Emergence: A newsletter of discovery, education, and outreach from the EMBRIO Institute

Issue 43: July 23, 2025

Dear EMBRIO Members:

Summer is always a time of energy and progress at EMBRIO—and this year is no exception. July has brought new milestones in outreach, scholarship, and community.

Earlier this month, EMBRIO investigators led a standing-room-only workshop on computational modeling at the International Zebrafish Conference (IZFS), and several of our researchers gave invited talks at the Society for Mathematical Biology meeting. We’re also proud to feature our summer undergraduate researchers, new publications, upcoming training events, and some exciting promotions and honors across the institute.

Don’t miss the call for submissions to our annual Scientific Figure and Video Awards—now extended through August 15. And if you haven’t scheduled your one-on-one evaluation interview with Soumi Mukherjee, please do so soon.

We encourage all EMBRIO members to check out the latest materials from our Summer School and Annual Retreat (links inside), and follow us on LinkedIn to help spread the word about our collaborative, interdisciplinary mission.

We hope the rest of your summer is both productive and rejuvenating.

Sincerely, Your EMBRIO Leadership Team

CONFERENCE TALKS AND WORKSHOPS

EMBRIO Leads Workshop on Computational Modeling and Quantitative Biology at IZFS 2025

On July 10, EMBRIO investigators led an engaging and well-attended workshop at the 19th International Zebrafish Conference (IZFS) in Madison, WI. With over 80 participants, the session titled “Integration of Computational Modeling and Quantitative Biology” explored the powerful intersection of experimental biology and computational approaches in zebrafish research.

The workshop began with a biology-focused overview of how computational modeling enhances our understanding of embryonic development in zebrafish, providing foundational insights into modeling strategies. Speakers then presented advanced workflows for multi-scale modeling from single-cell dynamics to complex tissue-level processes, followed by examples of how machine learning and AI techniques are accelerating image analysis, data quantification, and model optimization.

Throughout the session, attendees explored interdisciplinary case studies highlighting the collaboration between biologists and engineers. These included models of BMP patterning in early dorsal-ventral body-axis formation, mechanistic models of epiboly and notochord mechanics, and calcium signaling models in larval fin wound healing.

The workshop served as a forum for sharing innovative tools and approaches that bridge experimental and computational disciplines. Participants left with new perspectives and techniques to apply in their research, further advancing the zebrafish community’s capabilities in systems-level biology.

For more information on the IZFS program, visit: https://www.izfs.org/education/19izfc/program

Names (L to R):

Nissa Larson - Purdue University; Priyom Adhyapok - Duke University; Linlin Li - Purdue University; Bakary Samasa - University of Pennsylvania Perelman School of Medicine; Chang Ding - Purdue University; Nilay Kumar - Purdue University; Sharon Minsuk – Indiana University; Qing Deng (moderator) - Purdue University; (not pictured, but presenter or organizer: Shelly Tan - Purdue University; Michel Bagnat - Duke University; Mary Mullins - University of Pennsylvania Perelman School of Medicine)

Society for Mathematical Biology Annual Meeting

Both Sharon Minsuk (Postdoc Fellow, Glazier Lab, IU) and Taeyoon Kim (Asst. Prof., Kim Lab, Purdue) gave invited talks this month at the Society for Mathematical Biology Annual Meeting: https://2025.smb.org/

• Sharon’s talk was entitled "The Role of Embryo, Tissue, and Cell Shape in Morphogenesis: Modeling the Cellular Dynamics of Tissue Deformation,” given during the invited symposium of "Modeling the Role of Geometry and Topology in Shaping Cell Behavior, Function, and Tissue Patterns”. Abstract: https://2025.smb.org/MS05/MS-CDEV-06-Part-1.html 
• Taeyoon’s talk entitled "Reconstituting the Mechanical and Dynamic Behaviors of the Actin Cytoskeleton" was given during the invited mini-symposium of Agent-based modelling of cell cytoskeletal phenomena. Abstract: https://2025.smb.org/CDEV/MS-CDEV-08.html

Society for the Advancement of Biology Education Research Annual Meeting

The Gardner Lab has been conducting community of practice, interdisciplinary identity, and evaluation research with EMBRIO as part of our Thrust 4 efforts. This month Co-PI, Stephanie Gardner, with graduate students Soumi Mukherjee and Emily Georgopoulos, presented research at SABRE (Society for the Advancement of Biology Education Research). 

