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Karthik Shekhar, Ph.D.

University of California, Berkeley


Karthik Shekhar is an Assistant Professor in the Department of Chemical and Biomolecular Engineering at the University of California (UC) Berkeley and a member of the Helen Wills Neuroscience Institute. His research to understand the organization, development and evolution of neural diversity in the visual system. In this pursuit, his group combines single-cell molecular profiling approaches, mathematical modeling and machine learning methodologies to derive insights from genomic data. His prior scientific training spans engineering, neuroscience, immunology, single-cell genomics, and computational biology. As a Ph.D. student at MIT, he applied tools from statistical physics to study systems-level adaptive immunity to RNA viruses, and developed a framework to identify immunological “hotspots” in the viral genome from circulating strain data. Collaborating with clinicians at MGH, he designed novel immunogens for HIV that were preclinically tested. As an NIH K99 postdoctoral fellow in Aviv Regev’s lab the Broad Institute, he utilized high-throughput single-cell RNA-seq to construct and validate comprehensive neuronal atlases of the mouse retina and non-human primate retina together with the group of Prof. Joshua Sanes. As an independent investigator, his research has focused on understanding how neural diversity arises in postmitotic precursors within the retina and the primary visual cortex. His group has recently made inroads into understanding the role of sensory experience in shaping the molecular profiles and function of cell types. A parallel effort in his group aims to derive the evolutionary history of neural diversity in the visual system, which exhibits a remarkably conserved blueprint across vertebrates inhabiting distinct visuoecological niches. A third pillar of his research program is to leverage spatial transcriptomic approaches to study the multicellular ecosystem of neurodegeneration in glaucoma, an irreversible blinding disease. His work is distinguished by a high degree of collaboration with neurobiologists and clinical scientists.

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