This summer, Joshua Weitz, a professor with the School of Biological Sciences who is also the founding director of the Quantitative Biosciences Interdisciplinary Graduate Program (QBioS), organized a “Hands-On Modeling Virtual Workshop” focusing on epidemics.

The Weitz Group at Georgia Tech has created various models and figures to help explain the spread and epidemiology of Covid-19. Weitz has frequently shared his findings with local and national media outlets.

This year marked the fourth annual “Quantitative Biosciences Hands-On Modeling Workshop”. Due to Covid-19, the summer 2020 event was held virtually. Focused on the basics of epidemic modeling, the workshop was joined by more than 50 online attendees from around the globe.

Weitz delivered two lectures on epidemic theory and the latest Covid-19 research. In addition, ten QBioS students, two post-doctoral scientists from the Weitz group (David Demory and Stephen Beckett), and one external post-doctoral scientist (Bradford Taylor) served as instructors for small group sessions, focusing on the hands-on experience of coding deterministic and stochastic models to predict the spread of epidemics.

The QBioS Ph.D. student organizers collected surveys following the event, which provided feedback on both the content and format of the workshop. Some examples:

“The flow of the workshop is great. Learning introductory concepts to start, the ability to apply some of them with hands-on, and then finishing with applications and extensions. Having many participants from many backgrounds adds a lot to the small group sessions as well.”

“I thought it was a great workshop to get core concepts across. I think the online format was done as best as possible and appreciated the thoughtful instructors.”

Weitz and Pablo Bravo, a second year QBioS Ph.D. student in Quantitative Biosciences, share thoughts on how they ran the virtual workshop — along with ideas and advice for those looking to host similar online workshops:

What were the biggest lessons learned from your summer workshop?

Weitz: The survey results communicated two important lessons. First, positive
responses to the workshop structure reinforce just how critical it is to contextualize modeling in terms of a key biological challenge. Providing a biological scaffold helps to focus student work and keep their interest and attention on the technical material. The second lesson is that there is an adaptation period to hands-on learning online. We intentionally spaced out the coding sessions with a mid-day break and most of the issues appeared in the morning as students and instructors adjusted to their group's dynamic, including debugging code while in different locations, and indeed, countries.

Bravo: One aspect that made the workshop possible was the participation of many members in different roles: coordinators, advertising, lecturers, instructors, IT support.  Planning and working early as a team were essential.

What were the biggest challenges you had to overcome?

Bravo: There were two main problems that we had to solve. First, we offered support for three programming languages (MATLAB, Python, R), and given the high number of registrations, the first year QBioS cohort couldn't handle all of them. Members of the QBioS community, current and past members of the Weitz group stepped in and helped us in leading activity groups. It wouldn't have been possible without them!

Also, debugging was an issue. Debugging scripts over video calls was extremely difficult. Attendees were not keen on screen-sharing their code at the beginning, but as they got to know each other, this stopped being an issue. Delay between the video and audio feed remained an issue throughout the whole workshop.

What’s the one takeaway you want to stress to instructors looking to offer similar webinars and online workshops?

Weitz: Overall, we are optimistic about our ability to continue to develop and implement innovative teaching strategies in QBioS — but remain realistic that adjustment periods will be needed to foster an atmosphere conducive to small group learning when groups are dispersed.

Bravo: I think the biggest factor in the success of the workshop is that it was centered around interactive activity sessions, in which five students and an instructor would go through the material and write the scripts together. This promoted both active learning and discussion between the attendees, and also allowed attendees to follow up with questions and comments to their respective instructors ­­— even days after the workshop finalized.

This summer, Joshua Weitz, a professor with the School of Biological Sciences who is also the founding director of the Quantitative Biosciences Interdisciplinary Graduate Program (QBioS), organized a “Hands-On Modeling Virtual Workshop” focusing on epidemics.

The Weitz Group at Georgia Tech has created various models and figures to help explain the spread and epidemiology of Covid-19. Weitz has frequently shared his findings with local and national media outlets.

This year marked the fourth annual “Quantitative Biosciences Hands-On Modeling Workshop”. Due to Covid-19, the summer 2020 event was held virtually. Focused on the basics of epidemic modeling, the workshop was joined by more than 50 online attendees from around the globe.

Weitz delivered two lectures on epidemic theory and the latest Covid-19 research. In addition, ten QBioS students, two post-doctoral scientists from the Weitz group (David Demory and Stephen Beckett), and one external post-doctoral scientist (Bradford Taylor) served as instructors for small group sessions, focusing on the hands-on experience of coding deterministic and stochastic models to predict the spread of epidemics.

The QBioS Ph.D. student organizers collected surveys following the event, which provided feedback on both the content and format of the workshop. Some examples:

“The flow of the workshop is great. Learning introductory concepts to start, the ability to apply some of them with hands-on, and then finishing with applications and extensions. Having many participants from many backgrounds adds a lot to the small group sessions as well.”

“I thought it was a great workshop to get core concepts across. I think the online format was done as best as possible and appreciated the thoughtful instructors.”

Weitz and Pablo Bravo, a second year QBioS Ph.D. student in Quantitative Biosciences, share thoughts on how they ran the virtual workshop — along with ideas and advice for those looking to host similar online workshops:

What were the biggest lessons learned from your summer workshop?

Weitz: The survey results communicated two important lessons. First, positive
responses to the workshop structure reinforce just how critical it is to contextualize modeling in terms of a key biological challenge. Providing a biological scaffold helps to focus student work and keep their interest and attention on the technical material. The second lesson is that there is an adaptation period to hands-on learning online. We intentionally spaced out the coding sessions with a mid-day break and most of the issues appeared in the morning as students and instructors adjusted to their group's dynamic, including debugging code while in different locations, and indeed, countries.

