 at 9:01 PM
Our TRM modeling paper is now published in PLOS Computational Biology! In this paper, we fit dynamical (ODE) models to single-cell flow cytometry data using a variational autoencoder that has a GMM with time-dependent weights as prior. journals.plos.org/ploscompbiol...
Our manuscript on the effect of school closure on pre-vaccination SARS-CoV-2 transmission is now available on MedRxiv. Congrats to first authors Benedetta and Rey! www.medrxiv.org/content/10.1...
Retrospective evaluation of school-related measures on pre-vaccination transmission dynamics of SARS-CoV-2
Schools are important settings for respiratory virus transmission and a major focus of pandemic control measures in the absence of effective pharmaceutical interventions. During the COVID-19 pandemic,...
www.medrxiv.org
April 16, 2025 at 5:41 PM
Our manuscript on the effect of school closure on pre-vaccination SARS-CoV-2 transmission is now available on MedRxiv. Congrats to first authors Benedetta and Rey! www.medrxiv.org/content/10.1...
Reposted by Chris van Dorp
StanConnects are a series of one-day online conferences for the application of Stan to specific areas. This year, we're kicking off with Stan for biology (broadly defined), co-organized by @ericnovik.bsky.social and @vianeylb.bsky.social, on 30 May '25!!
stanbio.org
stanbio.org
StanBio Connect 2025 – StanBio Connect
Advancing Biomedical Research with Stan
stanbio.org
March 13, 2025 at 3:39 PM
StanConnects are a series of one-day online conferences for the application of Stan to specific areas. This year, we're kicking off with Stan for biology (broadly defined), co-organized by @ericnovik.bsky.social and @vianeylb.bsky.social, on 30 May '25!!
stanbio.org
stanbio.org
Reposted by Chris van Dorp
Nearly 20 years ago, theory predicted that evolution can evolve “mutation sensors” to improve evolvability. Michael Barnett et all et al. now show this in a beautiful experiment! ❤️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Experimental evolution of evolvability
Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...
www.science.org
February 21, 2025 at 2:37 PM
Nearly 20 years ago, theory predicted that evolution can evolve “mutation sensors” to improve evolvability. Michael Barnett et all et al. now show this in a beautiful experiment! ❤️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
In this preprint we quantify how resident-memory CD4 T cells are maintained in skin and lamina propria, and where they come from. We did this with a fate reporter mouse model, and of course Bayesian ODE models implemented in Stan.
doi.org/10.1101/2024...
doi.org/10.1101/2024...
Tissue resident memory CD4+ T cells are sustained by site-specific levels of self-renewal and replacement from precursors
Tissue-resident memory T cells (TRM) protect from repeated infections within organs and barrier sites. The breadth and duration of such protection is defined at minimum by three quantities; the rate a...
doi.org
February 15, 2025 at 10:14 PM
In this preprint we quantify how resident-memory CD4 T cells are maintained in skin and lamina propria, and where they come from. We did this with a fate reporter mouse model, and of course Bayesian ODE models implemented in Stan.
doi.org/10.1101/2024...
doi.org/10.1101/2024...
Our CD4 memory T cell paper is finally published in PLOS Biology (doi.org/10.1371/jour...).
Congratulations to Elise Bullock and other co-authors!
Congratulations to Elise Bullock and other co-authors!
The dynamics and longevity of circulating CD4+ memory T cells depend on cell age and not the chronological age of the host
The quality and longevity of CD4+ effector and central memory T cells change with age in mice. This study shows that these cells have longer lifespans and become more quiescent when the organism ages,...
doi.org
August 14, 2024 at 2:35 PM
Our CD4 memory T cell paper is finally published in PLOS Biology (doi.org/10.1371/jour...).
Congratulations to Elise Bullock and other co-authors!
Congratulations to Elise Bullock and other co-authors!
I this preprint we model lung memory T cell dynamics following influenza infection, and fit such models to "single cell" flow cytometry data directly. The idea is to identify T cell populations and their dynamics simultaneously. www.biorxiv.org/content/10.1...
July 12, 2024 at 12:39 AM
I this preprint we model lung memory T cell dynamics following influenza infection, and fit such models to "single cell" flow cytometry data directly. The idea is to identify T cell populations and their dynamics simultaneously. www.biorxiv.org/content/10.1...
Our Science paper is finally published!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Induction of durable remission by dual immunotherapy in SHIV-infected ART-suppressed macaques
The eradication of the viral reservoir represents the major obstacle to the development of a clinical cure for established HIV-1 infection. Here, we demonstrate that the administration of Anktiva (N-8...
www.science.org
March 4, 2024 at 6:59 PM
Our Science paper is finally published!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
My first publication of 2024! Thanks to Michiel van Boven and all other co-authors. This work required some creative Stan programming. doi.org/10.1371/jour...
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study
Author summary Households are a main setting for transmission of respiratory viruses. Here, we analyse data from a prospective household study to estimate the time-dependent hazards of introduction of...
doi.org
January 31, 2024 at 1:52 PM
My first publication of 2024! Thanks to Michiel van Boven and all other co-authors. This work required some creative Stan programming. doi.org/10.1371/jour...
I wrote a blog post about my efforts to add a distribution to Stan. It's work in progress. Check it out here: tbz533.blogspot.com/2023/12/cont...
Contributing code to Stan
This post is about me trying to contribute some code to the Stan codebase. My colleagues and I often use the Dirichlet-Multinomial distri...
tbz533.blogspot.com
December 9, 2023 at 5:15 PM
I wrote a blog post about my efforts to add a distribution to Stan. It's work in progress. Check it out here: tbz533.blogspot.com/2023/12/cont...
What would Alanis say about this?
December 2, 2023 at 8:56 PM
What would Alanis say about this?