Author

Grace H. Huynh

Allen InstituteORCID 0000-0002-3801-8041Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Assay:bulk RNA-seq· 2 Research Focus:clustering· 2 Approach:deep learning· 2 Organism:human· 2 Organism:mouse· 2 Approach:transformer / foundation model· 2 Assay:ATAC-seq· 1

Frequent Co-Authors

Abhejit RajagopaliD· 2 shared Aaron D. GarciaiD· 1 shared Adam W. HantmaniD· 1 shared Aditi ChandrashekariD· 1 shared Agata BudzilloiD· 1 shared Alex TraniD· 1 shared Alexander ViethiD· 1 shared Alfredo Rodriguez· 1 shared

Activity by Year

2019-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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2 shared papersNeuroscience

Abhejit RajagopalORCID

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Author profile →

4 papers

Recent·Most cited

Cross-species consensus atlas of the primate basal ganglia

Nelson Johansen, Yuanyuan Fu, Matthew T. Schmitz, Alma Dubuc, Niklas Kempynck, Morgan E. Wirthlin, Aaron D. Garcia, Madeleine N. Hewitt, Meghan A. Turner, Stephanie C. Seeman, Brian Long, Xiao-Ping Liu, Shu Dan, Michael DeBerardine, Inkar Kapen, , Trygve E. Bakken

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

bioRxiv · Dec 16, 2025 · PreprintNeuroscience

PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

Kuan Pang, Yanay Rosen, Kasia Kedzierska, Ziyuan He, Abhejit Rajagopal, Claire E. Gustafson, Grace H. Huynh, Jure Leskovec

PULSAR is a foundation model that integrates multi-scale biological data to predict disease and clinical outcomes in the human immune system.

bioRxiv · Nov 24, 2025 · PreprintBioinformatics

TabVI: Leveraging Lightweight Transformer Architectures to Learn Biologically Meaningful Cellular Representations

Aditi Chandrashekar, Rohan Gala, Andreas Tjärnberg, Saniya Khullar, Grace H. Huynh, Mariano I. Gabitto

TabVI improves cell type annotation and integration using a probabilistic transformer model, producing interpretable feature attention masks and robust performance across dataset sizes.

bioRxiv · Feb 13, 2025 · PreprintBioinformatics

Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution

Ruixuan Gao, Shoh M. Asano, Srigokul Upadhyayula, Igor Pisarev, Daniel Edward Milkie, Tsung‐Li Liu, Ved P. Singh, Austin R. Graves, Grace H. Huynh, Yongxin Zhao, John Bogovic, Jennifer I. Colonell, Carolyn M. Ott, Christopher T Zugates, Susan J. Tappan, , Eric Betzig

The paper combines expansion and lattice light sheet microscopy to enable high-speed, nanoscale molecular imaging of neural circuits across large volumes.

Science · Jan 17, 2019Peer-reviewedNeuroscience