Interdisciplinary (ID) STEM research allows researchers to cross-disciplinary boundaries and generate new knowledge. Emily’s poster discusses the ways BII graduate student trainees develop interdisciplinary research identities, and Soumi’s discusses the ways BII members develop as ID professionals. These will provide insights as we continue to evaluate the growth and development of EMBRIO, thereby enhancing institutional goals and outcomes. With the rise of ID research and centers, these studies provide insights into bolstering ID education, supporting students in crossing disciplinary and contextual boundaries, and preparing the next generation of ID scientists.

Mukherjee, S, Georgopoulos E, and Gardner SM. 2025, Mapping Success: A Member-Driven Competency-Based Approach to Interdisciplinary Professional Growth within a Biology Integration Institute. SABRE Annual Meeting, July 10-13, 2025.

Georgopoulos E, and Gardner SM. 2025. Exploring Interdisciplinary STEM Identity Development of Graduate Students in Interdisciplinary Biology Integration Institutes. SABRE Annual Meeting, July 10-13, 2025. 

NEW PUBLICATIONS

Let us know about new papers you want to highlight for the EMBRIO community!

See a more complete list of Scholarly Products produced under support of EMBRIO Institute

Weiwei Zhang and Chris Staiger are co-authors on a new publication in the New Phytologist with findings that propose MLO’s act downstream of FER to mediate Ca++ influx and promote ROS production to regulate root hair tip growth:

Ogawa, S.T., W. ZhangP, C.J. Staiger, and S.A. Kessler. 2025. MLO-mediated Ca2+ influx regulates root hair tip growth in Arabidopsis. New Phytol, July 13, 2025. https://doi.org/10.1111/nph.70378

MLO15 contributes to Arabidopsis root hair elongation



Check out EMBRIO’s publications and pre-prints on our Google Scholar Page

EMBRIO mandatory virtual Interviews with Soumi - please schedule yours asap

If you have not yet done so, please sign up for a follow-up virtual interview with Soumi Mukherjee to help capture your experience with collaborating and integrating in the EMBRIO research community. There are available times now through most of August. See the link and details from Soumi below.

Schedule link for signing up now https://www.when2meet.com/?30848105-sqcQL

UPCOMING OPPORTUNITIES & WORKSHOPS

EMBRIO Best Scientific Figure and Video Award Submission

Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu@gmail.com or visit www.compucell3d.org/Workshop25.

Register at: www.tinyurl.com/CC3D2025.

EMBRIO projects have included ten undergraduates this summer at Purdue working on research in multiple labs. Our summer interns will be presenting their work during the Purdue Summer Undergraduate Research Symposium, July 30 on campus: https://www.purdue.edu/undergrad-research/conferences/summer/index.php

QUICK LINKS

All-Hands Meetings Recordings

Institute Skills and Strengths Sharing Platform

Orientation to EMBRIO

Sign the Data Sharing Policy Agreement

EMBRIO Personnel List

Materials from Summer School & Annual Retreat

Annual Retreat Photos

Summer School Photos

Follow us on LinkedIN

Congrats to Clara Isaza for being promoted to Associate Professor at University of Puerto Rico at Mayagüez!

NEW LAB MEMBER?

Did you recently have new students or staff members join your EMBRIO projects? We want to add them to the listserv, Box account, demographics survey, and Personnel List for ensuring their inclusion in communications and participation. If they are not already on our Personnel spreadsheet, or they have graduated, let Brent know their names and email contacts (laddb@purdue.edu )

EMBRIO Website