Reza Abbasi-Asl, PhD

Photo of Reza Abbasi-Asl, PhD
Title(s)Associate Professor, Neurology
SchoolSchool of Medicine
Address675 Nelson Rising Lane
San Francisco CA 94158
ORCID ORCID Icon0000-0001-7824-4628 Additional info
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Overview 
    Collapse overview
    We are a research team at the University of California, San Francisco where we investigate the role of advanced computational tools in understanding brain functions and its related disorders. More specifically, our research program revolves around the development of interpretable machine learning tools to (1) integrate multi-modal data collected from the brain (and body) in both microscopic and macroscopic resolutions, (2) predict functions of biological systems in different resolutions, and (3) determine the functional differences across neurological disorders. We are a part of the Neuroscape Center and Cognitive Neuroscience division at UCSF and our team is supported through funding from NIH National Institute of Mental Health, NIH National Institute of Aging, Weill Neurohub, Sandler Program for Breakthrough in Biomedical Research, UCSF Innovation Ventures, and Google.

    Collapse Biography 
    Collapse education and training
    UC BerkeleyPhD05/2018Electrical Engineering and Computer Sciences
    UC BerkeleyMSc05/2018Electrical Engineering and Computer Sciences
    Sharif University of TechnologyMSc01/2013Biomedical Engineering
    Amirkabir University of TechnologyBSc09/2010Electrical Engineering
    Collapse awards and honors
    UC Noyce Initiative2026UC Noyce Award
    UCSF2025Weill Catalyst Award
    UCSF2023Kunal Patel Catalyst Award
    Weill Neurohub2021Next Great Ideas Award
    Sandler Program for Breakthrough Biomedical Research (PBBR)2021New Frontiers Research Award
    UC Berkeley, Department of Electrical Engineering and Computer Sciences2018Eli Jury Award
    UC Berkeley Graduate Division2017May J. Koshland Fund in Memory of H.A. Jastro Award
    Sharif University of Technology2010Excellence Award in Biomedical Engineering
    Amirkabir University of Technology2007Excellence Award in Electrical Engineering

    Collapse Research 
    Collapse research activities and funding
    Functional regionalization of the brain revealed by multi-modal neural and genomics dataintegration
    NIH R01LM014619Jun 10, 2025 - Apr 30, 2029
    Role: PI
    Determining the circuits and signals of sleep dysfunction in Parkinson’s disease through chronic intracranial recordings and closed-loop Deep Brain Stimulation
    NIH R01NS131405Jul 1, 2023 - Jun 30, 2028
    Role: co-Investigator
    Interpretable Machine Learning for Video-Assisted Diagnosis and Tracking of Parkinson’s Disease
    UCSF Innovation Ventures Catalyst AwardFeb 1, 2023 - Feb 1, 2025
    Role: PI
    Integrated functional and structural analysis of an entire column in mouse primary visual cortex
    NIH/NIMH RF1MH128672Aug 1, 2022 - Jul 31, 2025
    Role: PI
    Revealing regionalization in whole-organ spatial datasets via interpretable machine learning
    Sandler Program for Breakthrough Biomedical Research Jan 1, 2022 - Jan 1, 2023
    Role: PI
    Synthetic and Augmented MRI for a shared neuroimaging infrastructure across the Weill Neurohub
    Weill Neurohub Pillars Program AwardOct 1, 2021 - Sep 30, 2024
    Role: PI
    Revealing neural functions in primary visual cortex via interpretable and biologically realistic neural networks
    Sandler Program for Breakthrough Biomedical Research Jun 15, 2021 - Jun 14, 2022
    Role: PI
    Neural markers of impending task performance
    NIH R03AG065966May 1, 2021 - Apr 30, 2023
    Role: Co-Investigator
    Revealing Principal Patterns, Brain Areas and Local Gene Regulatory Networks in the Adult Mouse Brain by Interpretable Machine Learning
    Weill Neurohub - Next Great Ideas Program 7030453Apr 1, 2021 - Apr 1, 2023
    Role: PI

    Collapse Featured Content 

    Collapse Bibliographic 
    Collapse publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Functionally identified neuronal assemblies robustly encode stimuli and are structurally delineated by inhibition. Cell Rep. 2026 Sep 22; 45(9):117900. Wagner-Carena J, Kate S, Riordan T, Abbasi-Asl R, Aman J, Amster A, Arkhipov A, Bodor AL, Brittain D, Buchanan J, Buice MA, Bumbarger DJ, Collman F, Maçarico da Costa N, Daniel S, Denman DJ, de Vries SEJ, Joyce E, Kapner D, King CW, Larkin JD, Lecoq J, Mahalingam G, Millman D, Mölter J, Morrison C, Reid RC, Schneider-Mizell CM, Suckow S, Takasaki KT, Takeno M, Torres R, Vumbaco D, Waters J, Wyrick DG, Yin W, Zhuang J, Mihalas S, Berteau S. PMID: 42664054.
