journal articles

• Deep generative modeling of sample-level heterogeneity in single-cell genomics.
  Pierre Boyeau, Justin Hong, Adam Gayoso, Martin Kim, José L. McFaline-Figueroa, Michael I. Jordan, Elham Azizi, Can Ergen, and Nir Yosef.
  BioRxiv(2024, in press in Nature Methods)
• Calibrated Identification of Feature Dependencies in Single-cell Multiomics.
  Pierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan, and Nir Yosef.
  Genome Biology(2024)
• An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models.
  Pierre Boyeau, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, Romain Lopez, and Nir Yosef.
  Proceedings of the National Academy of Sciences(2023)
• CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models.
  Sebastian Prillo, Yun Deng, Pierre Boyeau, Xingyu Li, Po-Yen Chen, and Yun S. Song.
  Nature Methods(2023)
• DestVI identifies continuums of cell types in spatial transcriptomics data.
  Romain Lopez, Baoguo Li, Hadas Keren-Shaul, Pierre Boyeau, Merav Kedmi, David Pilzer, Adam Jelinski, et al.
  Nature Biotechnology(2022)
• A Python library for probabilistic analysis of single-cell omics data.
  Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, et al.
  Nature Biotechnology(2022)

conferences

• AutoEval Done Right: Using Synthetic Data for Model Evaluation.
  Pierre Boyeau, Anastasios N. Angelopoulos, Nir Yosef, Jitendra Malik, and Michael I. Jordan.
  International Conference on Machine Learning(2025)
• Decision-making with auto-encoding variational Bayes.
  Romain Lopez, Pierre Boyeau, Nir Yosef, Michael Jordan, and Jeffrey Regier.
  Advances in Neural Information Processing Systems(2020)

workshops

• Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics.
  Pierre Boyeau, Justin Hong, Adam Gayoso, Michael Jordan, Elham Azizi, and Nir Yosef.
  Machine Learning in Computational Biology(2022, Oral)
• Deep generative models for detecting differential expression in single cells.
  Pierre Boyeau, Romain Lopez, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, and Nir Yosef.
  Machine Learning in Computational Biology(2019, Oral)