Reza Abbasi Asl • UCSF Profiles

Reza Abbasi Asl, PhD

Title(s)	Assistant Professor, Neurology
School	School of Medicine
Address	Location Required
Phone	415-476-3199
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Other Positions


Title(s)	UCSF Weill Institute for Neurosciences

Biography

Education and Training

UC Berkeley	PhD	05/2018	Electrical Engineering and Computer Sciences
UC Berkeley	MSc	05/2018	Electrical Engineering and Computer Sciences
Sharif University of Technology	MSc	01/2013	Biomedical Engineering
Amirkabir University of Technology	BSc	09/2010	Electrical Engineering

Awards and Honors

Weill Neurohub	2021	Investigator
UC Berkeley, Department of Electrical Engineering and Computer Sciences	2018	Eli Jury Award
UC Berkeley Graduate Division	2017	May J. Koshland Fund in Memory of H.A. Jastro Award
Sharif University of Technology	2010	Excellence Award in Biomedical Engineering
Amirkabir University of Technology	2007	Excellence Award in Electrical Engineering

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.

Websites

Abbasi Lab

Research

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

Featured Content

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Bibliographic

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.

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.

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:
Neu Neurology
Translation:Animals Cells
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:
Bra Brain Neu Neurology
Translation:Animals
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:
Sci Science
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.
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.
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:
Com Computational Biology
Translation:Animals Cells
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.
Robust Image Registration via Empirical Mode Decomposition. arXiv:1711.04247. 2018. Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
Interpreting Convolutional Neural Networks Through Compression. NIPS 2017 Symposium on Interpretable Machine Learning. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
Structural Compression of Convolutional Neural Networks. arXiv:1705.07356. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
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.
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.
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.
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.