      View in: PubMed   Mentions:
    2. Diurnal step count patterns in progressive multiple sclerosis. Mult Scler. 2026 Aug 17; 13524585261475910. Behal A, Block VJ, Cree BA, Abbasi-Asl R. PMID: 42608793.
      View in: PubMed   Mentions:
    3. Multitarget brain implants enable generalized decoding of Parkinson's disease symptoms from chronic home recordings. Res Sq. 2026 May 15. Merk T, Olaru M, Rajamani N, Zvarova P, Purelku E, Yin Z, Köhler RM, Vanhoecke J, Oswal A, Zhu G, Zhang JG, Abbasi-Asl R, Hahn A, Little S, Horn A, Starr PA, Neumann WJ. PMID: 42183377; PMCID: PMC13193127.
      View in: PubMed   Mentions:
    4. State-Dependent Organization of Microscale Functional Circuitry in Visual Cortex. bioRxiv. 2026 Apr 03. Biswas R, Senevirathne HW, Wang Y, Zhang J, Mukherjee S, Abbasi-Asl R. PMID: 41959169; PMCID: PMC13060340.
      View in: PubMed   Mentions:
    5. Personalized supervised and unsupervised intracranial sleep decoding during deep brain stimulation. NPJ Digit Med. 2026 Jan 22; 9(1). Smyth C, Anjum MF, Zhang JX, Yao J, Abbasi-Asl R, Starr P, Little S. PMID: 41571940; PMCID: PMC13376363.
      View in: PubMed   Mentions:
    6. Data-driven fine-grained region discovery in the mouse brain with transformers. Nat Commun. 2025 Oct 07; 16(1):8536. Lee AJ, Dubuc A, Kunst M, Yao S, Lusk N, Ng L, Zeng H, Tasic B, Abbasi-Asl R. PMID: 41057352; PMCID: PMC12504640.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    7. Robustness tests for biomedical foundation models should tailor to specifications. NPJ Digit Med. 2025 Aug 29; 8(1):557. Xian RP, Baker NR, David T, Cui Q, Holmgren AJ, Bauer S, Sushil M, Abbasi-Asl R. PMID: 40883427; PMCID: PMC12397224.
      View in: PubMed   Mentions: 1  
    8. Imaging joy with generalized slice dithered enhanced resolution and SWAT reconstruction: 3T high spatial-temporal resolution fMRI. Front Neuroimaging. 2025; 4:1537440. Townsend JD, Muller AM, Naeem Z, Beckett A, Kalisetti B, Abbasi-Asl R, Liao C, Vu AT. PMID: 40529161; PMCID: PMC12170577.
      View in: PubMed   Mentions:
    9. Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies. bioRxiv. 2025 May 23. Wagner-Carena J, Kate S, Riordan T, Abbasi-Asl R, Aman J, Amster A, Bodor AL, Brittain D, Buchanan JA, Buice MA, Bumbarger DJ, Collman F, da Costa NM, Denman DJ, de Vries S, Joyce E, Kapner D, King CW, Larkin JD, Lecoq J, Mahalingam G, Millman D, Mölter J, Morrison C, Reid RC, Schneider-Mizell CM, Daniel S, Suckow S, Takasaki KT, Takeno M, Torres R, Vumbaco D, Waters J, Wyrick DG, Yin W, Zhuang J, Mihalas S, Berteau S. PMID: 40661630; PMCID: PMC12258723.
