Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation.
R. Lopez*, B. Li*, H. Keren-Shaul*, P. Boyeau, M. Kedmi, D. Pilzer, A. Jelinski, E. David, A. Wagner, Y. Addadi, M.I. Jordan, I. Amit†, N. Yosef†
bioRxiv, 2021
scvi-tools: a library for deep probabilistic analysis of single-cell omics data.
A. Gayoso*, R. Lopez*, G. Xing*, P. Boyeau, K. Wu, M. Jayasuriya, E. Mehlman, M. Langevin, Y. Liu, J. Samaran, G. Misrachi, A. Nazaret, O. Clivio, C. Xu, T. Ashuach, M. Lotfollahi, V. Svensson, E. Beltrame, C. Talavera-Lopez, L. Pachter, F.J. Theis, A. Streets, M.I. Jordan, J. Regier, N. Yosef.
bioRxiv, 2021
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, 2021
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
C. Xu*, R. Lopez*, E. Mehlman*, J. Regier, M.I. Jordan, N. Yosef.
Molecular Systems Biology, 2021
Decision-making with auto-encoding variational Bayes.
R. Lopez, P. Boyeau, N. Yosef, M. Jordan, J. Regier.
Advances in Neural Information Processing Systems, 2020
Interpretable factor models of single-cell RNA-seq via variational autoencoders.
V. Svensson, A. Gayoso, N. Yosef, L. Pachter.
Bioinformatics, 2020
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements.
R. Lopez*, A. Nazaret*, M. Langevin*, J. Samaran*, J. Regier*, M.I. Jordan, N. Yosef.
ICML Workshop on Computational Biology, 2019
Deep generative models for detecting differential expression in single cells.
P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef.
Machine Learning in Computational Biology meeting, 2019
Detecting zero-inflated denes in single-cell transcriptomics data.
O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef.
Machine Learning in Computational Biology meeting, 2019
Information constraints on auto-encoding variational Bayes.
R. Lopez, J. Regier, M. Jordan, N. Yosef.
Advances in Neural Information Processing Systems, 2018
A deep generative model for semi-supervised classification with noisy labels.
M. Langevin, E. Mehlman, J. Regier, R. Lopez, M.I. Jordan, N. Yosef.
Bay Area Machine Learning Symposium, 2018
Deep generative modeling for single-cell transcriptomics.
R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef.
Nature Methods, 2018