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Romain Lopez

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data
2019 · Samuel L. Wolock, Romain Lopez, et al. · Cell Systems · 2,712
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Deep generative modeling for single-cell transcriptomics
2018 · Romain Lopez, Jeffrey Regier, et al. · Nature Methods · 2,498
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A Python library for probabilistic analysis of single-cell omics data
2022 · Adam Gayoso, Romain Lopez, et al. · Nature Biotechnology · 806
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Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
2021 · Chenling Xu, Romain Lopez, et al. · Molecular Systems Biology · 680
Joint probabilistic modeling of single-cell multi-omic data with totalVI
2021 · Adam Gayoso, Zoë Steier, et al. · Nature Methods · 584
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The scverse project provides a computational ecosystem for single-cell omics data analysis
2023 · Isaac Virshup, Danila Bredikhin, et al. · Nature Biotechnology · 341
DestVI identifies continuums of cell types in spatial transcriptomics data
2022 · Romain Lopez, Baoguo Li, et al. · Nature Biotechnology · 271
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Information Constraints on Auto-Encoding Variational Bayes
2018 · Lopez, Romain, Regier, Jeffrey, et al. · arXiv (Cornell University) · 90
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Enhancing scientific discoveries in molecular biology with deep generative models
2020 · Romain Lopez, Adam Gayoso, et al. · Molecular Systems Biology · 82
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements
2019 · Lopez, Romain, Nazaret, Achille, et al. · arXiv (Cornell University) · 55
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Defining and benchmarking open problems in single-cell analysis
2025 · Malte D. Luecken, Scott Gigante, et al. · Nature Biotechnology · 54
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SpatialAgent: An autonomous AI agent for spatial biology
2025 · Hanchen Wang, Yichun He, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 49
An empirical Bayes method for differential expression analysis of single cells with deep generative models
2023 · Pierre Boyeau, Jeffrey Regier, et al. · Proceedings of the National Academy of Sciences · 49
Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative Models
2019 · Chenling Xu, Romain Lopez, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 24
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Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors
2024 · Kexin Huang, Romain Lopez, et al. · Lecture notes in computer science · 19
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Decision-Making with Auto-Encoding Variational Bayes
2020 · Lopez, Romain, Boyeau, Pierre, et al. · arXiv (Cornell University) · 18
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Disentangling shared and group-specific variations in single-cell transcriptomics data with multiGroupVI
2022 · Ethan Weinberger, Romain Lopez, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 14
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Large-Scale Differentiable Causal Discovery of Factor Graphs
2022 · Romain Lopez, Jan-Christian Huetter, et al. · neural information processing systems · 14
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Cost-Effective Incentive Allocation via Structured Counterfactual Inference
2020 · Romain Lopez, Chenchen Li, et al. · Proceedings of the AAAI Conference on Artificial Intelligence · 14
Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling
2022 · Lopez, Romain, Tagasovska, Nataša, et al. · arXiv (Cornell University) · 13
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Deep Generative Models for Detecting Differential Expression in Single Cells
2019 · Pierre Boyeau, Romain Lopez, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 13
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A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells
2019 · Adam Gayoso, Romain Lopez, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 12
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Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data
2019 · Oscar Clivio, Romain Lopez, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 11
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Learning from eXtreme Bandit Feedback
2021 · Lopez, Romain, Dhillon, Inderjit S., et al. · AAAI Publications (The Association for the Advancement of Artificial Intelligence (AAAI)) · 10
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A Supervised Contrastive Framework for Learning Disentangled Representations of Cell Perturbation Data
2024 · Xinming Tu, Jan-Christian Hütter, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 8
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Works count: 48
Citation count: 8,420
H-index: 14
I10-index: 22
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