Karthik Shekhar

About

Karthik Shekhar is the John F. Heil, Jr. Professor in Chemical & Biomolecular Engineering at the University of California, Berkeley. He completed his B.S. and M.S. at the Indian Institute of Technology, Bombay in 2008, and earned his Ph.D. from the Massachusetts Institute of Technology in 2015. Following his doctoral studies, he was a Postdoctoral Fellow at the Broad Institute of MIT and Harvard from 2015 to 2019. His research focuses on cellular and systems biology, utilizing high-throughput single-cell genomic measurements to understand cellular diversity in complex tissues such as the mouse retina, and exploring their conservation across vertebrates including humans and non-human primates. He develops computational approaches rooted in machine learning to make precise biological inferences, aiming to reveal general mechanistic principles underlying cellular organization and molecular networks.

Research topics

• Pathology
• Biology
• Cancer research
• Psychology
• Medicine
• Immunology
• Neuroscience
• Genetics
• Cell biology

Selected publications

• Solving neurodegeneration: common mechanisms and strategies for new treatments

  Molecular Neurodegeneration · 2022 · 296 citations

  Across neurodegenerative diseases, common mechanisms may reveal novel therapeutic targets based on neuronal protection, repair, or regeneration, independent of etiology or site of disease pathology. To address these mechanisms and discuss emerging treatments, in April, 2021, Glaucoma Research Foundation, BrightFocus Foundation, and the Melza M. and Frank Theodore Barr Foundation collaborated to bring together key opinion leaders and experts in the field of neurodegenerative disease for a virtual…

  DOI

• Cell Atlas of The Human Fovea and Peripheral Retina

  Scientific Reports · 2020-06-17 · 295 citations

  articleOpen access

  Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retin…

  PublisherOA PDFDOI

• Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis

  Cell stem cell · 2021 · 137 citations

  DOI

• A standardized nomenclature for the rods and cones of the vertebrate retina

  PLoS Biology · 2025-05-07 · 16 citations

  articleOpen access

  Vertebrate photoreceptors have been studied for well over a century, but a fixed nomenclature for referring to orthologous cell types across diverse species has been lacking. Instead, photoreceptors have been variably-and often confusingly-named according to morphology, presence/absence of 'rhodopsin', spectral sensitivity, chromophore usage, and/or the gene family of the opsin(s) they express. Here, we propose a unified nomenclature for vertebrate rods and cones that aligns with the naming syst…

  PublisherDOI

• Comparative transcriptomic insights into the evolution of vertebrate photoreceptor types

  Current Biology · 2025-04-17 · 15 citations

  articleOpen accessSenior author

  To explore the molecular similarities and potential evolutionary origins of vertebrate photoreceptor types, we analyzed single-cell and -nucleus transcriptomic atlases from six vertebrate species: zebrafish, chicken, lizard, opossum, ground squirrel, and human. Comparative analyses identified conserved transcriptional signatures for the five ancestral photoreceptor types: red, blue, green, and UV cones, as well as rods. We further identified and validated molecular markers of the principal and a…

  PublisherDOI

Recent grants

• Uncovering the molecular identity of retinal cell types, and their responses to nerve injury using single-cell transcriptomics

  NIH · $740k · 2018–2023

• NIH Grant K99EY028625

  NIH · $215k · 2020

Frequent coauthors

• Aviv Regev

  Broad Institute

  109 shared

• Joshua R. Sanes

  Harvard University Press

  88 shared

• Salwan Butrus

  University of California, Berkeley

  75 shared

• Yvonne Kölsch

  Max Planck Institute of Neurobiology

  43 shared

• Yi-Rong Peng

  University of California, Los Angeles

  43 shared

• Arup K. Chakraborty

  Massachusetts Institute of Technology

  39 shared

• Semir Beyaz

  Cold Spring Harbor Laboratory

  37 shared

• Irene E. Whitney

  Harvard University

  36 shared

Education

• Postdoctoral Fellow, Cell Circuits and Epigenomics

  Broad Institute

  2019

Awards & honors

• 2023 McKnight Foundation Scholar Award
• 2023 The Donald Sterling Noyce Prize for Excellence in Under…
• 2023 The Dr. Douglas H Johnson Award (National Glaucoma Rese…
• 2023 Scialog Fellow, Microbiome, Neurobiology and Disease
• 2022 Society of Hellmann Fellows

Similar researchers at University of California, Berkeley

• Peidong Yangh-262
• Jennifer A. Doudnah-230
• Jeffrey R. Longh-189