Research

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.

Raghavan, Srivatsan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DelAdel, Kristen E. Lowder, Jennyfer Galvez-Reyes, et al. 2021. “Microenvironment Drives Cell State, Plasticity, and Drug Response in Pancreatic Cancer”. Cell.

Kedzierska, Kasia Z., Lorin Crawford, Ava P. Amini, and Alex X. Lu. 2023. “Assessing the Limits of Zero-Shot Foundation Models in Single-Cell Biology”. BioRxiv.