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Regional Node Meeting

GEP Regional Node Meeting Virtual

Puerto Rico Regional Node Meeting – February 6 & 8, 2024

On the 6th and the 8th of February of 2024, the Puerto Rico Regional Node had a two-day Pathways Project training with Dr. Laura Reed. Node members met through Zoom each day from 4:30 to 6:00 pm AST (2:30 to 4:00 pm CST). Ten (10) GEP faculty and one (1) undergraduate student participated in the three-hour online training. 

As part of their GEP onboarding, all Puerto Rico Node members have been trained in the F Element annotation methodology. However, few have worked with other GEP Projects. During the 2023 Faculty Workshop, attending Node members expressed an interest in professional development activities that would help them acquire the knowledge and skills necessary to participate in other GEP research activities. A Pathways Project training was identified as a logical next step towards achieving this goal. 

The first session started with an overview of the overarching research questions, implementation ideas and an introduction to the project walkthrough. The second session covered topics such as common annotation mistakes, project claiming and submission protocols, managing report forms, and an overview of the microPublication pipeline. It also offered an opportunity to ask general questions and learn about different Pathways support initiatives. Members of the Puerto Rico Node have a special interest in the Pathways and Puerto Rican Parrot Projects and this training provided valuable knowledge and methodological insights that will serve them well as they venture (with their students) into other GEP annotation projects.

The Puerto Rico Node thanks Pathways Project Leader, Laura Reed, for setting time aside to train the Node members. A special thanks to the Regional Node Director and Co-Director, Melinda Yang and Jenni Kennell for answering many questions, sending helpful follow-up messages, and making sure the Node Leaders had the resources necessary to organize the training. Thanks to Sarah Potts for supporting the event registration, facilitating access to training materials and managing Zoom channel logistics. The planning of the training was a collaborative effort of the Node Leader and Co-Leader, Ángel O Custodio and Sheylda Díaz.

What worked well for your event that might help others plan similar events?

We had an online event during weekdays. This activity didn’t require organizing a venue or having people travel to the meeting location. It served our purpose well. Also, scheduling the training on a date removed from the beginning of the semester promoted faculty participation.

What lessons were learned from challenges in the planning or execution of the event?

Communicate often with headquarters or the Regional Node Directors before sending information to Node members. Also, remember that the Central Office will give the Node support with registrations and surveys.

What would your Node do differently based on your experiences?

Node leaders will write emails to headquarters more often to make sure they are not duplicating efforts doing some transactions that the Central Office can handle with ease. Also, they will set up a local checklist that will help plan and follow-up on certain tasks.

GEP Regional Node Meeting Virtual

Midwest Regional Node Meeting – February 1, 2024

The Midwest Regional Node held an online, professional development meeting for faculty on February 1st from 7-8:30 pm CST. The planning of the meeting was a collaborative effort of the Node, with special thanks to Node Leader Dr. Jenny Mierisch for taking a primary role in organization and participant recruitment. Nine current members of the Midwest Node attended, four of whom presented on different pieces or uses of curriculum. The schedule for the meeting was:

  • 7:00-7:20 pm Intro to HIV Curriculum by Don Paetkau
  • 7:20-7:35 pm Development of AI-Focused Curriculum by Ken Luzynski 
  • 7:40-8:10 pm Using R in the Classroom by Sarah Justice and Ken Saville
  • 8:10-8:30 pm Time for Socializing and Node Event Planning


Topics for these sessions were proposed both at the Node’s in-person fall meeting as well as a planning session that occurred in November as areas of interest to Node members. Presentations included faculty walking participants through the curriculum as well as discussions of how faculty have integrated these curricula in different classes. For anyone who is interested, a recording of the meeting and materials from the session can be found on the Midwest Node’s Trello card and in the associated Google Drive folder.

In addition to the sessions themselves, the last bit of time was used to discuss an upcoming student-focused virtual event the Node will be hosting in April.

What worked well for your event that might help others plan similar events?

Gathering contributions from Node members of what would be topics of interest as well as having different faculty present on interesting pieces of curriculum that aren’t traditional GEP materials.

What would your Node do differently based on your experiences?

