[Embrio-list] Emergence Newsletter Issue 42: June 23, 2025

Mon Jun 23 14:48:21 EDT 2025

[cid:df688f5a-0ed9-4e6e-a2e0-bd66c028916e]

Dear EMBRIO Members:

It was great to see the membership come together during our EMBRIO Summer School and Annual Meeting hosted at Purdue University, June 9-13. Altogether for the week, we had over fifty members representing Purdue, Notre Dame, Indiana, Penn, UPRM, and Texas A&M, as well as a number of first-time attendees and new members.

Highlights of the summer school include a series of tutorials on using AI in Research from Purdue Rosen Center for Advanced Computing scientists, Purdue faculty librarians, and from Lucas Wiese, Ph.D. Candidate in the Magana Lab at Purdue, a hands-on tutorial from Scott Bolton on data management for EMBRIO member labs, and introductory mini workshops from Pedro dal Castro on CompuCell3D, and from Sharon Minsuk on Tissue Forge. You can access slides from the sessions on our Box account under Summer Workshops and Annual Retreats > Summer School 2025<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2F6gz327g52a13i3r2p5pl156t3unxs2eu&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037796028%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=b08wzq49NQcNfzYlINfWNDhoSdRnLcnqpOrNmSR7%2FOk%3D&reserved=0>.

Highlights of the Annual Retreat include journal club presentations highlighting their manuscript submissions for peer-review publication:

  *
Ca++ Signaling and Actin Club Pre-Print:
     *
Li,  L.; Gazzo,  D.; Saad,  S.; Larson,  N.; Kim,  E.; Kumar,  N.; Mim,  M.; Krishnan,  M.; Speybroeck,  B.; Ding,  C.; Mullins,  M.; Pascuzzi,  A.; Deng,  Q.; Pienaar,  E.; Evans,  J.; Umulis,  D.; Zartman,  J. 2025. Rules of Life at the Interface of Calcium Signaling and Mechanobiology. Preprints 2025, 2025060387. https://doi.org/10.20944/preprints202506.0387.v1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.20944%2Fpreprints202506.0387.v1&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037817525%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=fz9Cre7jCgUX4EmF13WM2IcnB4caj6QKpSf%2BBeOOl8k%3D&reserved=0>. Submitted to APL Bioengineering (June 2025)

  *
Ca++ Imaging and Analysis Club Pre-Print:
     *
Suarez-Gomez, D., N.C. Perez-Rosas, G.I. Miranda-Contreras, S.R. Colom-Braña, W. ZhangP, M.S. Mim, S. Tan, D. Gazzo, A. Buganza Tepole, Q. Deng, G. Reeves, C.E. Isaza-Brando, C.J. Staiger, D. Umulis, J. Zartman, M. Cabrera-Ríos*. 2025. CalciumInsights: An open-source, tissue-agnostic graphical interface for high-quality analysis of calcium signals. June 9, 2025, biorxiv. https://doi.org/10.1101/2025.06.04.657923<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1101%2F2025.06.04.657923&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037831138%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=h65fl2o3s%2F%2BVL3sywp787T1Ou8qS2XBaXMSdX2xrV1c%3D&reserved=0>  Submitted to Nature Methods (June 2025)

A panel discussion (that probably broke records) with thirteen members representing graduate students, postdocs, staff research scientists, thrust co-leads, and affiliate faculty and student members: "Toward Integration in the Interdisciplinary Research Framework of EMBRIO Institute: An Open Discussion on Cross-Systems Communications and Collaborations.” Thank you to Steph Gardner and Elsje Pienaar for moderating the panel, and to each of the panelists:

  *   Chrissy Boody, Ph.D. Student (Purdue, T1B, Evans Lab)
  *   Agnes Doszpoly, Ph.D. Candidate (Purdue, T1A, Kinzer Ursem Lab)
  *   David Gazzo, Ph.D. Candidate (Notre Dame, T2B, Zartman Lab)
  *   Nilay Kumar, Sr. Research Scientist (Purdue, Core, T2, T3, Cross-Systems Coordination Team, Pienaar Lab and Buganza-Tepole Lab)
  *   Linlin Li, Sr. Research Scientist (Purdue, Core, T2,T3, Cross-Systems Coordination Team, Umulis Lab)
  *   Allison McCarthy (Purdue, T1B, Evans Lab)
  *   Sharon Minsuk, Research Fellow (IU, Core, T3A, Glazier Lab)
  *   Greg Reeves, Associate Professor (Core – affiliate, TAMU)
  *   Bakary Samasa, Ph.D. Candidate (UPenn, T3A, Mullins Lab)
  *   Razeen Shaikh, Ph.D. Candidate (TAMU, Core - affiliate, Reeves Lab)
  *   Chris Staiger, Distinguished Professor (T2A Co-Lead, Purdue)
  *   Aby Udosen, Ph.D. Candidate (Purdue, T4, Magana Lab)
  *   Weiwei Zhang, Sr. Research Scientist (Purdue, T2A, Cross-Systems Coordination Team, Staiger Lab

