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Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
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.
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
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.
Adapting systems biology to address the complexity of human disease in the single-cell era
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.
Consequences of training data composition for deep learning models in single-cell biology
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.
Hierarchical cross-entropy loss improves atlas-scale single-cell annotation models
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.
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation.
Labade, Ajay S, Zachary D Chiang, Caroline Comenho, Paul L Reginato, Andrew C Payne, Andrew S Earl, Rojesh Shrestha, et al. 2025. “Expansion in Situ Genome Sequencing Links Nuclear Abnormalities to Aberrant Chromatin Regulation.”. Science (New York, N.Y.) 389 (6758): eadt2781.
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.
Kotliar, Dylan, Michelle Curtis, Ryan Agnew, Kathryn Weinand, Aparna Nathan, Yuriy Baglaenko, Kamil Slowikowski, et al. 2025. “Reproducible Single-Cell Annotation of Programs Underlying T Cell Subsets, Activation States and Functions.”. Nature Methods.
Next-generation characterization of the Cancer Cell Line Encyclopedia
Ghandi, Mahmoud, Franklin Huang, Judit Jané-Valbuena, Gregory Kryukov, Christopher Lo, Robert McDonald, Jordi Barretina, et al. 2019. “Next-Generation Characterization of the Cancer Cell Line Encyclopedia”. Nature 569 (7757): 503-8.
The landscape of cancer cell line metabolism
Li, Haoxin, Shaoyang Ning, Mahmoud Ghandi, Gregory Kryukov, Shuba Gopal, Amy Deik, Amanda Souza, et al. 2019. “The Landscape of Cancer Cell Line Metabolism”. Nat Med 25 (5): 850-60.