Link to all publications: 

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Selected Publications/PREPRINTs 

* denotes equal contributions
^ denotes corresponding author(s)
Underlined authors are lab members

He S*, Zhu Y*, Tavakol DN*, Ye H, Lao YH, Zhu ZX, Xu C, Chauhan S, Garty G, Tomer R, Vunjak-Novakovic G, Zou J^, Azizi E^, Leong KW^. Squidiff: Predicting cellular development and perturbation response with diffusion model. Nature Methods. 2025. (code)

Boyeau P*, Hong J*, Gayoso A, Kim M, McFaline-Figueroa JL, Jordan MI, Azizi E, Ergen C, Yosef N, Deep generative modeling of sample-level heterogeneity in single-cell genomics. Nature Methods, 2025.
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Hong J*, Desai K*, Nguyen TD, Nazaret A, Levy N, Ergen C, Plitas G, Azizi E^, AMICI: Attention Mechanism Interpretation of Cell–cell Interactions. bioRxiv, 2025.​

Zweig A*, Zhang M*, Azizi E, Knowles D. Energy Guided Geometric Flow Matching. arXiv, 2025.

Perez M*, Hong J*, Zweig A, Azizi E^, Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data, AI4Science Workshop at NeurIPS, 2025. 

​Zweig A, Lin Z, Azizi E and Knowles DA, Towards identifiability of interventional stochastic differential equations, arXiv, 2025.

Shi L*, Uzuni A*, Wang XK*, Pressler M, Harle DW, Chakrabarti S, Macedo R, Belay K, Gordillo CA, Raps E, Zhang JY, Nazaret A, Fan JL, Jin Y, Shen X, Fuller JS, Azad T, Huang J, Chainani P, Abrams JA, Del Portillo A, Mapara MY, Alhamar M, Sykes M, McFaline-Figueroa JL, Azizi E^, Reshef R^. Spatiotemporal single‑cell analysis reveals T cell clonal dynamics and phenotypic plasticity in human graft‑versus‑host disease. bioRxiv, 2025. 

​​Nazaret A*, Fan JL*, Lavallée V-P*, Burdziak C, Cornish AE, Kiseliovas V, Masilionis I, Chun J, Bowman RL, Eisman SE, Wang J, Shi L, Levine RL, Mazutis L, Blei D, Pe'er D^, Azizi E^, Joint representation and visualization of derailed cell states with Decipher. Genome Biology, 2025 (highlights, code)

​Maurer K*, Park CY*, Mani S, Borji M, Raths F, Gouin III KH, Penter L, Jin Y, Zhang JY, Shin C, Brenner JR, Southard J, Krishna S, Lu W, Lyu H, Abbondanza D, Mangum C, Olsen LR, Neuberg DS, Bachireddy P, Glezer EN, Farhi SL, Li S, Livak KL, Ritz J, Coiffeur RJ, Wu CJ^, Azizi E^. Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy, Science Immunology, 2025.

• Link to data files and details 
• Spotlight article

Fan JLF*, Zhang M*, O’Brien W, Myers J, Melms J, Biermann J, D’Souza E, Tagore S, Beltran-Velez N, Hoffer-Hawlik K, Preau A, Arora I, Chatterjee S, Izar B^, Azizi E^. Echidna: A Bayesian framework for quantifying gene dosage effect impacting phenotypic plasticity. bioRxiv 2024.

Park C*, Mani S*, Beltran-Velez N, Maurer K, Gohil S, Li S, Huang T, Knowles DA, Wu CJ, Azizi E^. A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Research. 2024.(featured on the cover, highlights, code).

Nazaret A*^, Hong J*^, Azizi E^, Blei D^. Stable Differentiable Causal Discovery, Proceedings of International Conference in Machine Learning (ICML), 2024 (code).​

He S*, Jin Y*, Nazaret A*, Shi L, Chen X, Rampersaud R, Dhillon BS, Valdez I, Friend LE, Fan JL, Park CY, Mintz Y-H, Carrera D, Fang KW, Mehdi K, Rohde M, McFaline-Figueroa JL, Blei D, Leong KW, Rudensky AY^, Plitas G^, Azizi E^. Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs, Nature Biotechnology, 2024 (code, press release)

Liu Y, Jin Y, Azizi E^, Blumberg AJ^.  CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport. BMC Bioinformatics.. 24, 480. 2023.

