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Alumni Workshop

Group photo from the 2024 National Genomics Education Partnership Faculty Workshop.

2024 National GEP Faculty Workshop

A total of 75 participants (64 GEP faculty members, three staff, three student reconcilers, one student Virtual TA, and four collaborators) participated in the 2024 National GEP Faculty Workshop held at Washington University in St. Louis.

The national workshop allowed GEP members to gather to share their experiences teaching GEP materials, develop new curriculum, work on potential scientific and education research publications, identify future funding avenues, and undergo professional development via keynotes, a lecture, and working groups. 

Steering Committee Working Day

The Steering Committee arrived on June 17 to hold a working day packed with recaps from the prior academic year and the status of GEP grants, identifying future funding mechanisms, Committee-specific planning sessions, and opportunities for informal networking. 

Faculty Workshop

The official workshop kicked off on the evening of June 18 and ran through the midday of June 21. Dr. Emma Farley from UC San Diego and Dr. Mica B. Estrada from UC San Francisco provided keynote talks. There were two sessions of implementation lightning talks and Working Groups. GEP staff member, Katie Sandlin, provided a one-hour lecture on “Long-read Sequencing Technology.” GEP External Evaluator, Dr. Christine Pribbenow (Wisconsin Center for Education Research), provided an Implicit Bias Training called Fair Play

Science Keynote by Dr. Emma Farley - Affinity-optimizing enhancer variants disrupt development

Enhancers control the location and timing of gene expression and harbor the majority of variants associated with phenotypic variation and disease. As such, enhancers provide the instructions for tissue-specific gene expression, development, and cellular integrity. The majority of variants associated with phenotypic variation, evolutionary adaptations, and disease are thought to lie within enhancers. Yet, pinpointing causal enhancer variants from the sea of inert variants is a major challenge. Transcription factors bind to sites within the enhancers to regulate the timing and location of gene expression. Despite decades of study, how enhancers encode tissue-specific activity and the mechanisms by which single nucleotide variants (SNVs) alter phenotypes are poorly understood. I will discuss our work to pinpoint and predict what changes within enhancers lead to phenotypic changes across different species, including the heart of the marine invertebrate Ciona robust and the mouse and human limb. We discover that many enhancers contain suboptimal affinity binding sites (also known as low-affinity sites). Strikingly, we find that single nucleotide changes that increase the affinity of these sites, even slightly, cause organismal-level phenotypes such as extra digits or a second beating heart. Genomic analysis of many enhancers illustrates affinity optimizing SNVs lead to gain of function gene expression across a variety of cell types and enhancers. Our studies illustrate that the prevalence of suboptimal affinity binding sites in enhancers creates a vulnerability within genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs within genomes provides a generalizable approach to identify causal variants that underlie enhanceropathies.

Emma Farley providing introduction to her talk on how "Affinity-optimizing enhancer variants disrupt development"
Dr. Emma Farley providing introduction to her talk

Diversity, Equity, and Inclusion Keynote by Dr. Mica B. Estrada – Creating pathways of kindness and inclusion in STEM education

An ongoing tension exists between breaking apart and coming together that happens at every level of the biosphere, including among people. STEM education has historically focused on providing knowledge to integrate people into an academic community. Data shows that not all people became equally integrated into this academic community. With all this in mind, Dr. Estrada will describe findings from her research program in which she longitudinally tracks and examines what types of mentorship, experiences and supports are more likely to result in students integrating into their professional fields and persisting in STEM career pathways. She will describe findings regarding persons historically excluded because of ethnicity and race. Further, she will talk about how institutional policies and climate that provide kindness cues that affirm social inclusion may impact the integration experience for historically underrepresented college students, faculty and administrators in STEM training and professional settings.

Extra Working Day

All GEP faculty members were welcome to stay for an extra Committee Working Day. The day began with a Field Trip to one of many locations across the city of St. Louis. The only requirement was willingness to contribute to the project for one of the Working Groups organized by the GEP Committees. The extra Committee Working Day ran midday June 21 through midday June 22. 

Four GEP faculty pose in front of the Gateway Arch
Group Photo of 2023 National GEP Faculty Workshop attendees

2023 National GEP Faculty Workshop

A total of 87 participants (78 GEP faculty members, three staff, two Virtual TAs, and four collaborators) participated in the 2023 National GEP Faculty Workshop (formerly called Alumni Workshop) held at Washington University in St. Louis. This was the first time the Partnership was able to meet in-person for the annual event since 2019. 

The national workshop allowed GEP members to gather to share their experiences teaching GEP materials, develop new curriculum, and work on potential scientific and education research publications including future funding avenues.

Throughout the Workshop, many folks continued to mention how different it was to be able to gather in person rather than virtually on Zoom. Initially it almost felt as if we were meeting each other for the first time rather than having worked closely for several years. Many folks were surprisingly taller or younger (we agreed that Zoom ages us). 

