Decipher: A New Framework for Visualizing Transcriptional Disruption in Disease Progression
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A new study from the Azizi, Pe’er, and Blei labs introduces Decipher, a deep generative model for integrating and visualizing single-cell data across healthy and disease contexts. Published in Genome Biology, this work, led by Achille Nazaret, Joy Linyue Fan, Vincent-Philippe Lavallée, and colleagues, demonstrates how Decipher reconstructs cell-state transitions and reveals disrupted regulatory programs in cancers such as AML, gastric cancer, and pancreatic tumors.
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IICD Featured in 2025 JSM TV Film Series
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We’re honored to share that IICD has been selected for inclusion in the 2025 JSM TV Film Series, a global showcase of innovative research in the statistical sciences. Produced by WebsEdge and presented during the Joint Statistical Meetings in Nashville, the video highlights our mission and interdisciplinary work at the intersection of data science, mathematics, and cancer biology.
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IICD Seminar Series: September Seminar
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AI-Powered Genome Technology for Tracking Cancer Evolution & Immune Resistance
Hosted by Jellert Gaublomme, PhD
Date: September 10, 2025
Time: 2:00 PM (ET)
Location: Schermerhorn
Hall 603 and via Zoom
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We’re pleased to welcome Nicolas Beltran-Velez, a PhD student in Computer Science working with the Azizi Lab and advised by David Blei. Nicolas focuses on probabilistic machine learning and scientific discovery using foundation models.
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Congratulations to Dr. Apoorva Singh (Rane Lab) who received a Travel Award to attend the NITMB MathBio Convergence Conference in Chicago last month. She presented her latest research on “Dissecting Mechanisms of Marginal Zone B Cell Ontogenesis and Homeostasis.”
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Recent Publications from IICD Researchers
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Asynchronous Aging and Turnover of Human Circulating and Tissue-Resident Memory T Cells across Sites. Lam, N.; Angel, J. C.; Buchholz, B. A.; Lee, Y.; Weisberg, S. P.; Brown, B. H.; Davis-Porada, J.; Caron, D. P.; Jensen, I. J.; Szabo, P. A.; Ural, B. B.; Wells, S. B.; Kubota, M.; Matsumoto, R.; Brusko, M.; Brusko, T. M.; Lu, C.; Yates, A. J.; Farber, D. L. Immunity 2025, in press.
Convergence and Divergence of Individual Immune Responses over the Life Course. Metcalf, C. J. E.; Graham, A. L.; Yates, A. J.; Cummings, D. A. T Science 2025, 389 (6760), 604-609.
GPX4 Regulates Lipid Peroxidation and Ferroptosis of Stored Red Blood Cells. Stephenson, D.; Keele, G. R.; Hay, A.; Dzieciatkowska, M.; Reisz, J. A.; Haiman, Z. B.; Moore, A. L.; Nemkov, T.; Deng, X.; Stone, M.; Hansen, K. C.; Kleinman, S.; Norris, P. J.; Busch, M. P.; Churchill, G. A.; Stockwell, B. R.; Roubinian, N.; Zimring, J. C.; Page, G. P.; D’Alessandro, A. Blood Red Cells & Iron 2025, 100020.
Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign. Shi, H.; Zatzman, M.; Shah, S.; McPherson, A. Cancer Bioinformatics 2025, 137-152.
Model Directions, Not Words: Mechanistic Topic Models Using Sparse Autoencoders. Zheng, C.; Beltran-Velez, N.; Karlekar, S.; Shi, C.; Nazaret, A.; Mallik, A.; Feder, A.; Blei, D. M. arXiv 2025.
Spatiodynamic Inference Using Vision-Based Generative Modelling. Park, J. W.; Zhao, K.; Rane, S. arXiv 2025, 2507.
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Catch up on the latest from our IICD community! Here are some highlights you might have missed on our social channels.
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