      View in: PubMed   Mentions:
    10. Motor learning leverages coordinated low-frequency cortico-basal ganglia activity to optimize motor preparation in humans with Parkinson's disease. Front Neurosci. 2025; 19:1542493. Presbrey KN, Wozny TA, Louie KH, Little S, Starr PA, Abbasi-Asl R, Wang DD. PMID: 40433500; PMCID: PMC12106502.
      View in: PubMed   Mentions:
    11. Data-driven fine-grained region discovery in the mouse brain with transformers. bioRxiv. 2025 Feb 26. Lee AJ, Dubuc A, Kunst M, Yao S, Lusk N, Ng L, Zeng H, Tasic B, Abbasi-Asl R. PMID: 38766132; PMCID: PMC11100623.
      View in: PubMed   Mentions:
    12. Compression-enabled interpretability of voxelwise encoding models. PLoS Comput Biol. 2025 02; 21(2):e1012822. Kamali F, Suratgar AA, Menhaj M, Abbasi-Asl R. PMID: 39970189; PMCID: PMC11867343.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. Deep brain stimulation-entrained gamma oscillations in chronic home recordings in Parkinson's disease. Brain Stimul. 2025 Mar-Apr; 18(2):132-141. Olaru M, Hahn A, Shcherbakova M, Little S, Neumann WJ, Abbasi-Asl R, Starr PA. PMID: 39894343.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    14. Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology. Proc Natl Acad Sci U S A. 2024 09 10; 121(37):e2319804121. Cahill R, Wang Y, Xian RP, Lee AJ, Zeng H, Yu B, Tasic B, Abbasi-Asl R. PMID: 39226356; PMCID: PMC11406299.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    15. Structurally-constrained encoding framework using a multi-voxel reduced-rank latent model for human natural vision. J Neural Eng. 2024 07 26; 21(4). Ranjbar A, Suratgar AA, Menhaj MB, Abbasi-Asl R. PMID: 38986451.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    16. Interpretable video-based tracking and quantification of parkinsonism clinical motor states. NPJ Parkinsons Dis. 2024 Jun 25; 10(1):122. Deng D, Ostrem JL, Nguyen V, Cummins DD, Sun J, Pathak A, Little S, Abbasi-Asl R. PMID: 38918385; PMCID: PMC11199701.
      View in: PubMed   Mentions: 8  
    17. Practical considerations for machine learning-enabled discoveries in spatial transcriptomics. GEN Biotechnol. 2024 Jun; 3(3):130-135. Lee AJ, Cahill R, Abbasi-Asl R. PMID: 41438128; PMCID: PMC12721806.
      View in: PubMed   Mentions:
    18. Motor network gamma oscillations in chronic home recordings predict dyskinesia in Parkinson's disease. Brain. 2024 Jun 03; 147(6):2038-2052. Olaru M, Cernera S, Hahn A, Wozny TA, Anso J, de Hemptinne C, Little S, Neumann WJ, Abbasi-Asl R, Starr PA. PMID: 38195196; PMCID: PMC11146421.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    19. The entropic heart: Tracking the psychedelic state via heart rate dynamics. bioRxiv preprint. 2023. F. E. Rosas, P. A. M. Mediano, C. Timmermann, A. I Luppi, D. Candia-Rivera, R. Abbasi-Asl, A. Gazzaley, M. L. Kringelbach, S. D. Muthukumaraswamy, D. Bor, S. Garfinkel, R. Carhart-Harris. View Publication.
    20. Interpretable prototype discovery in deep learning based time series classification. Integrated Systems: Innovations and Applications, Springer book chapter. 2023. Gaurav Ghosal, R. Abbasi-Asl. .
    21. Neurology. Diurnal Step Count Patterns in Progressive Multiple Sclerosis. 2023. D. Navani, V. Block, B. Cree, R. Abbasi-Asl. . View Publication.
    22. Journal of Vision. Reconstructing visual experience from a large-scale biologically realistic model of mouse primary visual cortex. 2023. R. Abbasi-Asl, Y. Chi, H. Yang, K. Dai, A. Arkhipov. View Publication.
    23. Machine Learning for Uncovering Biological Insights in Spatial Transcriptomics Data. ArXiv. 2023 Mar 29. Lee AJ, Cahill R, Abbasi-Asl R. PMID: 37033464; PMCID: PMC10081350.
