Sotabase

Career

· Assistant Professor of Computer Science and Biology, New York University2025–
· Postdoctoral Researcher, Genentech2021–2025
· Postdoctoral Researcher, Genentech & Stanford Medicine2021–2025
· Diplôme d'Ingénieur; M.S. Applied Mathematics, Ecole polytechnique2016–
· PhD (Computer Science), University of California, Berkeley2016–2021
· PhD in Electrical Engineering & Computer Sciences, University of California, Berkeley2016–2021
· MSc in Applied Mathematics, Ecole polytechnique2013–2016

Publications (58)

AUTO-ENCODING VARIATIONAL BAYES
2020
21,128
cited
Deep Generative Modeling for Single-cell Transcriptomics
Nature Methods · 2018
2,033
cited
Scrublet: computational identification of cell doublets in single-cell transcriptomic data
bioRxiv · 2018
1,978
cited
A Python library for probabilistic analysis of single-cell omics data
Nature Biotechnology · 2022
541
cited
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
bioRxiv · 2019
473
cited
Joint probabilistic modeling of single-cell multi-omic data with totalVI
Nature Methods · 2021
409
cited
The scverse project provides a computational ecosystem for single-cell omics data analysis
Nature Biotechnology · 2023
213
cited
DestVI identifies continuums of cell types in spatial transcriptomics data
Nature Biotechnology · 2022
163
cited
Information Constraints on Auto-Encoding Variational Bayes
Neural Information Processing Systems · 2018
143
cited
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements
arXiv.org · 2019
127
cited
Enhancing scientific discoveries in molecular biology with deep generative models
Molecular Systems Biology · 2020
73
cited
scvi-tools: a library for deep probabilistic analysis of single-cell omics data
bioRxiv · 2021
59
cited
Large-Scale Differentiable Causal Discovery of Factor Graphs
Neural Information Processing Systems · 2022
58
cited
Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling
CLEaR · 2022
53
cited
Bayesian Inference for a Generative Model of Transcriptome Profiles from Single-cell RNA Sequencing
bioRxiv · 2018
39
cited
An empirical Bayes method for differential expression analysis of single cells with deep generative models
bioRxiv · 2022
34
cited
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation
bioRxiv · 2021
29
cited
Learning from eXtreme Bandit Feedback
AAAI Conference on Artificial Intelligence · 2020
26
cited
Cost-Effective Incentive Allocation via Structured Counterfactual Inference
AAAI Conference on Artificial Intelligence · 2019
20
cited
Deep Generative Models for Detecting Differential Expression in Single Cells
bioRxiv · 2019
18
cited
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Romain Lopez | Researcher Profile | Sotabase | Sotabase