Author

Hsin-Yu Lai

Allen InstituteORCID 0000-0002-5783-3156Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:statistical model· 4 Research Focus:cell type annotation· 3 Assay:scRNA-seq· 3 Research Focus:benchmarking· 2 Research Focus:differential expression· 2 Assay:bulk RNA-seq· 1 Approach:deep learning· 1

Frequent Co-Authors

Kyle J. TravagliniiD· 4 shared Mariano I. GabittoiD· 4 shared Anamika AgrawaliD· 3 shared Ed S. LeiniD· 3 shared Eitan S KaplaniD· 3 shared Omar Z. KanaiD· 3 shared Alana A. OyamaiD· 2 shared Amy TorkelsoniD· 2 shared

Activity by Year

2026-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersNeuroscience

Kyle J. TravagliniORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

The SEA-AD DREAM Challenge: Community benchmarking human and AI agent solutions for Alzheimer's disease neuropathology prediction from single-nucleus transcriptomics

Hsin-Yu Lai, Nikolaos Kalavros, Verena Chung, Eitan S Kaplan, Julio Sáez-Rodríguez, Lingyi Cai, Dimitris Anastassiou, Erica Chen, Ignacio Garach Vélez, Gamze Gürsoy, Luis Javier Herrera, Xiaoting Li, Eric R. Londin, Phillipe Loher, Iliza Nazeraj, , Mariano I. Gabitto

The paper presents a benchmarking challenge to predict Alzheimer's disease neuropathology from single-nucleus transcriptomics using human and AI models, finding that top methods achieve near-perfect categorical staging predictions.

bioRxiv · Aug 11, 2026 · PreprintNeuroscience

Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer's disease

Kyle J. Travaglini, Mariano I. Gabitto, Yi Ding, Anamika Agrawal, Nadia O. Postupna, Joseph T. Mahoney, Eitan S Kaplan, Erica J. Melief, Jeff Goldy, Anish Bhaswanth Chakka, Ming Xiao, Tejas S Bajwa, Andreas Tjärnberg, Jeanelle Ariza, Song‐Lin Ding, , Ed S. Lein

This study uses single-nucleus RNA-seq, ATAC-seq, and Multiome to analyze Alzheimer's disease across multiple brain regions, revealing shared and region-specific cellular vulnerabilities.

bioRxiv · Jul 2, 2026 · PreprintNeuroscience

scVIP: personalized modeling of single-cell transcriptomes for developmental and disease phenotypes

Hsin-Yu Lai, Yehchan Yoo, Andreas Tjärnberg, Kyle J. Travaglini, Ziyuan He, Qi Qiao, Anamika Agrawal, Omar Z. Kana, Cindy T. J. van Velthoven, Jeffrey B. Carroll, Mark Gillespie, Shubhabrata Mukherjee, David W. Fardo, Xiaojun Li, Ed S. Lein, Mariano I. Gabitto

scVIP models single-cell transcriptomes to predict phenotypes and infer trajectories in development and disease.

bioRxiv · Jun 27, 2026 · PreprintBioinformatics

The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease

Omar Z. Kana, Nadia O. Postupna, Anamika Agrawal, Brian Long, Kyle J. Travaglini, Mariano I. Gabitto, Hsin-Yu Lai, Joseph T. Mahoney, Ming Xiao, Tejas S Bajwa, Heino Hulsey-Vincent, Sora L Oyaizu, Gonzalo E. Mena, Janna Hong, Emily C. Gelfand, , Jennie Close

The paper maps AD-related pathological changes in the caudate nucleus at cellular resolution, identifying distinct features and cell type-specific responses.

bioRxiv · Jan 15, 2026 · PreprintNeuroscience