Q&A with 2025 IICD SRP Interns
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Each summer, the IICD Summer Research Program welcomes exceptional undergraduates from across the country to explore interdisciplinary research at the intersection of biology, math, and computer science. This yearâs cohort features ten driven students with unique interests, big ambitions, and inspiring stories. Read the full Q&A to learn more about their backgrounds, research goals, and what brought them to IICD.
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A TRENDY New Approach to Modeling Gene Regulation with AI
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Dr. Yue Wang, Associate Research Scientist at the Herbert and Florence Irving Institute for Cancer Dynamics and the Department of Statistics at Columbia University, has developed a novel approach to improve the accuracy and interpretability of gene regulatory network inference using deep learning. The results were recently published in Bioinformatics.
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Welcome to Our New IICD Members
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Weâre thrilled to welcome three new members to the IICD community:
- Pamela Felix, Executive Assistant at IICD
- Beatrice Grauman, PhD student in the VickoviÄ Lab
- Ren-Yi Wang, Postdoctoral Researcher in the Tavaré Lab
Weâre excited to have them on board and look forward to the contributions theyâll bring to our dynamic community.
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SRP intern Marina Milea has been awarded the Edmund Baermann Award, the Slagowitz Family Scholarship, and the City College Fellowship. These honors recognize her academic excellence and commitment to pursuing a PhD in biomedical research focused on womenâs health.
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Congratulations to MD/PhD student Cody Slater (Vickovic Lab), recipient of an IICD Travel Award enabling him to attend a hands-on workshop at Stanford University focused on in vivo experimental design in neuroscience. The workshop offered a valuable opportunity to translate his molecular research to live models.
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Dr. Yue Wang, Associate Research Scientist, has accepted a new position at Amazon and is departing IICD. Weâre grateful for his contributions and were glad to celebrate his last day with the teamâwishing him all the best in this next chapter! Stay in touch with Yue here.
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Congratulations to postdoc Aaron Zweig on receiving the prestigious Damon Runyon Quantitative Biology Fellowshipâone of just five awarded nationwide. His work uses geometric deep learning and CRISPR data to model gene regulation and support targeted cancer therapies.
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Our second annual 5-day workshop on 'Methods in Single-Cell Data Integration and Optimal Transport' was a success! Graduate students and postdocs explored cutting-edge methods and toolsâcheck out our social media for photos and highlights from the week.
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Recent Publications from IICD Researchers
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Are Machine Learning Interpretations Reliable? A Stability Study on Global Interpretations. Gan, L.; Zikry, T. M.; Allen, G. A. arXiv 2025.
Between Cluster Analysis: Supervised Dimensionality Reduction for Trajectory Inference. Strzalkowski, A.; Zeira, R.; Raphael, B. J. Bioinformatics 2025, in press.
FOXA2 Promotes Metastatic Competence in Small Cell Lung Cancer. Kawasaki, K.; Salehi, S.; Zhan, Y. A.; Chen, K.; Lee, J. H.; Salataj, E.; Zhong, H.; Manoj, P.; Kinyua, D.; Mello, B. P.; Sridhar, H.; Tischfield, S. E.; Linkov, I.; Ceglia, N.; Zatzman, M.; Havasov, E.; Shah, N. J.; Meng, F.; Loomis, B.; Bhanot, U. K.; Redin, E.; de Stanchina, E.; Hamard, P.-J.; Koche, R. P.; McPherson, A.; Quintanal-Villalonga, Ă.; Shah, S. P.; MassaguĂ©, J.; Rudin, C. M. Nature Communications 2025, 16 (1), 4865.
Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease. Shi, L.; Uzuni, A.; Wang, X. K.; Pressler, M.; Harle, D. W.; Chakrabarti, S.; Macedo, R.; Belay, K.; Gordillo, C. A.; Raps, E.; Zhang, J. Y. A.; Nazaret, A.; Fan, J. L.; Jin, Y.; Shen, X.; Fuller, J. S.; Azad, T.; Huang, J.; Chainani, P.; Abrams, J. A.; Del Portillo, A.; Mapara, M. Y.; Alhamar, M.; Sykes, M.; McFaline-Figueroa, J.; Azizi, E.; Reshef, R. bioRxiv 2025.
Towards Identifiability of Interventional Stochastic Differential Equations. Zweig, A.; Lin, Z.; Azizi, E.; Knowles, D. arXiv 2025.
TRENDY: Gene Regulatory Network Inference Enhanced by Transformer. Tian, X.; Patel, Y.; Wang, Y. Bioinformatics 2025, 41 (6).
Unsupervised Machine Learning for Scientific Discovery: Workflow and Best Practices. Chang, A.; Tang, T. M.; Zikry, T. M.; Allen, G. I. arXiv 2025.
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