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Wang Y*, Fan JL*, Melms JC*, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodriguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan S, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E^, Izar B^, Multi-modal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nature Genetics. 55, 19-25.2023. (press release)

Nazaret A*, Fan JL*, Pe'er D, Azizi E^, Probabilistic basis decomposition for characterizing temporal dynamics of gene expression, Workshop on Computational Biology at ICML. 2022.

Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT,  [et al. including Azizi E]. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell. 2022 Jul 7;185(14):2591-608.

He S, Xu C, Lao YH, Chauhan S, Xiao Y, Willner MJ, Jin Y, McElroy S, Rao SB, Gogos JA, Tomer R, Azizi E, Xu B, Leong KW. Mapping morphological malf ormation to genetic dysfunction in blood vessel organoids with 22q11. 2 Deletion Syndrome. bioRxiv. 2021.
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Bachireddy P*^, Azizi E*^, Burdziak C, Nguyen VN, Ennis C, Maurer K, Park CY, Choo Z-N, Li S, Gohil, SH, Ruthen NG, Ge Z, Keshin D, Cieri N, Livak K, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea E, Pe'er D^, Wu CJ^. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Reports, 37, no. 6: 109992, 2021.​ (Link to processed data) (Featured in top 10 Best of Cell Reports 2021-2022). ​

Jin Y*, Toberoff A*, Azizi E^, Transfer learning framework for cell segmentation with incorporation of geometric features, NeuriPS LMRL Worksho, 2020. 

Alonso-Curbelo D, Ho YJ, Burdziak C, [et al. including Azizi E], A gene–environment-induced epigenetic program initiates tumorigenesis. Nature. 2021 Feb;590(7847):642-8.

Burdziak C*, Azizi E*, Prabhakaran S, & Pe'er D, ​A Nonparametric Multi-view model for Estimating Cell Type-Specific Gene Regulatory Networks, arXiv 1902.08138, 2019. 

Hemmers S, Schizas M, Azizi E, Dikiy S, Zhong Y, Feng Y, Altan-Bonnet G, Rudensky AY. IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus. Journal of Experimental Medicine, 2019 Nov 4;216(11):2466-78.

Viny AD, Bowman RL, Liu Y, [et al. including Azizi E]. Cohesin members Stag1 and Stag2 display distinct roles in chromatin accessibility and topological control of HSC self-renewal and differentiation. Cell Stem Cell, 2019 Nov 7;25(5):682-96.

Azizi E*, Carr AJ*, Plitas G*, Cornish AE*, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme, R.M., Dao P, McKenney P.T., Wasti, R.C., Kadaveru, K., Mazutis L, Rudensky AY^, Pe'er D^, Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment, Cell 174 (5): 1293-1308, 2018 (Featured as Cover Story) (outreach piece by NCI Cancer Systems Biology Consortium) 
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Azizi E*, Prabhakaran* S, Carr A, Pe'er D, Bayesian Inference for Single-cell Clustering and Imputing,  Genomics and Computational Biology 3 (1), 46, 2017. 

Prabhakaran S*, Azizi E*, Carr A, Pe'er D, Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data,  Proceedings of International Conference in Machine Learning (ICML), PMLR 48:1070-1079, 2016 (R code) (Recipient of Dataminr Poster Presentation Award, NYAS Machine Learning Symposium 2016).

Azizi E, Airoldi EM, Galagan JE, Learning Modular Structures from Network Data and Node Variables,  Proceedings of International Conference in Machine Learning (ICML), PMLR 32(2):1440-1448, 2014 (Recipient of IBM Best Student Paper Award, NESS 2014) (Extended version).

Galagan JE, Minch K*, Peterson M*, Lyubetskaya A*, Azizi E*, Sweet L*, Gomes A*, Rustad T, Dolganov G, Glotova I, et al., The Mycobacterium tuberculosis regulatory network and hypoxia, Nature. 2013 Jul 11; 499 (7457): 178-183. doi: 10.1038/nature12337 (pdf)