Research

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Papers


  1. Lee, Alex J., Shenqin Yao, Nicholas Lusk, Lydia Ng, Michael Kunst, Hongkui Zeng, Bosiljka Tasic, and Reza Abbasi-Asl. "Data-Driven Fine-Grained Region Discovery in the Mouse Brain with Transformers." Nature Communications, 2025. https://doi.org/10.1038/s41467-025-64259-4. [doi, pdf]
  2. Brown, Jesse A., Alex J. Lee, Kristen Fernhoff, Taylor Pistone, Lorenzo Pasquini, Amy B. Wise, et al. "Atrophy-Driven Functional Network Collapse in Neurodegenerative Disease." Nature Communications, 2025. https://doi.org/10.1038/s41467-025-65156-6. [doi, pdf]
  3. Flagan, Taru M., Chu, Stephanie A., Hakkinen, Suvi, Zhang, Liwen, et al. "Functional Connectivity Associations with Markers of Disease Progression in GRN Pathogenic Variant Carriers." Annals of Clinical and Translational Neurology, 2025. http://doi.org/10.1002/acn3.70170. [doi]
  4. Rui, Patrick X., Alex J. Lee, Satvik Lolla, Vincent Wang, Russell Ro, Qiming Cui, and Reza Abbasi-Asl. "Assessing Biomedical Knowledge Robustness in Large Language Models by Query-Efficient Sampling Attacks." Transactions in Machine Learning Research, 2024. https://arxiv.org/abs/2402.10527. [doi, pdf]
  5. Cahill, Robert, Yu Wang, R. Patrick Xian, Alex J. Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, and Reza Abbasi-Asl. "Unsupervised Pattern Identification in Spatial Gene Expression Atlas Reveals Mouse Brain Regions beyond Established Ontology." Proceedings of the National Academy of Sciences of the United States of America 121, no. 37 (September 10, 2024): e2319804121. https://doi.org/10.1073/pnas.2319804121. [doi, pdf]
  6. Pasquini, Lorenzo, Felipe L. Pereira, Sahba Seddighi, Yi Zeng, Yongbin Wei, Ignacio Illán-Gala, Sarat C. Vatsavayai, et al. "Frontotemporal Lobar Degeneration Targets Brain Regions Linked to Expression of Recently Evolved Genes." Brain: A Journal of Neurology 147, no. 9 (September 3, 2024): 3032–47. https://doi.org/10.1093/brain/awae205. [doi]
  7. Zhang, Liwen, Taru M. Flagan, Suvi Häkkinen, Stephanie A. Chu, Jesse A. Brown, Alex J. Lee, Lorenzo Pasquini, et al. "Network Connectivity Alterations across the MAPT Mutation Clinical Spectrum." Annals of Neurology 94, no. 4 (October 2023): 632–46. https://doi.org/10.1002/ana.26738. [doi, pdf]
  8. Pasquini, Lorenzo, Susanna L. Fryer, Stuart J. Eisendrath, Zindel V. Segal, Alex J. Lee, Jesse A. Brown, Manish Saggar, and Daniel H. Mathalon. "Dysfunctional Cortical Gradient Topography in Treatment-Resistant Major Depressive Disorder." Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 8, no. 9 (September 2023): 928–39. https://doi.org/10.1016/j.bpsc.2022.10.009. [doi, pdf]
  9. Chow, Tiffany E., Christina R. Veziris, Renaud La Joie, Alex J. Lee, Jesse A. Brown, Jennifer S. Yokoyama, Katherine P. Rankin, et al. "Increasing Empathic Concern Relates to Salience Network Hyperconnectivity in Cognitively Healthy Older Adults with Elevated Amyloid-β Burden." NeuroImage. Clinical 37, no. 103282 (2023): 103282. https://doi.org/10.1016/j.nicl.2022.103282. [doi, pdf]
  10. Pasquini, Lorenzo, Fatemeh Noohi, Christina R. Veziris, Eena L. Kosik, Sarah R. Holley, Alex Lee, Jesse A. Brown, et al. "Dynamic Autonomic Nervous System States Arise during Emotions and Manifest in Basal Physiology." Psychophysiology 60, no. 4 (April 2023): e14218. https://doi.org/10.1111/psyp.14218. [doi, pdf]
  11. Brown, Jesse A., Alex J. Lee, Lorenzo Pasquini, and William W. Seeley. "A Dynamic Gradient Architecture Generates Brain Activity States." NeuroImage 261, no. 119526 (November 1, 2022): 119526. https://doi.org/10.1016/j.neuroimage.2022.119526. [doi, pdf]
  12. Mantyh, William G., Salvatore Spina, Alex Lee, Leonardo Iaccarino, David Soleimani-Meigooni, Elena Tsoy, Taylor J. Mellinger, et al. "Tau Positron Emission Tomographic Findings in a Former US Football Player with Pathologically Confirmed Chronic Traumatic Encephalopathy." JAMA Neurology 77, no. 4 (April 1, 2020): 517–21. https://doi.org/10.1001/jamaneurol.2019.4509. [doi, pdf]
  13. Pasquini, Lorenzo, Gianina Toller, Adam Staffaroni, Jesse A. Brown, Jersey Deng, Alex Lee, Katarzyna Kurcyus, et al. "State and Trait Characteristics of Anterior Insula Time-Varying Functional Connectivity." NeuroImage 208, no. 116425 (March 2020): 116425. https://doi.org/10.1016/j.neuroimage.2019.116425. [doi, pdf]