      View in: PubMed   Mentions:
    24. Editorial: Functional microcircuits in the brain and in artificial intelligent systems. Front Comput Neurosci. 2023; 17:1135507. Lee JH, Choe Y, Ardid S, Abbasi-Asl R, McCarthy M, Hu B. PMID: 36761841; PMCID: PMC9904200.
      View in: PubMed   Mentions: 1  
    25. Robust Registration of Medical Images in the Presence of Spatially-Varying Noise. Algorithms. 2022; 15(2):58. Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
    26. Journal of Vision. A large-scale standardized survey of neural receptive fields in an entire column in mouse V1. 2021. R. Abbasi-Asl, A. Muslim, J. Larkin, K. Takasaki, D. Millman, D. Denman, J. Lecoq, A, Arkhipov, N. W Gouwens, J. Waters, R C. Reid, S. EJ de Vries. View Publication.
    27. Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification. arxiv. 2021. Gaurav R Ghosal, Reza Abbasi-Asl. . View Publication.
    28. Structural Compression of Convolutional Neural Networks with Applications in Interpretability. Front Big Data. 2021; 4:704182. Abbasi-Asl R, Yu B. PMID: 34514381; PMCID: PMC8427695.
      View in: PubMed   Mentions: 4  
    29. Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex. Neuron. 2020 05 06; 106(3):388-403.e18. Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A. PMID: 32142648.
      View in: PubMed   Mentions: 141     Fields:    Translation:AnimalsCells
    30. Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain. eNeuro. 2020 Jan/Feb; 7(1). Takasaki K, Abbasi-Asl R, Waters J. PMID: 31907211; PMCID: PMC6984806.
      View in: PubMed   Mentions: 59     Fields:    Translation:Animals
    31. Definitions, methods, and applications in interpretable machine learning. Proc Natl Acad Sci U S A. 2019 10 29; 116(44):22071-22080. Murdoch WJ, Singh C, Kumbier K, Abbasi-Asl R, Yu B. PMID: 31619572; PMCID: PMC6825274.
      View in: PubMed   Mentions: 314     Fields:    
    32. 3-Photon Calcium Imaging of Deep Cortical Layers for Functional Connectomics. Optics and the Brain. 2019. Kevin Takasaki, Josh Larkin, Reza Abbasi-Asl, Dan Denman, Dan Millman, Saskia de Vries, Marc Takeno, Nuno M da Costa, R Clay Reid, Jack Waters. View Publication.
    33. Brain-Computer Interface in Virtual Reality. 9th International IEEE EMBS Conference on Neural Engineering (NER). 2019. R. Abbasi-Asl, M. Keshavarzi, D. Y. Chan. View Publication.
    34. Visual physiology of the layer 4 cortical circuit in silico. PLoS Comput Biol. 2018 11; 14(11):e1006535. Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Abbasi-Asl R, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-Llavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C. PMID: 30419013; PMCID: PMC6258373.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    35. The DeepTune framework for modeling and characterizing neurons in visual cortex area V4. bioArxiv. 2018. Reza Abbasi-Asl, Yuansi Chen, Adam Bloniarz, Michael Oliver, Ben DB Willmore, Jack L Gallant, Bin Yu. View Publication.
    36. Interpreting Convolutional Neural Networks Through Compression. NIPS 2017 Symposium on Interpretable Machine Learning. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
    37. Do retinal ganglion cells project natural scenes to their principal subspace and whiten them?. IEEE Proceedings of 50th Asilomar Conference on Signals, Systems and Computers. 2016. R. Abbasi-Asl, C. Pehlevan, B. Yu and D. B. Chklovskii. View Publication.
    38. Automatic b-spline image registration using histogram-based landmark extraction. IEEE-EMBS Conference on Biomedical Engineering and Sciences. 2012. Abdollah Ghanbari, Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
    39. Estimation of muscle force with emg signals using hammerstein-wiener model. 5th Kuala Lumpur International Conference on Biomedical Engineering. 2011. Reza Abbasi-Asl, Rahman Khorsandi, Shahrokh Farzampour, Edmond Zahedi. View Publication.
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