|
Link to all publications:
|
|
Selected Publications/PREPRINTs
* denotes equal contributions
^ denotes corresponding author(s)
Underlined authors are lab members
Nazaret A*^, Hong J*^, Azizi E^, Blei D^. Stable Differentiable Causal Discovery, ICML 2024 (code)
Maurer K*, Park CY*, Mani S, Borji M, 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, Garhi SL, Li S, Livak KL, Ritz J, Coiffeur RJ, Wu CJ^, Azizi E^. Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy, bioRxiv. 2024
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)
Park C*, Mani S*, Beltran-Velez N, Maurer K, Gohil S, Li S, Huang T, Knowles DA, Wu CJ, Azizi E^. DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. bioRxiv. 2023. RECOMB 2024 (acceptance rate 16%) (highlights, code)
Nazaret A*, Fan JL*, Lavallée V-P*, 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^, Deep generative model deciphers derailed trajectories in acute myeloid leukemia. bioRxiv. 2023.11. 11.566719. (highlights, code)
Liu Y, Jin Y, Azizi E^, Blumberg AJ^. CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport. BMC Bioinformatics. 24, 480. 2023.
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)
Boyeau P*, Hong J*, Gayoso A, Jordan MI, Azizi E, Yosef N, Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics, bioRxiv. 2022.
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.
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).
^ denotes corresponding author(s)
Underlined authors are lab members
Nazaret A*^, Hong J*^, Azizi E^, Blei D^. Stable Differentiable Causal Discovery, ICML 2024 (code)
Maurer K*, Park CY*, Mani S, Borji M, 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, Garhi SL, Li S, Livak KL, Ritz J, Coiffeur RJ, Wu CJ^, Azizi E^. Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy, bioRxiv. 2024
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)
Park C*, Mani S*, Beltran-Velez N, Maurer K, Gohil S, Li S, Huang T, Knowles DA, Wu CJ, Azizi E^. DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. bioRxiv. 2023. RECOMB 2024 (acceptance rate 16%) (highlights, code)
Nazaret A*, Fan JL*, Lavallée V-P*, 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^, Deep generative model deciphers derailed trajectories in acute myeloid leukemia. bioRxiv. 2023.11. 11.566719. (highlights, code)
Liu Y, Jin Y, Azizi E^, Blumberg AJ^. CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport. BMC Bioinformatics. 24, 480. 2023.
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)
Boyeau P*, Hong J*, Gayoso A, Jordan MI, Azizi E, Yosef N, Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics, bioRxiv. 2022.
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.
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, LMRL Workshop at NeurIPS, 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)
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 The 33rd International Conference on 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 the 31st International Conference on 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)
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)
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 The 33rd International Conference on 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 the 31st International Conference on 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)
