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Project 3: Social Determinants of Infections Disease Dynamics (SDIDD or Social-Epi)

Working Group leader: Bert Baumgaertner

Group members: Steve Krone, Craig Miller, Ben Ridenhour, Florian Justwan

Originated: Summer 2015

Description:

We develop and analyze epidemiological models of infectious disease to understand how social and behavior factors affect disease dynamics. We work with both analytical models (e.g., ODEs) and generative models (e.g., ABMs).  We also design surveys and behavioral experiments to validate our models.

Publications:

Planning horizon affects prophylactic decision-making and epidemic dynamics

Nardin LG, Miller CR, Ridenhour BJ, Krone SM, Joyce P, Baumgaertner BO. (2016Planning horizon affects prophylactic decision-making and epidemic dynamicsPeerJ4:e2678

Opinion strength influenced the spatial dynamics of opinion formation

Baumgaertner B, Tyson R, Krone S, (2016) Opinion strength influenced the spatial dynamics of opinion formation. The Journal of Mathematics Sociology. 2016. NIHMSID 825394.

The Influence of Political Ideology and Trust on Willingness to Vaccinate

Baumgaertner, B., Carlisle, J. E., & Justwan, F. (2018). The influence of political ideology and trust on willingness to vaccinate. PLoS ONE13(1), e0191728. http://doi.org/10.1371/journal.pone.0191728

Phage

Working Group leader: Craig Miller

Group members: Holly Wichman, JT Van Leuven, Yesol Sapozhnikov, Keera Paull, Jacob Schow, Tessa Wedmyer

Originated: June 2015

Description:

This working group focuses on phage and phage-host interactions. We have several research directions. One project involves attenuating the bacteriophage phiX174 using synonymous recoding and asking questions about how mutational effects combine and how fitness recovery transpires. This work is funded by an NIH R01 grant. A second project is focused on how altering the stability of phage capsid proteins alters fitness. Here we are asking asking how well can molecular and statistical models predict viral fitness. This work is funded by an NSF Track II grant. A third (and recently begun) branch of work involves testing how bacterial host cells evolve resistance to different phage using whole genome sequencing and bioinformatics tools.

Publications:

Selecting among three basic fitness landscape models: additive, multiplicative and stickbreaking

Miller, C.R., Leuven, J.T., Wichman, H.A., & Joyce, P. (2017). Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical population biology.

Modeling Community Dynamics of Microbiomes

Working Group leader: Christopher Remien

Group members: Ben Ridenhour, Tuan Phan

Originated: June 2015

Description:

We are developing new methods to study and analyze microbial community dynamics and applying the methods to publicly available data and data collected by members of the group. If a grant is funded, the working group will last as long as the funding exists.  If we are unable to obtain funding within the next year and a half, we will reassess our focus or dissolve.

Statistical Genomics (StaGe)

Working Group leader: Audrey Fu

Group members: Bandita Karki, Jarred Kvamme, Elijah Danquah Darko, Chenangnon Tovissode

Originated: June 2015

Description:

We develop statistical models and machine learning algorithms to analyze data in human genomics, with an emphasis on causal network inference and high-dimensional data.

Modeling Variability in Persistence Induced From Within by a Toxic Metabolite (MetToxin)

Working Group leader: Chris Marx

Group members: Andreas Vaskekis, Chris Remien, Marty Ytreberg, Jill Johnson, Sergey Stolyar, Ben Ridenhour, Tomislav Ticak, Jannell Bazurto, Jagdish Patel, Saiavash Riazi, Eric Bruger, Isaiah Jordan

Originated: May 2015

Description:

Our group is taking a very broad, integrated approach to understanding the mechanism and consequences of sensing the toxic metabolite formaldehyde and its interaction with the ribosome that leads to growth cessation and protection from increased damage.