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Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer

Publication: Journal Article

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.

Hongming Shang

Person: Research Technician, Dana Farber Cancer Institute

Hongming Shang

Adapting systems biology to address the complexity of human disease in the single-cell era

Publication: Journal Article

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

Publication: Journal Article

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

Publication: Journal Article

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.

Xiang Zhang

Person: Postdoctoral Associate, Dana Farber Cancer Institute

Xiang Zhang PhD Xiang is a Research Fellow in the Raghavan Lab at the Dana-Farber Cancer Institute. He specializes in developing machine learning approaches to integrate diverse genomic data, infer biological networks, and identify novel therapeutic targets. Originally from Shenzhen, Xiang received...

Alex Stanley

Person: Research Associate, Broad Institute

Alex Stanley Alex is a Research Associate I at the Broad working to decipher cell state shifts and WNT pathway dependencies as potential therapeutic targets. She completed her B.S. in Neuroscience and Classical and Early Mediterranean Studies with a minor in Mathematics at Brandeis University in...

Lanjing Wei

Person: Postdoctoral Associate, Dana Farber Cancer Institute

Langjing Wei, PhD

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

Publication: Journal Article

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.

scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics

Publication: Journal Article

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