Preprints


  1. Yang, Kevin K.*, Sarah Alamdari*, Alex J. Lee*, Kaeli Kaymak-Loveless, Samir Char, Garyk Brixi, Carles Domingo-Enrich, Chentong Wang, Suyue Lyu, Nicolo Fusi, Neil Tenenholtz, Ava P. Amini. "The Dayhoff Atlas: Scaling Sequence Diversity for Improved Protein Generation." (*co-first authors) bioRxiv, 2025. https://doi.org/10.1101/2025.07.21.665991. [doi]
  2. Lee, Alex Jihun, and Reza Abbasi-Asl. "Opportunities in Deep Learning Methods Development for Computational Biology." arXiv [q-Bio.QM], June 12, 2024. arXiv. http://arxiv.org/abs/2406.08686. [doi]

Conference abstracts


  1. Alex Jihun Lee, Alma Dubuc, Shenqin Yao, Nicholas Lusk, Lydia Ng, Michael Kunst, Hongkui Zeng, Bosiljka Tasic, Reza Abbasi-Asl. "Multimillion Cell Self-Supervised Representation Learning Enables Organ-Scale Tissue Niche Discovery." ICML Multi-modal Foundation Models and Large Language Models for Life Sciences workshop, 2025.
  2. Alex Jihun Lee, Sarah Alamdari, Chentong Wang, Reza Abbasi-Asl, Kevin Yang, Ava Amini. "Structure-Based Synthetic Data Augmentation for Protein Language Models." ICLR Generative and Experimental Perspectives for Biomolecular Design (GEM) workshop, 2025. https://openreview.net/forum?id=XAhcYXdqSJ. [doi, pdf]
  3. Chen, Yu., Winson Fu Zun Yang, Myrthe G. Rijpma, Jesse A. Brown, Alex Lee, Gianina Toller, Howard J. Rosen, Joel H. Kramer, Bruce L. Miller, Katherine P. Rankin. "The Hierarchical Organization of the Salience, Default, and Executive Networks in Social Inferences." Organization for Human Brain Mapping, 2024.
  4. Alex Jihun Lee, Hongkui Zeng, Bosiljka Tasic, Reza Abbasi-Asl. "Masked Autoencoders for Spatial Clustering in the Mouse Brain." In Machine Learning in Computational Biology, 2023. https://sites.google.com/cs.washington.edu/mlcb2023/accepted-abstracts. [doi]
  5. Brown, Jesse A., Alex J. Lee, Lorenzo Pasquini, Adit Friedberg, Gil D. Rabinovici, Joel H. Kramer, Maria Luisa Gorno Tempini, Howard J. Rosen, Bruce L. Miller, and William W. Seeley. "Local Neurodegeneration and Global Connectivity Adaptation across the FTD-AD Spectrum." Alzheimer's & Dementia 17, no. S6 (2021): e055308. https://doi.org/10.1002/alz.055308. [doi]
  6. Flagan, Taru M., Stephanie A. Chu, Suvi Häkkinen, David McFall, Carolin Heller, Jonathan D. Rohrer, Jesse A. Brown, et al. "Complement and NfL Associations with Brain Structure and Functional Connectivity Alterations in Presymptomatic and Symptomatic GRN Mutation Carriers." In Alzheimers. Dement., 17:e050737. Wiley, 2021. https://doi.org/10.1002/alz.050737. [doi]
  7. Zhang, Liwen, Taru M. Flagan, Stephanie A. Chu, Suvi Häkkinen, Jesse A. Brown, Alex Jihun Lee, Lorenzo Pasquini, et al. "Presymptomatic and Symptomatic MAPT Mutation Carriers Feature Functional Connectivity Alterations." In Alzheimers. Dement., 17:e054128. Wiley, 2021. https://doi.org/10.1002/alz.054128. [doi]

News coverage


Quanta Magazine — Fed on Reams of Cell Data, AI Maps New Neighborhoods in the Brain

Fed on Reams of Cell Data, AI Maps New Neighborhoods in the Brain

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The Transmitter — How neuroscientists are using AI

How neuroscientists are using AI

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Microsoft Research — The Dayhoff Atlas: scaling sequence diversity improves protein design

The Dayhoff Atlas: scaling sequence diversity improves protein design

Microsoft Research · Jul 25, 2025