Publications


Preprints

Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells.
Adam Gayoso*, Zoë Steier*, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef.
bioRxiv, 2020. [Paper]

Journal Articles

Enhancing scientific discoveries in molecular biology with deep generative models.
Romain Lopez, Adam Gayoso, Nir Yosef.
Molecular Systems Biology, 2020.

Interpretable factor models of single-cell RNA-seq via variational autoencoders.
Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter.
Bioinformatics, 2020. [Paper]

Characterization of cell fate probabilities in single-cell data with Palantir.
Manu Setty, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, Dana Pe’er.
Nature Biotechnology, 2019. [Paper]

Stress-adaptive responses associated with high-level carbapenem resistance in kpc-producing klebsiella pneumoniae.
Sheila Adams-Sapper, Adam Gayoso, Lee. W. Riley.
Journal of Pathogens, 2018. [Paper]

Refereed Workshop Papers

A joint model of RNA expression and surface protein abundance in single cells.
Adam Gayoso, Romain Lopez, Zoë Steier, Jeffrey Regier, Aaron Streets, Nir Yosef
Machine Learning in Computational Biology (MLCB), 2019. [bioRxiv]

Detecting zero-inflated genes in single-cell transcriptomics data
Oscar Clivio, Romain Lopez, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, Nir Yosef
Machine Learning in Computational Biology (MLCB), Spotlight talk, 2019. [bioRxiv]

Deep generative models for detecting differential expression in single cells.
Pierre Boyeau, Romain Lopez, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, Nir Yosef.
Machine Learning in Computational Biology (MLCB), 2019. [bioRxiv]