Steering Committee Working Day

The Steering Committee arrived on June 5th to hold a working day packed with recaps from the prior academic year, the current status of GEP grants, Committee-specific planning sessions for final preparations of Working Groups, and opportunities for informal networking. 

Faculty Workshop

The official workshop kicked off on the evening of June 6 and ran through midday of June 9. Professor Jef D. Boeke from NYU Langone Health and Professor Erin Dolan from the University of Georgia provided keynote talks. There were four sessions of implementation lightning talks and three sessions of Working Groups.

Science Keynote - Transposable elements: part of the dark matter of the genome

Keynote Jef D Boeke PhD Talk is on Transposable elements: part of the dark matter of the genome At 2pm in Rebstock 215 Dr. Boeke is a Professor in the Department of Biochemistry and Molecular Pharmacology at NYU Grossman School of Medicine and the Sol and Judith Bergstein Director of the Institute of System Genetics

Dr. Jef D. Boeke provided the scientific research keynote talk in which he shared his expertise on genome engineering and transposable elements. His keynote presentation on the Dark Matter Project (e.g., creating a humanized mouse model of ACE2 to study the pathology of COVID-19), and on the mutations induced by LINE-1 retrotransposons that drive human evolution (e.g., loss of the tail) were fascinating.

We also appreciated Dr. Boeke’s insights on the best way to incorporate transposons into the introductory biology curriculum. The Working Group K discussions provided members with several ideas on how students can use the Genome Browser to investigate transposons in the human genome — such as examining transposon insertions found in a subset of the human population, and investigating genes (e.g., Hox genes) that have low transposon density.

Lastly, Dr. Boeke shared his experiences (and the challenges) associated with his botanical expedition to the tropical Andes Mountains in the 1970s. We look forward to continuing our collaboration with him on the transposon curriculum, and to explore potential ways to incorporate genome engineering (e.g., “humanize” a section of the mouse genome) into the GEP curriculum.

Education Keynote - What Makes CUREs “Work?” Insights from experience sampling and instructor talk

Keynote Erin L Dolan PhD Talk is on What Makes CUREs “Work?” Insights from experience sampling and instructor talk At 1:15pm in Rebstock 215 Dr. Dolan is a Professor, Biochemistry & Molecular Biology at University of Georgia and the Georgia Athletic Association Professor of Innovative Science Education

Most of Dr. Dolan’s data hasn’t yet been published. We respect her wishes to avoid sharing any of it until she has a chance to publish pre-prints this coming academic year.

Extra Working Day

All GEP faculty members were welcome to stay for an extra Committee Working Day. The only requirement was willingness to contribute to the project for one of the Working Groups organized by the GEP Committees. The extra Committee Working Day ran midday June 9 through midday June 10. 

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GEP 2021 Alumni Faculty Workshop

The 2021 Alumni Workshop of the Genomics Education Partnership was held June 12-13 and followed a week of one-hour Pre-Workshop events. Over 125 GEP faculty members took part in the online proceedings. GEP Program Director, Dr. Laura Reed, launched the Pre-Workshop events with a “State of the Union” address by outlining GEP’s accomplishments over the 2020/2021 academic year, including the addition of 75 new members (25% increase in membership and 27% increase in institutions). Laura also touched on how the GEP had successfully adapted to remote-learning challenges by establishing an online network of virtual TAs who provided invaluable assistance to GEP students and faculty alike. A highlight of the conference was hearing from lead TA Leon Laskowski regarding the overwhelmingly positive response to the virtual TA network. Equally effective were the ever-popular “implementation lightning talks” – fast-paced, succinct overviews of how faculty have incorporated the GEP curriculum over the past academic year.

The GEP was honored to have Drs. Christopher Miller and Ting Wang, both from Washington University School of Medicine, present illuminating professional development talks on genomics research. Dr. Miller described cutting-edge clinical approaches to treating cancer via personalized genomic medicine, while Dr. Wang presented a fascinating overview of transposable elements and epigenome evolution. Both talks engendered lively discussion among the faculty and were rated as a highlight of the conference.

In addition to learning about cutting-edge genomics research, faculty members were able to actively invest their own knowledge and experience into program projects by taking part in numerous Working Groups based on their areas of interest and expertise. The Working Group format truly allows faculty to engage in the inner workings of the partnership and creates ownership as members participate in collaborative discussions, outline practical next steps, and report back to the faculty body at large with actionable goals and deliverables.

After an extremely challenging year of navigating the challenges of online instruction, many GEP faculty wistfully reminisced about bygone days of reconnecting face-to-face and enjoying the camaraderie and networking that only in-person meetings can offer. However, as Dr. Reed reminded us, we look forward to “next year in St. Louis” and walk away from yet another online event with a renewed sense of resolve and commitment to our shared community.