preprints

• Pierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan, and Nir Yosef. Calibrated Identification of Feature Dependencies in Single-cell Multiomics.(2023)

conferences & workshops

• Pierre Boyeau, Justin Hong, Adam Gayoso, Michael Jordan, Elham Azizi, and Nir Yosef. Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics. MLCB(2022)
• Romain Lopez, Pierre Boyeau, Nir Yosef, Michael Jordan, and Jeffrey Regier. Decision-making with auto-encoding variational Bayes. NeurIPS(2020)
• Pierre Boyeau, Romain Lopez, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, and Nir Yosef. Deep generative models for detecting differential expression in single cells. MLCB(2019)

journal articles

• Pierre Boyeau, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, Romain Lopez, and Nir Yosef. An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models. PNAS(2023)
• Sebastian Prillo, Yun Deng, Pierre Boyeau, Xingyu Li, Po-Yen Chen, and Yun S. Song. CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models. Nature Methods(2023)
• Romain Lopez, Baoguo Li, Hadas Keren-Shaul, Pierre Boyeau, et al. DestVI identifies continuums of cell types in spatial transcriptomics data. Nature Biotechnology(2023)
• Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau et al. A Python library for probabilistic analysis of single-cell omics data. Nature Communications(2022)