Bravo: One aspect that made the workshop possible was the participation of many members in different roles: coordinators, advertising, lecturers, instructors, IT support.  Planning and working early as a team were essential.

What were the biggest challenges you had to overcome?

Bravo: There were two main problems that we had to solve. First, we offered support for three programming languages (MATLAB, Python, R), and given the high number of registrations, the first year QBioS cohort couldn't handle all of them. Members of the QBioS community, current and past members of the Weitz group stepped in and helped us in leading activity groups. It wouldn't have been possible without them!

Also, debugging was an issue. Debugging scripts over video calls was extremely difficult. Attendees were not keen on screen-sharing their code at the beginning, but as they got to know each other, this stopped being an issue. Delay between the video and audio feed remained an issue throughout the whole workshop.

What’s the one takeaway you want to stress to instructors looking to offer similar webinars and online workshops?

Weitz: Overall, we are optimistic about our ability to continue to develop and implement innovative teaching strategies in QBioS — but remain realistic that adjustment periods will be needed to foster an atmosphere conducive to small group learning when groups are dispersed.

Bravo: I think the biggest factor in the success of the workshop is that it was centered around interactive activity sessions, in which five students and an instructor would go through the material and write the scripts together. This promoted both active learning and discussion between the attendees, and also allowed attendees to follow up with questions and comments to their respective instructors ­­— even days after the workshop finalized.

Ribonucleotides, units of RNA that can become rooted in DNA during processes such as replication and repair, generally are associated with genomic instability, an increase in mutations, and DNA fragility.

Researchers have been aware of the abundance of ribonucleotides for about a decade, and the lab of Francesca Storici at the Georgia Institute of Technology has been at the forefront, researching the relationship between RNA and DNA in genome stability and instability, and DNA modification. 

“There is much that is unknown about the phenomenon of ribonucleotides in DNA, andit needs to be uncovered,” says Storici, professor in the School of Biological Sciences and a researcher in the Petit Institute of Bioengineering and Bioscience at Georgia Tech, where her lab’s previous studies have led to the development of new-age tools and techniques, to collect and analyze data and answer some of the questions surrounding ribonucleotides.

“It’s important to establish a framework for better directing future studies to uncover physiological roles of ribonucleotides in DNA,” she says. And that’s exactly what she and her colleagues have done in their latest research paper, “Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine,” published recently in the journal Nature Communications.

Namely, they use the tools and techniques they’ve developed over the past few years to characterize sites of ribonucleotide incorporation in DNA, demonstrating clearly that ribonucleotides in yeast DNA are not randomly distributed but show preferences for being incorporated in specific DNA sequence contexts. “We specifically reveal a bias for ribonucleotide incorporation both in yeast mitochondrial and nuclear DNA,” Storici says.

In a previous study published in January 2015, the lab introduced ribose-seq, a high-throughput sequencing technique that allows researchers to establish a full profile of ribonucleotides embedded in genomic DNA, generating large, complex data sets. In late 2018, the lab published its work on a new bioinformatics toolkit called Ribose-Map, which effectively and efficiently transforms the massive amounts of raw sequencing data obtained from the ribose-seq process into summary datasets and publication-ready results.

For their latest work described in Nature Communications, the team deployed ribose-seq to generate the data and Ribose-Map to analyze it, identifying sites of ribonucleotides in yeast DNA and explore their genome-wide distribution. Consequently, the paper’s four co-lead authors included Sathya Balachander (part of the ribose-seq development team and co-author of that paper, now licensing associate for the Bill Harbert Institute for Innovation and Entrepreneurship/University of Alabama-Birmingham) and Alli Gombolay (lead author of the Ribose-Map study).

Contributing equally as co-lead authors of the new research were Taehwan Yang and Penghao Xu, who, like Gombolay, are Ph.D. students in Storici’s lab (where Balachander was a Ph.D. student and postdoctoral researcher).

The team studied three different yeast species and detected a number of similar patterns. In all three species, the deoxyribonucleotide that is immediately upstream of the ribonucleotide was shown to have the greatest impact on the incorporation of ribonucleotides in DNA. “This rule was not clear before,” Storici says. “The study also highlights hotspots of ribonucleotides in DNA sequences containing di- and tri-nucleotide repeats, showing that specific sequence contexts have higher likelihood of ribonucleotide incorporation in DNA. This might be associated with ribonucleotide physiological/pathological functions that are yet to be discovered.”

The lab is now working toward better understanding of how cells control and benefit from ribonucleotide incorporation in DNA by uncovering the patterns and hotspots of incorporation in yeast cells of different genotypes, as well as cells from other species and organisms.

“Now we are interested to see if the rule that we have discovered for yeast applies to other cell types beyond yeast, like human cells for example, and to what extent,” says Storici. “As long term goal, we aim to determine whether there is a sort of language of ribonucleotide incorporation that cells utilize for regulating different cell metabolic functions.”

In addition to those mentioned, other authors of this multi-institutional study were Fredrik Vannberg (former professor in the School of Biological Sciences at Georgia Tech and former Petit Institute researcher), Gary Newnam (manager of the Storici Lab), Anton Bryksin (director of the Petit Institute’s Molecular Evolution Core), Havva Keskin (former Storici grad student, now a researcher with Omega Bio-tek), Kyung Duk Koh (former member of Storici lab, now a researcher at the University of California-San Francisco),  Waleed M. M. El-Sayed (former visiting scholar in the Storici’s lab, now researcher at the National Institute of Oceanography and Fisheries in Egypt), and Sijia Tao, Nicole Bowen, Raymond Schinazi, and Baek Kim from the Emory School of Medicine’s Department of Pediatrics.