Maybe consider a different time or recruit harder. 

Northeast Regional Node Meeting participants group photo

New England Regional Node Meeting – January 4-5, 2024

Eight faculty members, one staff member/TA, and seven students of the New England Regional Node gathered together at Siena College in Loudonville, NY on January 4-5, 2024 for an exciting two-day conference. Dr. Brittany Miller and Dr. Tom Giarla gave upper level course implementation talks entitled, “Using GEP Annotation Projects as a Launching Point for More Advanced Bioinformatics” and “Piloting the ZAD-ZNF Gene Family Evolution Project,” respectively. Dr. Rachel Sterne-Marr led a training session, “Wasp Venom Gene Annotation” and GEP TA and staff member, Logan Cohen, engaged us in a discussion, “Why students make mistakes: the underlying concepts behind common errors.” Five students from the Pathways Project presented in a lively poster session. 
Brittany Miller posing before beginning her talk entitled Using GEP annotation projects as a launching point in an advanced bioinformatics course
Rachel Sterne-Marr providing talk on PPT slide entitled Challenges: Incomplete Transcript Examples
  • Kate Putnam (Siena College, Giarla lab), presented “Akt and srl Genes.”
  • Forrest Veilleux (Franklin Pierce University, Page lab) presented “Glycogen Synthase in D. bipectinata: How Fruit Flies Store Their Sugar.” 
  • Caleb Casey (Siena College, Tom Giarla’s Genomics and Bioinformatics course) enlightened us on “Discovery of a Putative Paralog to wat in Drosophila willistoni.”
  • Chris Shulman (Siena College, Biochemistry course) gave a progress report on the wet lab wasp CURE (a collaboration with Lindsey Long, Marisol Santisteban and Nate Mortimer) in a poster entitled “Role of Glycolytic Enzymes in Parasitoid Wasp Infection of Drosophila: Heterologous Expression of Three Wasp Venom Pyruvate Kinases.” 
  • Tommy Anderson (Siena College, Sterne-Marr lab in collaboration with Nate Mortimer, Oregon State University) shared novel images from the SUNY Albany timsTOF MALDI instrument in a poster entitled, “Using Classical Histology and Mass Spectrometry Imaging to Study Parasitoid Wasp Infection of Drosophila Larvae.”
Members of the New England Node have a long-standing interest in learning R for their courses and research projects. The two final sessions, “An Introduction to R: Data Import, Simple Statistics, and Plotting” presented by Tom Giarla, and “Differential Gene Expression in R: Walkthrough of Primary Component Analysis and Volcano Plots” presented by Shallee Page, accomplished an important first step in getting the Node members comfortable working in the R environment and being exposed to very common uses of R for life scientists.
Shallee Page providing a talk on using R

Special thanks to all our presenters and other participants for making this meeting highly successful! Thanks to Melinda Yang and Jenni Kennel, the Regional Node Director and Co-Director, for perfectly scheduling the planning benchmarks. Thanks to Sarah Potts for taking care of financial logistics allowing us to focus on the meeting itself. Thanks to student participant Isaiah Korostil (Siena College) for facilitating during the R workshops. Rachel Sterne-Marr, Tom Giarla, Daron Barnard, and Evan Merkhofer all contributed to making this meeting actually happen.

What worked well for your event that might help others plan similar events?

The timeframe that was set up by Melinda Yang, the Regional Node Director, was perfect for prodding us to complete the various steps in a timely manner. Working with Sarah Potts to take care of financial logistics was such a relief. We are lucky in having two GEP members at our institution so the organizer had help in making decisions and on-the-spot problem solving (no lighting in the room we were having dinner!).

What would your Node do differently based on your experiences?

Have a detailed checklist for the week before the event to include name tags, poster boards, clips, maps, uploading presentations, and confirming times with caterers.

