Adaptive Nonparametric Perturbations of Parametric Bayesian Models. Wu, B.; Weinstein, E. N.; Salehi, S.; Wang, Y.; Blei, D. M. arXiv 2024. 

Automated Cell Type Annotation with Reference Cluster Mapping. Galanti, V.; Shi, L.; Azizi, E.; Liu, Y.; Blumberg, A. J. bioRxiv 2024.

Characterizing the Evolutionary Dynamics of Cancer Proliferation in Single-Cell Clones with SPRINTER. Lucas, O.; Ward, S.; Zaidi, R.; Bunkum, A.; Frankell, A. M.; Moore, D. A.; Hill, M. S.; Liu, W. K.; Marinelli, D.; Lim, E. L.; Hessey, S.; Naceur-Lombardelli, C.; Rowan, A.; Purewal-Mann, S. K.; Zhai, H.; Dietzen, M.; Ding, B.; Royle, G.; Aparicio, S.; McGranahan, N.; Jamal-Hanjani, M.; TRACERx Consortium; PEACE Consortium; Kanu, N.; Swanton, C.; Zaccaria, S. Nature Genetics 2024, in press.
 

Coordinated Immune Networks in Leukemia Bone Marrow Microenvironments Distinguish Response to Cellular Therapy. Maurer, K.; Park, C. Y.; Mani, S.; Borji, M.; Raths, F.; Gouin, K. H.; Penter, L.; Jin, Y.; Zhang, J. Y.; Shin, C.; Brenner, J. R.; Southard, J.; Krishna, S.; Lu, W.; Lyu, H.; Abbondanza, D.; Mangum, C.; Olsen, L. R.; Lawson, M. J.; Fabani, M.; Neuberg, D. S.; Bachireddy, P.; Glezer, E. N.; Farhi, S. L.; Li, S.; Livak, K. J.; Ritz, J.; Soiffer, R. J.; Wu, C. J.; Azizi, E.  Science Immunology 2025, 10 (103), eadr0782.

Echidna: A Bayesian Framework for Quantifying Gene Dosage Effect Impacting Phenotypic Plasticity. Fan, J. L.; Zhang, M.; O'Brien, W. G.; Myers, J. D.; Melms, J. C.; Biermann, J.; D'Souza, E.; Tagore, S.; Beltran-Velez, N.; Hoffer-Hawlik, K.; Preau, A.; Arora, I.; Chatterjee, S.; Izar, B.; Azizi, E. bioRxiv 2024.

Ferroptosis—Disease Perils and Therapeutic Promise. Brown, A. R.; Hirschhorn, T.; Stockwell, B. R. Science 2024, 386 (6724), 848-849.

Glioma-Induced Alterations in Excitatory Neurons are Reversed by mTOR Inhibition. Goldberg, A. R.; Dovas, A.; Torres, D.; Pereira, B.; Viswanathan, A.; Das Sharma, S.; Mela, A.; Merricks, E. M.; Megino-Luque, C.; McInvale, J. J.; Olabarria, M.; Shokooh, L. A.; Zhao, H. T.; Chen, C.; Kotidis, C.; Calvaresi, P.; Banu, M. A.; Razavilar, A.; Sudhakar, T. D.; Saxena, A.; Chokran, C.; Humala, N.; Mahajan, A.; Xu, W.; Metz, J. B.; Bushong, E. A.; Boassa, D.; Ellisman, M. H.; Hillman, E. M. C.; Hargus, G.; Bravo-Cordero, J. J.; McKhann, G. M.; Gill, B. J. A.; Rosenfeld, S. S.; Schevon, C. A.; Bruce, J. N.; Sims, P. A.; Peterka, D. S.; Canoll, P. Neuron 2025.

Interpretable Neural ODEs for Gene Regulatory Network Discovery under Perturbations. Lin, Z.; Chang, S.; Zweig, A.; Azizi, E.; Knowles, D. A. arXiv 2025. 

Luminal Breast Epithelial Cells of BRCA1 or BRCA2 Mutation Carriers and Noncarriers Harbor Common Breast Cancer Copy Number Alterations. Williams, M. J.; Oliphant, M. U. J.; Au, V.; Liu, C.; Baril, C.; O’Flanagan, C.; Lai, D.; Beatty, S.; Van Vliet, M.; Yiu, J. C. H.; O’Connor, L.; Goh, W. L.; Pollaci, A.; Weiner, A. C.; Grewal, D.; McPherson, A.; Norton, K.; Moore, M.; Prabhakar, V.; Agarwal, S.; Garber, J. E.; Dillon, D. A.; Shah, S. P.; Brugge, J. S.; Aparicio, S. Nature Genetics 2024, in press.

Posterior Mean Matching: Generative Modeling through Online Bayesian Inference. Salazar, S.; Kucer, M.; Wang, Y.; Casleton, E.; Blei, D. arXiv 2024. 

Subsampling, Aligning, and Averaging to Find Circular Coordinates in Recurrent Time Series. Blumberg, A. J.; Carrière, M.; Fung, J. H.; Mandell, M. A. arXiv 2024.