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.
Publications
2024
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.
2023
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.
2021
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.