GEP Regional Node Meeting Virtual

Southeast Regional Node Meeting – November 17, 2023

On November 17, 2023, the Southeast Regional Node faculty and students came together for the Fall 2023 Virtual Symposium to highlight excellent student research in gene annotations of F-element and Pathways Projects. In addition, we were very fortunate to have as a keynote speaker Jason Williams of the Cold Spring Harbor Laboratory DNA Learning Center, where he gave some valuable insight into how his career came about in terms of computational biology, bioinformatics, and skills-based instruction and pedagogy with high school and college students. Jason Williams is also the founder of Life Science Trainers, as per a Hudson Alpha article. 

Many thanks to everyone for spending their Friday with us to share their work and ideas, we are looking forward to future virtual symposium events for more excellence.

What worked well for your event that might help others plan similar events?

Zoom was used to facilitate the event. Two breakout rooms were set up and students were assigned to one or the other. The schedule was sent out a day or two ahead of time, so that the students knew which breakout room they would be presenting in. Each breakout room was locally recorded and is available to watch on Box (contact Sarah Crocker-Buta for access).

What would your Node do differently based on your experiences?

It remains difficult to limit student presentations and Q&A to 5 minutes because of unexpected computer issues. In the future, Node organizers might need to consider having a moderator receive all presentations and share it on a working laptop for each speaker, in order to mitigate the technical difficulties. One breakout room had finished their presentations approximately 15 minutes before the other, which resulted in the guest speaker waiting in the main room for a period of time before the breakout rooms were closed. It was definitely a learning experience. 

Zoom meeting screenshot of six participants

DMV Regional Node Meeting – October 21, 2023

The D.C., Maryland, and Virginia (DMV) Regional Node held a faculty-focused professional development event on Oct 21, 2023. In this virtual workshop, faculty from our Node spent a half day having quality discussions about curriculum and pedagogy. Specifically, we walked through a curriculum developed by Dr. Rivka Glaser related to analysis of conserved domains. Portions of this curriculum were designed for intro level students, while others were designed for advanced students. This led to a conversation about course design for students at different levels. These active, hands-on discussions were capped off with a short planning discussion about things our Node would like to achieve in the coming year.

All participating Node members had a hand in planning the event, but special thanks goes to Dr. Rivka Glaser for sharing her curriculum, Dr. Christy Fleet for helping to refine our schedule and guiding questions for pedagogy discussion, Dr. Matt Wawersik as Node Leader and lead organizer for the workshop, and Sarah Crocker-Buta, Dr. Melinda Yang and Dr. Norma Velazquez for additional help with event planning. 

What worked well for your event that might help others plan similar events?

Node organizers began planning well ahead of time. This allowed discussion on what the faculty really wanted to talk about, and adaptation of the schedule so that the event could be pulled off. It also allowed for distribution of the workload. 

What would your Node do differently based on your experiences?

Not much differently for this event, even though it would have been nice to have more satellite Node members show up. This didn’t happen even after some individual contacts, and it made for a high quality and fun discussion with core members. For the future, regular events with a smaller/active group might feel repetitive if done without students, so alternating years with an in-person event with undergrads participating, and then faculty focused events the next year is a good plan. For faculty focused events, Node leaders might consider inviting another Node and have a multi-Node event to get insight from GEP members outside our Node.

GEP Regional Node Meeting Virtual

Pacific Northwest Regional Node Meeting – November 4, 2023

The Pacific Northwest (PNW) Regional Node had a successful virtual event on November 4th, organized by Dr. Norma Velazquez and Dr. Jack Vincent, Leader and Co-Leader of the PNW Node. Five current GEP faculty, 4 graduate students, and 10 undergraduates attended the event. We had 5 student talks on the F-Element and Pathways research projects. The talks were given by current undergraduates and recent graduates from Linfield University, Southern Oregon University, the University of Washington-Tacoma, and the University of the Fraser Valley, which is a great representation for the small Node that we are. 

The second part of the event was a graduate school panel, which started with an engaging introduction on graduate school myths by Dr. Nate Mortimer, from Oregon State University, followed by unstructured conversations between graduate students and undergraduate attendees. While the students talked, faculty moved to a breakout room to discuss implementation challenges and brainstorm solutions. We all reconvened in the main Zoom room at the end of the event to close the event and thank everyone for their participation.

What worked well for your event that might help others plan similar events?

