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Articles and other press 2024: Beth Cimini is interviewed in special episode on Mental Health on Peter O'Toole's podcast series "The Microscopists" [ Link to video] 2024. Beth Cimini is interviewed in "Enhancing Global Access: interview with CZI grantee Beth Cimini" (Focal Plane/ The Company of...

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.

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To nominate individuals and/or teams for the Merkin Prize, please confirm you've reviewed the eligibility requirements and then fill out the nomination form below. FAQs can be viewed here. For additional questions or technical difficulties, contact merkinprize@broadinstitute.org. Nomination Deadline...

David Husselbee

Person: Research Associate II

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https://www.ncbi.nlm.nih.gov/myncbi/seungmin.hwang.1/bibliography/public/ 1. Park J, Seo T, Hwang S, Lee D, Gwack Y, Choe J. 2000. The K-bZIP protein from Kaposi's sarcoma-associated herpesvirus interacts with p53 and represses its transcriptional activity. J Virol 74:11977-82. 2. Lim C, Gwack Y...

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.