| The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans The Tabula Sapiens Consortium*, RC Jones, J Karkanias, MA Krasnow, ... Science 376 (6594), eabl4896, 2022 | 456 | 2022 |
| Characterization of cell fate probabilities in single-cell data with Palantir M Setty, V Kiseliovas, J Levine, A Gayoso, L Mazutis, D Pe’Er Nature biotechnology 37 (4), 451-460, 2019 | 419 | 2019 |
| Cell2location maps fine-grained cell types in spatial transcriptomics V Kleshchevnikov, A Shmatko, E Dann, A Aivazidis, HW King, T Li, ... Nature biotechnology 40 (5), 661-671, 2022 | 356 | 2022 |
| Joint probabilistic modeling of single-cell multi-omic data with totalVI A Gayoso, Z Steier, R Lopez, J Regier, KL Nazor, A Streets, N Yosef Nature methods 18 (3), 272-282, 2021 | 279 | 2021 |
| A Python library for probabilistic analysis of single-cell omics data A Gayoso, R Lopez, G Xing, P Boyeau, V Valiollah Pour Amiri, J Hong, ... Nature biotechnology 40 (2), 163-166, 2022 | 274* | 2022 |
| Mapping single-cell data to reference atlases by transfer learning M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M Büttner, ... Nature biotechnology 40 (1), 121-130, 2022 | 273 | 2022 |
| Interpretable factor models of single-cell RNA-seq via variational autoencoders V Svensson, A Gayoso, N Yosef, L Pachter Bioinformatics 36 (11), 3418-3421, 2020 | 146 | 2020 |
| Enhancing scientific discoveries in molecular biology with deep generative models R Lopez, A Gayoso, N Yosef Molecular systems biology 16 (9), e9198, 2020 | 57 | 2020 |
| The scverse project provides a computational ecosystem for single-cell omics data analysis I Virshup, D Bredikhin, L Heumos, G Palla, G Sturm, A Gayoso, I Kats, ... Nature biotechnology 41 (5), 604-606, 2023 | 53 | 2023 |
| DoubletDetection A Gayoso, J Shor, AJ Carr, R Sharma, D Pe’er Zenodo, DOI 10, 2018 | 53* | 2018 |
| PeakVI: A deep generative model for single-cell chromatin accessibility analysis T Ashuach, DA Reidenbach, A Gayoso, N Yosef Cell reports methods 2 (3), 2022 | 47 | 2022 |
| Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells A Gayoso, P Weiler, M Lotfollahi, D Klein, J Hong, A Streets, FJ Theis, ... Nature methods 21 (1), 50-59, 2024 | 23 | 2024 |
| Deep generative models for detecting differential expression in single cells P Boyeau, R Lopez, J Regier, A Gayoso, MI Jordan, N Yosef bioRxiv, 794289, 2019 | 19 | 2019 |
| An empirical Bayes method for differential expression analysis of single cells with deep generative models P Boyeau, J Regier, A Gayoso, MI Jordan, R Lopez, N Yosef Proceedings of the National Academy of Sciences 120 (21), e2209124120, 2023 | 15 | 2023 |
| Detecting zero-inflated genes in single-cell transcriptomics data O Clivio, R Lopez, J Regier, A Gayoso, MI Jordan, N Yosef bioRxiv, 794875, 2019 | 11 | 2019 |
| Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics P Boyeau, J Hong, A Gayoso, MI Jordan, E Azizi, N Yosef BioRxiv, 2022.10. 04.510898, 2022 | 9 | 2022 |
| A joint model of RNA expression and surface protein abundance in single cells A Gayoso, R Lopez, Z Steier, J Regier, A Streets, N Yosef biorxiv, 791947, 2019 | 9 | 2019 |
| Stress-adaptive responses associated with high-level carbapenem resistance in kpc-producing klebsiella pneumoniae S Adams-Sapper, A Gayoso, L Riley Journal of pathogens 2018, 2018 | 8 | 2018 |
| Defining and benchmarking open problems in single-cell analysis M Luecken, S Gigante, D Burkhardt, R Cannoodt, D Strobl, N Markov, ... | | 2024 |
| Scvi-hub: an actionable repository for model-driven single cell analysis C Ergen, VV Pour Amiri, M Kim, A Streets, A Gayoso, N Yosef bioRxiv, 2024.03. 01.582887, 2024 | | 2024 |
Nir YosefAssociate Professor, Department of Systems Immunology, Weizmann Institute of ScienceVerified email at berkeley.edu