The students gave great oral presentations and there were questions after each one. The presentations were bundled by research project topic (Pathways vs. F-Element), so there were similarities in the presentations according to topic. Yet, the several Pathway presentations all had their own focus on different aspects of the project, so they did not feel repetitive.

What would your Node do differently based on your experiences?

There needed to be at least 30 minutes more for the event. There ended up being  more student presentations than originally thought, which complicated the final scheduling. Getting a better idea about who will present before deciding the duration of the event would be helpful next time. The other way would be to cap the number of presentations, but it’s always great to have more students present and adjust the time as needed.

Two students present their work on the gene annotation of Myc gene in D. suzukii and D. bipectinata

Midwest North Regional Node Meeting – September 16-17, 2023

The Midwest North Regional Node held its third in-person meeting at Loyola University Chicago on September 16-17, 2023. This meeting included 16 GEP Midwest Node faculty, 8 undergraduate students, a prospective GEP faculty member, and two keynote speakers: Dr. Sara Lipshutz (Duke University) and Dr. Alondra Diaz Lamerio (University of Puerto Rico-Mayaguez), who joined us virtually via Zoom.

The two day event included research talks from both the faculty and undergraduates, as well as panel discussions around curriculum and implementation.

The keynote presentation from Dr. Alondra Diaz Lamerio focused on the new Puerto Rican Parrot Project and was followed by a walkthrough of the related curriculum, led by Dr. Don Paetkau (Saint Mary’s College). The keynote presentation from Dr. Sara Lipshutz focused on the use of genomics to explore female aggression in birds. The meeting wrapped up with a planning session for future Midwest North Regional Node events.

What worked well for your event that might help others plan similar events?

There was a mix of events that included presentations, opportunities for talking about curriculum, and learning about new curricula (such as the Puerto Rican Parrot Project). This encouraged discussion over meals. It was also very helpful that Dr. Jennifer Mierisch’s (event organizer; Loyola University Chicago) department assisted with room reservations, which was made possible because students from the university were included in the event.

What would your Node do differently based on your experiences?

Recently, the Midwest North and Midwest South Regional Nodes were combined into a single Midwest Node, making the geographical area that the Node encompasses even larger. The Node leaders feel that it is good to continue having the meeting location move around the Node, as the Node covers a large geographical area, in an effort to promote more faculty participation over time. 

Group photo of student participants

DMV Regional Node Meeting – September 17-18, 2022

The GEP’s D.C., Maryland, and Virginia (DMV) Regional Node held its Fall 2022 Regional Node Meeting on Saturday, Sept 17th at the University of Richmond. A total of 30 engaged students and faculty participated, in our full day in-person event, from the following schools: Catholic University, Radford University, Community College of Baltimore County, Stevenson University, Emory & Henry College, William & Mary, and the University of Richmond. 
Faculty from three GEP projects were represented (i.e., F Element, Pathways, and Parasitoid Wasps), and undergraduate students had the opportunity to share results and lessons learned from their GEP annotation projects conducted through GEP Course-based Undergraduate Research Experiences (CUREs). Emily Oh, a student reconciler at Washington University in St. Louis, joined us to give a virtual talk about the “Next Steps in Gene Annotation.” There were afternoon sessions where students and faculty reviewed GEP curriculum, and then research talks by faculty. The event then retired to Bryan Park to bond over BBQ and lawn games. A Sunday morning hike at Belle Isle with faculty and friends helped further build the community; most of whom were meeting for the first time in person! This couldn’t have been done without a great group of motivated students and faculty brought together by the common cause of the GEP!!!

What worked well for your event that might help others plan similar events?

General organization was good, with a morning session that included student talks preceded by a short faculty intro of the different projects. After lunch, there was a working group to examine the curriculum, and then the event concluded with short faculty research talks about other work that might not be GEP related. The morning session worked particularly well. For this, 3 GEP projects were represented by faculty, so it was great to hear about them, and the student experiences. This session was capped off by a virtual talk about next steps in annotation from Emily Oh. She’s an undergrad who has worked on F-element reconciliation, and showed some specific data related to repeat elements. Ending with this talk provided a great perspective to understand what happens to submitted projects after they leave our hands.

