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Covid-19 Event Risk Assessment Planning Tool makes headlines as Thanksgiving approaches

November 23, 2021 by adavidson38 Leave a Comment

Last November the Covid-19 Event Risk Assessment Planning Tool made headlines as people around the United States planned their holiday travel amidst rising Covid-19 cases and uncertainty. Now, the tool is in the news again.

So far, the tool has been featured in national news outlets such as National Geographic, The Hill, and Fast Company, as well as in a number of regional news outlets, including:

CBS-17 in Raleigh, NC
The Courier Journal in Louisville, KY
The Tri-City Herald in Kennewick, WA
The Akron Beacon Journal in Akron, OH
The Des Moines Register in Des Moines, IA
The Springfield News-Leader in Springfield, MO
The Courier-Post in Cherry Hill, NJ
Mass Live in Springfield, MA

Follow the tool at @covid19riskUSA to stay up to date on additional media features, risk updates, and news.

More about the tool

Since its inception in July of 2020, over 8 million people have used the Covid-19 Event Risk Assessment Planning Tool to gauge Covid-19 exposure risk. Created by members of the Weitz Group, (Prof. Weitz, Dr. Stephen Beckett, and Quan Nguyen) in collaboration with the Applied Bioinformatics Laboratory and Clio Andris, a professor of city and regional planning and interactive computing at Georgia Tech, this tool uses real-time Covid-19 case data to calculate the county-level risk of exposure to Covid-19 at events of different sizes. For example, the tool can estimate how likely it is that at least one person has Covid-19 at a 15-person Thanksgiving celebration.

As the tool has grown its development has continued. A new collaboration with cognitive neuroscientists at Duke University has led to the addition of interactive elements to the site. Users can now see examples of events of different sizes, such as noting that a 50-person event is similar to what one would encounter at a restaurant or a grocery store. People are also encouraged to test their knowledge of the risk levels in their area with a risk quiz.

To learn more about the science behind the tool, read our paper in Nature Human Behavior. Visit our Covid-19 Research page to learn more about our other research on Covid-19.

I’m worried about the risk in my area – what can I do?

If the risk levels in your area have you worried about seeing family over the holiday season, there are things you can do to reduce the chance of spreading Covid-19.

Get vaccinated. If you or your loved ones haven’t already, getting the Covid-19 vaccine will vastly reduce your chance of infection, the severity of breakthrough infections, and the risk of spreading infection.
Improve ventilation. Hosting celebrations outdoors when possible dramatically decreases the chance of spread. If that is not feasible, increasing ventilation in indoor areas by opening windows or using air purifiers can help.
Reduce the size of your gathering. With fewer people, the chances that at least one person has Covid-19 are reduced.
Keep your distance. Social distancing when possible is a great preventative step.
Wear a mask. Wearing a mask when possible will reduce the risk of spread.

Ashley successfully defends her dissertation, earning her Ph.D. in Physics.

November 22, 2021 by adavidson38 Leave a Comment

On November 18th, 2021, Ashley Coenen successfully defended her dissertation entitled “Inferring ecological interactions from dynamics in phage-bacteria communities,’’ earning her Ph.D. in physics.

To learn more about Ashley’s dissertation, read the abstract below.

Characterizing how viruses interact with microbial hosts is critical to understanding microbial community structure and function. However, existing methods for quantifying bacteria-phage interactions are not widely applicable to natural communities. First, many bacteria are not culturable, preventing direct experimental testing. Second, “-omics” based methods, while high in accuracy and specificity, have been shown to be extremely low in power. Third, inference methods based on time-series or co-occurrence data, while promising, have for the most part not been rigorously tested. This thesis work focuses on this final category of quantification strategies: inference methods.

In this thesis, we further our understanding of both the potential and limitations of several inference methods, focusing primarily on time-series data with high time resolution. We emphasize the quantification of efficacy by using time-series data from multi-strain bacteria-phage communities with known infection networks. We employ both in silico simulated bacteria-phage communities as well as an in vitro community experiment. We review existing correlation-based inference methods, extend theory and characterize tradeoffs for model-based inference which uses convex optimization, characterize pairwise interactions in a 5×5 virus-microbe community experiment using Markov chain Monte Carlo, and present analytic tools for microbiome time-series analysis when a dynamical model is unknown. Together, these chapters bridge gaps in existing literature in inference of ecological interactions from time-series data.

Graduate student feature: Marian Dominguez-Mirazo

October 29, 2021 by adavidson38 Leave a Comment

Quantitative Biosciences Ph.D. student Marian Dominguez-Mirazo successfully defended her thesis proposal on October 19th, 2021. We are delighted to feature Marian to commemorate her successful defense and progression to Ph.D. candidate.

