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Adam Gayoso
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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
5172022
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
4412019
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
4282022
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
306*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
3002021
Mapping single-cell data to reference atlases by transfer learning
M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M BŁttner, ...
Nature biotechnology 40 (1), 121-130, 2022
2982022
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
1512020
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
672023
Enhancing scientific discoveries in molecular biology with deep generative models
R Lopez, A Gayoso, N Yosef
Molecular systems biology 16 (9), e9198, 2020
612020
DoubletDetection
A Gayoso, J Shor, AJ Carr, R Sharma, D Pe’er
Zenodo, DOI 10, 2018
55*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
532022
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
312024
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
192023
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
192019
Detecting zero-inflated genes in single-cell transcriptomics data
O Clivio, R Lopez, J Regier, A Gayoso, MI Jordan, N Yosef
bioRxiv, 794875, 2019
112019
Deep generative modeling of sample-level heterogeneity in single-cell genomics
P Boyeau, J Hong, A Gayoso, M Kim, JL McFaline-Figueroa, MI Jordan, ...
BioRxiv, 2022.10. 04.510898, 2022
102022
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
92019
Stress‐Adaptive Responses Associated with High‐Level Carbapenem Resistance in KPC‐Producing Klebsiella pneumoniae
S Adams-Sapper, A Gayoso, LW Riley
Journal of pathogens 2018 (1), 3028290, 2018
82018
Defining and benchmarking open problems in single-cell analysis
MD Luecken, S Gigante, DB Burkhardt, R Cannoodt, DC Strobl, ...
Research Square, 2024
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
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