What would your Node do differently based on your experiences?

The Node event organizers wouldn’t change a thing from the morning session, though not sure there should be such a student focused event every year. The afternoon sessions were a bit crunched for time, which caused the event to run behind and shorten breaks a bit more than was ideal. There also wasn’t much time as a faculty to meet and discuss curriculum as hoped. For the future, the Node Leader would like to expand time spent on a curriculum hack-a-thon by faculty. 

group photo at dinner of GEP members in attendance

MN/IA/Dakotas Regional Node Meeting – April 21, 2023

The Minnesota, Iowa, and Dakotas Regional Node held the GEP’s first, and largest, NIH-funded Regional Node Genomics Research Symposium in Saint Paul, MN, at Saint Catherine University, on April 21st, 2023. This was completely an in person event. The meeting was organized by Dr. Kellie Agrimson with support from Dr. Paula Croonquist and Dr. Andy Arsham.

The 80 attendees included 20 faculty, 1 postdoc, 1 postbac, 1 graduate student and 55 undergraduates from 10 institutions (Anoka Ramsey Community College, Bemidji State University, Crown College, Macalester College, Minneapolis Community and Technical College, Normandale Community College, North Hennepin Community College, Saint Catherine University, University of Minnesota, and Wartburg College).

The Genomics Research Symposium Included:

Adapting GEP Tools to Study Gene Family Evolution Across Insecta” guest speaker: Dr. Andy Arsham, Assistant Professor of Biology, Bemidji State University

Student Workshop - Research Experience Search

Genomics of a Partnership: Exploring the Lichen Symbiosis” guest speaker: Dr. Tami McDonald, Associate Professor of Biology, Saint Catherine University

Searching for a Genetic Basis to Feeding & Sleeping Behaviors in Cavefish” guest speaker: Dr. Emilie Richards, NIH IRACDA Postdoctoral Fellow, University of Minnesota

Student Poster Presentations

Computational Techniques and Tools to Improve Genetic Testing in the Clinic” guest speaker: Dr. Getiria Onsongo, Assistant Professor of Computer Science, Macalester College

Student Workshop – CV Design

Transcriptional Regulation by the Polycomb Repressive Complex 1.1 in Placental Development” guest speaker: Dr. Micah Gearhart, Research Assistant Professor, University of Minnesota

What worked well for your event that might help others plan similar events?

Having short (20-30 min) research talks throughout the day seemed to be a highlight.

Student presenting on Divergence of Species in the Insulin/TOR Pathway

TX/OK Regional Node Meeting – July 21, 2023

The Texas and Oklahoma Regional Node held their first in-person Regional Node Meeting at the University of Texas at Austin on July 21, 2023. The meeting was organized by several Node members, including Node Leader Dr. Lindsey Long (Oklahoma Christian University). Attendees included 8 GEP faculty and 9 GEP students. Seven Universities/Colleges across Texas and Oklahoma were represented at the meeting including: University of Houston-Clear Lake, East Central University, Texas Wesleyan University, University of Texas San Antonio, St. Mary’s University, Oklahoma Christian University, and University of Texas at Austin. 

The morning session included training on the GEP R curriculum by Dr. Nolan Bentley (University of Texas at Austin) and research lightning talks by the GEP students. Additionally, Dr. Tom Juenger from UT Austin talked to the group about his research and how he uses it as a CURE project for several undergraduate students. While the students visited the Wonderspaces immersive and interactive art museum together in the afternoon, the faculty continued the meeting which included updates about the Parasitoid Wasps wet lab project and the National GEP meeting. Several faculty also gave implementation talks where there was valuable sharing of ideas and feedback. Finally, the group ate supper together at True Food Kitchen in downtown Austin before returning home.

What worked well for your event that might help others plan similar events?

The registration process was very smooth and the involvement with the students was great. They were included for the professional development portion, the guest speaker, and they gave lightning talks about their research. In the afternoon, they went as a group to the museum which helped with the community building aspect. The events program came together well.

What would your Node do differently based on your experiences?

Book a cheaper hotel slightly further from the meeting location and use a ride share service to transport the participants to the meeting site.