Steph Gardner led us in an excellent professional development session to up our game with thinking clearly about crafting and delivering an effective elevator pitch that best represents our skills, experiences, and ideas to potential collaborators, employers, investors, clients, etc. We all gained more insight and knowledge from presentations and discussion from each Thrust level project throughout Thursday and Friday, along with two poster sessions.  Thanks to all who presented and helped prepare presentations and posters. Our day and a half retreat helped to represent the impactful research that is now available to the public and the broader scientific community in more than 25 pre-print manuscripts, as well as over 32 peer-reviewed journal publications as a result of research and collaborations in EMBRIO!  Congrats to all for your excellent scientific research and continued collaborations that advance the mission of the Institute. You can quickly view the list and get the direct links to these manuscripts and publications and more at the Institute’s Google Scholar page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3D-gQWba8AAAAJ%26view_op%3Dlist_works%26authuser%3D1%26gmla%3DAH70aAVM8yPeKYknph-fu5nB09Nm1PGoxA5jWkVbnlBqFCJlbiXFEYwKI9S1weQ1_OFaXNCWtNkps95_OQkY7uGI&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037843983%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=cCPmABZM1UgSj6sEvCIw5oXItCuy9gtBsMmmEr7ZGIs%3D&reserved=0>. A more comprehensive list of products is available on our research page<https://www.purdue.edu/research/embrio/research/scholarly-products.php>. Presentations at the retreat concluded with a show and tell of the new Multiscale Modeling E-Book<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fembrio-modeling-course.readthedocs.io%2Fen%2Flatest%2F&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037857245%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pcPTX3nuz7cEceGN3T01h%2BCUrberjvCz30bs2R%2FNlC0%3D&reserved=0> from Hayden Fennell that we can all benefit from in the Institute and beyond.

Thrust 4 Interview Scheduling for Institute Evaluations, Community of Practice, and Interdisciplinary Research
A reminder that Thrust 4 researchers are capturing, analyzing, and synthesizing findings of our integrative activities, please take a moment to schedule your interview with Soumi Mukherjee (see previous emails for details. Reminders will continue to be shared out):

Just a quick note from Soumi – there is a wide range of available dates throughout the summer semester, from June through the first two weeks of August (before the fall semester begins. There is plenty of flexibility in scheduling the online interviews, so if you're not available right away, feel free to pick a time in the later weeks. Thank you for taking the time to schedule!

Here is the link : https://www.when2meet.com/?30848105-sqcQL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2meet.com%2F%3F30848105-sqcQL&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037870882%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=2sse7oXmpcOV2rWed4PBt9camuBg6JU3YgJH5sih4ro%3D&reserved=0>

Congratulations to EMBRIO 2025 Best Paper Awardees!!

  *   BEST PAPER 2025 to CO-FIRST AUTHORS: MAYESHA MIM and NILAY KUMAR for their Cell Reports paper:
     *   Mim M.S., Kumar, N., Levis,M..,  Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and  Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.celrep.2024.114398&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037884073%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=p5ffOT6TIMMMsHZYqHFSrAVP2C3ZLBm7Ir6c6WoQf2c%3D&reserved=0>

  *   Runner Up: RAZEEN SHAIKH for her npj Systems Biology and Applications paper with multiple EMBRIO labs:
     *   Shaikh, R., Larson, N. J., Kam, J., Hanjaya-Putra, D., Zartman, J.J., Umulis, D. M., Li, L., & Reeves, G. T. (2024). *Optimal performance objectives in the highly conserved bone morphogenetic protein signaling pathway. Npj Systems Biology and Applications, 10(1), 103. https://doi.org/10.1038/s41540-024-00430-9<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1038%2Fs41540-024-00430-9&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037893918%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aIbKcmSHL9ork8q6nx1Yv77GlrVjdj1gZvmr5zXlIlM%3D&reserved=0>

 Best Scientific Figure and Video Award Submission
    A call for Best Scientific Figure and Video Award Submission – these have been extended, with the deadline of August 1st. Extended Deadline for 2025 Best Scientific Figure or Live Video Awards
 https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca1.qualtrics.com%2Fjfe%2Fform%2FSV_9X3KHxUUz0bg6Pk&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037903212%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=avOt8zrvCDDH9%2Fz9OdqWV5IVecH%2B%2BfVHAUxEdrO8SQM%3D&reserved=0>

EMBRIO Annual Report Accepted by NSF
    Our Fourth Annual Report to the National Science Foundation was accepted by our program officer. You can access both the Executive Summary and the Full Report via our shared Box account: Annual Reporting > BII NSF Annual Report 2025 (Year 4)<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2F815sk1rm0gcy6nm4cm3ydr2n11uontvp&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037912232%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=53uHRZKscudl%2BAwU764Cg8FTo2M69edAwjqBzy0soNA%3D&reserved=0>

Opportunities and Workshops for EMBRIO Members
2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon

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 at gmail.com<mailto:compucell3d.iu at gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compucell3d.org%2FWorkshop25&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037922908%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=z7ypNRJy7lbgE6vO2B1SIkrJ8m6RFJ8swNmKUu3ZNtg%3D&reserved=0>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyurl.com%2FCC3D2025&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C39144ec4a180439dd86f08ddb28686a9%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638863013037931709%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hiU482bnanITQtiea4v5s3RJsj1seok%2F4AD6TYnsHaE%3D&reserved=0>.

Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/>
Weldon School of Biomedical Engineering, Purdue University
Office: Hall for Discovery Learning and Research, Ste. 203
207 S. Martin Jischke Drive
West Lafayette, IN 47907
laddb at purdue.edu

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