A Twist on Traditional Computational Methods to Advance Mathematical Modeling
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Dr. Khanh N. Dinh’s group has developed a more efficient random forest-based Approximate Bayesian Computation method to enable more reliable and robust mathematical modeling across many fields of science. They share their findings in a new study published in Statistics and Computing.
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Squidiff: A Diffusion AI Model to Accelerate Precision Medicine
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The Azizi and Leong labs at Columbia University and the Zou group at Stanford University have developed a diffusion artificial intelligence model named Squidiff to predict cellular responses to developmental and chemical cues and accelerate precision medicine. Their work was recently published in Nature Methods.
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Research Highlights of 2025
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As 2025 comes to a close, we look back on a year of innovation and discovery at IICD. These nine research spotlights showcase our researchers’ continued commitment to advancing cancer research.
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IICD Seminar Series: December Seminar
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Capsule-Based Genome Sequencing and Lineage Tracing
Hosted by José McFaline-Figueroa, PhD
Date: December 10, 2025
Time: 2:00 PM (ET)
Location: Schermerhorn
Hall 603 and via Zoom
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Some seminars are recorded and available for viewing on the IICD YouTube channel.
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Dr. Khanh Dinh and collaborators made the cover of the Journal of Pathology. They study multiple types of biological data to uncover the key factors that drive bladder cancer development, starting from early changes in the bladder lining before tumors form. Their work was also highlighted in Nature Reviews Urology.
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Justin Hong and Mathias Perez (Alliance's 25) were accepted to present a poster at the AI4Science Workshop at NeurIPS 2025. They will share their new computational framework for Multiple Instance Learning, which enables more robust precision diagnostics using patients' single-cell RNA sequencing data.
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The IICD welcomes two new members to the Vicković lab. Ishaq Kothari joins as a Research Associate developing computational tools for optics-free “omics” imaging methods. Cody Slater is an MD-PhD student designing synthetic systems to target and perturb highly specific cell types in their native context.
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Sanja Vicković and Maroš Pleška published an opinion article discussing a recent Nature Method paper. Their piece highlights Deep-STARmap and Deep-RIBOmap, fluorescent imaging techniques that advance spatial transcriptomic and translatomic profiling by significantly improving performance in thick, intact samples. Read more.
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IICD SRP 2026: Now Accepting Applications
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The Irving Institute for Cancer Dynamics at Columbia University offers a 10-week research opportunity for talented undergraduate students to perform cutting-edge research at the intersection of cancer biology and mathematical sciences. Areas of research span from cancer biology to computer science, mathematics, statistical bioinformatics, engineering, and more. Deadline to apply is February 1, 2026.
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Recent Publications from IICD Researchers
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Cellular States Associated with Metastatic Organotropism and Survival in Patients with Pancreatic Ductal Adenocarcinoma. Chalabi Hajkarim, M.; May, M.; Amin, A. D.; Jamison, J.; Tagore, S.; D’Souza, E.; Caprio, L.; Walsh, Z. H.; Fan, J. L.; Zhang, M.; Shah, P.; Abuzaid, S.; Michel, A.; Dajiang, S.; Wong, W.; Shaikh, N.; Ramaradj, P.; Bakir, B.; Kluger, M. D.; Chabot, J.; Azizi, E.; Hibshoosh, H.; Rustgi, A. K.; Raufi, A. G.; Manji, G. A.; Izar, B. Nature Genetics 2025, in press.
Compressibility Barriers to Neighborhood-Preserving Data Visualizations. Snoeck, S.; Bergam, N.; Verma, N. ArXiv 2025.
Deep Generative Modeling of Sample-Level Heterogeneity in Single-Cell Genomics. Boyeau, P.; Hong, J.; Gayoso, A.; Kim, M.; McFaline-Figueroa, J. L.; Jordan, M. I.; Azizi, E.; Ergen, C.; Yosef, N. Nature Methods 2025, in press.
Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data. Perez, M.; Hong, J.; Zweig, A.; Azizi, E. bioRxiv 2025.
From Slices to Deep Dishes: Spatial Transcriptomics and Translatomics of Thick Tissue Blocks. Pleška, M.; Vickovic, S. Nature Methods 2025, in press.
Lipidomic Changes in Persister Cancer Cells Drive Enhanced Ferroptosis Sensitivity. Reznik, E.; Zandkarimi, F.; Csuka, J. M.; Zhu, Q.; Jin, J.; Neelakantan, T. V.; Zheng, J.; Polychronidou, V.; Fongheiser, M.; Brown, A.; Qiu, B.; Rodriguez, M.; DeVine, L.; Subramaniam, P. S.; Gu, W.; Califano, A.; Stockwell, B. R. Ferroptosis Oxid Stress 2025, 1 (1).
Multi-Parameter Module Approximation: An Efficient and Interpretable Invariant for Multi-Parameter Persistence Modules with Guarantees. Loiseaux, D.; Carrière, M.; Blumberg, A. J. Journal of Applied and Computational Topology 2025, 9 (4), 26.
Squidiff: Predicting Cellular Development and Responses to Perturbations Using a Diffusion Model. He, S.; Zhu, Y.; Tavakol, D. N.; Ye, H.; Lao, Y.-H.; Zhu, Z.; Xu, C.; Chauhan, S.; Garty, G.; Tomer, R.; Vunjak-Novakovic, G.; Zou, J.; Azizi, E.; Leong, K. W. Nature Methods 2025, in press.
t-SNE Exaggerates Clusters, Provably. Bergam, N.; Snoeck, S.; Verma, N. ArXiv 2025.
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Stay up to date with the latest from our IICD community, and be sure to follow us on X, Bluesky, IG, LinkedIn, and YouTube! Below are some recent highlights you may have missed.
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