Reza Abbasi Asl, PhD

Title(s)Assistant Professor, Neurology
SchoolSchool of Medicine
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences

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    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
    Weill Neurohub2021Investigator
    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 Overview 
    Collapse Overview
    The Abbasi Lab develops interpretable models and algorithms based on machine learning principles to understand functions of the brain and related disorders. To discover and model the functions of neurons, the lab studies applications of machine learning in the analysis of large-scale multi-modal datasets including electrophysiology, calcium imaging, electron microscopy, and spatial gene expression profiles. In the next step and to reconcile our understanding of the brain with related disorders, the Abbasi Lab builds computational tools for scientific discovery in large-scale neurological clinical datasets. This involves interpretable analysis and visualization of medical images, multi-omics datasets, and electronic health records.
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    Collapse Research 
    Collapse Research Activities and Funding
    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

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    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.
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    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. 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: 12     Fields:    Translation:AnimalsCells
    2. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    3. 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.
      View in: PubMed   Mentions: 26     Fields:    
    4. 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.
    5. 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.
    6. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    7. 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.
    8. Robust Image Registration via Empirical Mode Decomposition. arXiv:1711.04247. 2018. Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
    9. Interpreting Convolutional Neural Networks Through Compression. NIPS 2017 Symposium on Interpretable Machine Learning. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
    10. Structural Compression of Convolutional Neural Networks. arXiv:1705.07356. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
    11. 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.
    12. 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.
    13. 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.
    14. Hammerstein-Wiener model: A new approach to the estimation of formal neural information. Basic and Clinical Neuroscience. 4(3):45-51. Reza Abbasi-Asl, Rahman Khorsandi, Bijan Vosooghi-Vahdat. View Publication.
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