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Link to all publications:
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Selected Publications/PREPRINTs
* denotes equal contributions
^ denotes corresponding author(s)
Underlined authors are lab members
Nazaret A*, Fan J*, Pe'er D, Azizi E^, Probabilistic basis decomposition for characterizing temporal dynamics of gene expression, Workshop on Computational Biology at ICML. 2022.
Park C*, Mani S*, Gohil S, Maurer K, Wu CJ, Azizi E^, DIISCO: Dynamic Intercellular Interactions in Single Cell transcriptOmics, accepted in Workshop on Computational Biology at ICML. 2022.
Wang Y*, Fan JL*, Melms JC*, Amin AD, Georgis Y, Ho P, Tagore S, Abril-Rodriguez G, Biermann J, Hofree M, Caprio L, Berhe S, Khan S, Henick BS, Ribas A, Taylor AM, Schwartz GK, Carvajal RD, Azizi E^, Izar B^, Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications. bioRxiv. 2022.
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 malformation 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)
Chen X, Fan L, Park CY, Friend L, Rampersaud S, Plitas G, Rudensky Y, Azizi E^. Semi-supervised Deconvolution of Spatial Transcriptomics in Breast Tumors, Workshop on Computational Biology at ICML, 2021.
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 (Acceptance rate: 24%) (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 (Acceptance rate: 22%)(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)
^ denotes corresponding author(s)
Underlined authors are lab members
Nazaret A*, Fan J*, Pe'er D, Azizi E^, Probabilistic basis decomposition for characterizing temporal dynamics of gene expression, Workshop on Computational Biology at ICML. 2022.
Park C*, Mani S*, Gohil S, Maurer K, Wu CJ, Azizi E^, DIISCO: Dynamic Intercellular Interactions in Single Cell transcriptOmics, accepted in Workshop on Computational Biology at ICML. 2022.
Wang Y*, Fan JL*, Melms JC*, Amin AD, Georgis Y, Ho P, Tagore S, Abril-Rodriguez G, Biermann J, Hofree M, Caprio L, Berhe S, Khan S, Henick BS, Ribas A, Taylor AM, Schwartz GK, Carvajal RD, Azizi E^, Izar B^, Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications. bioRxiv. 2022.
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 malformation 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)
Chen X, Fan L, Park CY, Friend L, Rampersaud S, Plitas G, Rudensky Y, Azizi E^. Semi-supervised Deconvolution of Spatial Transcriptomics in Breast Tumors, Workshop on Computational Biology at ICML, 2021.
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 (Acceptance rate: 24%) (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 (Acceptance rate: 22%)(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)
