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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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David Husselbee

Person: Research Associate II

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation.

Publication: Journal Article

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.

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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...

Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.

Publication: Journal Article

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.

Dylan Mercado

Person: Broad 2025 BSSP

Dylan joined the Broad Summer Scholars Program eager to explore how tiny changes in DNA can ripple outward to affect brain function and health. At the Stanley Center, he worked on understanding the functional effects of missense mutations in the CACNA1A gene, which encodes the CaV2.1 calcium channel...

Lanjing Wei

Person: Postdoctoral Associate, Dana Farber Cancer Institute

Langjing Wei, PhD

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https://www.ncbi.nlm.nih.gov/myncbi/seungmin.hwang.1/bibliography/public/ 68. Soriaga L, Balce D, Bartha I, Park A, Wong E, McAllaster M, Mueller EA, Barauskas O, Carabajal E, Kowalski B, Lee S, Lo G, Mahoney TF, Metruccio M, Sahakyan A, Somasundaram L, Steinfeld T, Wang L, Wedel L, Yim SS, Yin L...