Publications

D’Ascenzo, Davide, and Sebastiano Cultrera_di_Montesano. 2025. “ScDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics”. ArXiv.

Cultrera_di_Montesano, Sebastiano, Davide D’Ascenzo, Srivatsan Raghavan, Ava P. Amini, Peter S. Winter, and Lorin Crawford. 2025. “Hierarchical Cross-Entropy Loss Improves Atlas-Scale Single-Cell Annotation Models”. BioRxiv.

Fischer, David S., Martin A. Villanueva, Peter S. Winter, and Alex K. Shalek. 2025. “Adapting Systems Biology to Address the Complexity of Human Disease in the Single-Cell Era”. Nature Review Genetics.

Nadig, Ajay, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, and Lorin Crawford. 2025. “Consequences of Training Data Composition for Deep Learning Models in Single-Cell Biology”. BioRxiv.

Dilly, Julien, Megan T. Hffman, Laleh Abbassi, Ziyue Li, Francesca Paradiso, Brendan D. Parent, Connor J. Hennessey, et al. 2024. “Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer”. Cancer Discovery.

DenAdel, Alan, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, and Lorin Crawford. 2024. “Evaluating the Role of Pre-Training Dataset Size and Diversity on Single-Cell Foundation Model Performance”. BioRxiv.

DelAdel, Alan, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, and Lorin Crawford. 2024. “A Knockoff Calibration Method to Avoid Over-Clustering in Single-Cell RNA-Sequencing”. BioRxiv.

Winter, Peter S., Michelle L. Ramseier, Andrew W. Navia, Sachit Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, et al. 2024. “Mutation and Cell State Compatibility Is Required and Targetable in Ph+ Acute Lymphoblastic Leukemia Minimal Residual Disease”. BioRxiv.

Nwizu, Chibuikem, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, and Lorin Crawford. 2024. “Scalable Nonparametric Clustering With Unified Marker Gene Selection for Single-Cell RNA-Seq Data”. BioRxiv.

Liu, Nuo, Walaa Kattan, Benjamin Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jamie H. Cheah, et al. 2024. “Scalable, Compressed Phenotypic Screening Using Pooled Perturbations”. Nature Biotechnology.