Originally hailing from Iguala, Guerrero, Mexico, Marian joined the Weitz Group in 2018 after completing a bachelor’s degree in Genomics at the National University of Mexico (UNAM). We asked Marian some questions about her work, her time in the Weitz Group, her advice for the science-minded, and her plans for the future.

Describe your primary research project in 5 words or less.
“How do viruses shape populations?”

What initially interested you in viral ecology/quantitative/theoretical science?
There are very few things I like, but the ones I do like, I like A LOT. I really like viruses cause they are constantly defying our understanding of biology. I also like math a bunch, pretty much since I was a kid. So theoretical virology just made sense as a science path for me.

What three words would you use to describe your time in the Weitz Group?
Challenging, fun, insightful.

What is one thing you wish more people knew about being a scientist?
Science can only exist within society, therefore it is not isolated from social problems.

What are your plans for the future?
I would like to stay in science and travel the world while doing it.

Join Our Group: Ph.D. and Postdoctoral Positions Available

October 28, 2021 by adavidson38 Leave a Comment

Multiple professional opportunities in quantitative viral dynamics research are available in the Weitz Group, including Ph.D. and postdoctoral positions.

Ph.D. Positions

Ph.D. positions are available in quantitative viral dynamics spanning viral ecology (i.e., phage-microbe dynamics) and epidemic dynamics (i.e., SARS-CoV-2 modeling) starting in Aug 2022. The Weitz Group recruits from Ph.D. programs at the Georgia Institute of Technology, including Quantitative Biosciences, Physics, Biological Sciences, Electrical and Computational Engineering, and Bioinformatics. Applicants interested in starting in August 2022 should apply to programs this fall, with some deadlines as early as December 1st. For more information about applying to Ph.D. programs at Georgia Tech, visit grad.gatech.edu.

Postdoctoral Positions

Multiple postdoctoral positions (2+ years) are also available in our group via the School of Biological Sciences at the Georgia Institute of Technology in Atlanta, GA with potential cross-appointment at the Institut de Biologie of the École Normale Supérieure in Paris, France where Prof. Weitz holds the Blaise Pascal Chair. The postdoc positions are in (i) theory and models of viral life-history evolution; (ii) impacts of viral infections on marine microbial population dynamics and ecosystem functioning. In both positions, postdocs will have the opportunity to develop mechanistic, eco-evolutionary models of virus-microbe interactions, connect quantitative model predictions with experimental datasets, and take on leadership roles in international collaborations supported by the Simons Foundation.

Preferences for postdoctoral applicants include: (1) Ph.D. in quantitative biosciences, physics, ecology, evolutionary biology, applied mathematics, or related area; (2) Strong quantitative & computational skills; (3) Excellent communication skills; (4) Interest and experience in model-data integration and some experience in pathogen and/or virus dynamics.

Postdoctoral positions are projected to start approximately March 2022, but the start date is negotiable. Postdoctoral positions include competitive salary, benefits, collaborative opportunities in the USA, France, and Israel, and a travel budget. Screening of applicants will begin immediately and applications will be considered until positions are filled. To apply, e-mail Joshua Weitz (jsweitz @ gatech DOTedu) with a CV, a 1-page cover letter detailing how your research interests are related to the position(s), and include contact information for 3 references.

About Atlanta

Those considering joining the Weitz Group will be based out of Georgia Tech, located in Atlanta, GA in the Midtown neighborhood – a vibrant, urban community. Depending on circumstances, postdocs may also be based at IBENS located in Paris near the Pantheon in the heart of a multidisciplinary research community.

Georgia Tech is a unit of the University System of Georgia and an Affirmative Action/Equal Opportunity Employer.

Paris Sciences et Lettres University to host Winter School Chaired by Prof. Weitz

October 27, 2021 by adavidson38 Leave a Comment

Paris Sciences et Lettres (PSL) University has announced a winter school centered around Quantitative Viral Dynamics Across Scales. The school will run for one week (March 21-25, 2022), and aims to “bring thought leaders in dialogue with the next generation of early-career scientists to advance the integrative study of quantitative viral dynamics across scales.” Prof. Weitz will serve as a lecturer and Scientific Committee Chair. Other guest lecturers include Weitz Group research scientist David Demory, postdoctoral fellow Jacopo Marchi, and several group collaborators.

With 25 slots available in the course, applications for attending the school will be accepted until January 7, 2022. Early-career scientists and Ph.D. students are especially encouraged to apply. See the event poster or visit the QLife website for additional details.