Shekhar Lab University of California, Berkeley

Publications

2026

  1. Sex-specific APOE4-dependent innate immunity regulates meningeal lymphatics, brain lipids, neuroinflammation, and cognition
    Delivanoglou, N. ; Todd, K. T. ; Almeida, F. ; Rego, S. ; Changavi, A. ; Spajer, M. ; Ayuso, V. E. ; Pinho-Correia, L. M. ; Sanchez, G. ; Neves, S. P. ; Barber, M. J. ; Schrader, R. ; Sacilotto, P. ; Martens, Y. A. ; Heckman, M. G. ; Bu, G. ; Tanzi, R. E. ; Thomas, J. L. ; Fryer, J. D. ; Oliveira, T. G. ; Shekhar, K. ; Da Mesquita, S.
    Neuron, Mar 2026
    citations ...
  2. Thickness effects in the electromechanical stability of charged biological membranes
    Ning, S. ; Omar, Y. A. ; Shekhar, K.‡ ; Mandadapu, K. K.‡
    arXiv preprint arXiv:2603.23477, Mar 2026
    arXiv: 2603.23477 - arXiv preprint
    citations ...
  3. The Extreme Diversity Of Retinal Amacrine Cells Has Deep Evolutionary Roots
    Tommasini, D. ; Monavarfeshani, A. ; Dinesh, V. ; Hahn, J. ; Tangeman, J. ; Marre, O. ; Blackshaw, S. ; Puthussery, T. ; Sanes, J. R. ; Shekhar, K.‡
    bioRxiv, Mar 2026
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  4. Single-cell atlas of the transcriptome and chromatin accessibility in the human retina
    Li, J. ; Wang, J. ; Ibarra, I. L. ; Cheng, X. ; Luecken, M. D. ; Lu, J. ; Monavarfeshani, A. ; Yan, W. ; Zheng, Y. ; Zuo, Z. ; Colborn, S. L. Z. ; Cortez, B. S. ; Owen, L. A. ; Wick, B. ; Bao, X. ; Choi, J. ; Haeussler, M. ; Tran, N. M. ; Shekhar, K. ; Sanes, J. R. ; Stout, J. T. ; Chen, S. ; Li, Y. ; DeAngelis, M. M. ; Theis, F. J. ; Chen, R.
    Nature Genetics, Feb 2026
    citations ...
  5. Electrochemical response of biological membranes to localized currents and external electric fields
    Fernandes, J. B. ; Row, H. ; Mandadapu, K. K.‡ ; Shekhar, K.‡
    Physical Review Research, Feb 2026
    arXiv: 2508.14001 - arXiv preprint
    citations ...

2025

  1. Establishing a continuum of cell types in the visual cortex
    Yoo, J. ; Xie, F. ; Butrus, S. ; Xu, R. ; Tan, Z. ; Gorzek, R. ; Mirshahidi, P. ; Tring, E. ; Suresh, S. ; Kim, J. ; Fleishman, G. ; Tan, L. ; Ringach, D. ; Trachtenberg, J. ; Xu, X. ; Zipursky, S. L.‡ ; Shekhar, K.‡ ; Jain, S.‡
    bioRxiv, Feb 2025
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  2. Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma
    Nimkar, K. ; Tsai, N. Y. ; Zhao, M. ; Yi, Y. ; Lum, M. R. ; Garrett, T. R. ; Wang, Y. ; Toma, K. ; Caval-Holme, F. ; Reddy, N. ; Ehrlich, A. T. ; Kriegstein, A. R. ; Do, M. T. H. ; Hu, Y. ; Sivyer, B. ; Shekhar, K.‡ ; Duan, X.‡
    Neuron, Feb 2025
    citations ...
  3. Capacitive response of biological membranes
    Farhadi, J. ; Fernandes, J. B. ; Shekhar, K.‡ ; Mandadapu, K. K.‡
    Physical Review E, Feb 2025
    citations ...
  4. Molecular states underlying neuronal cell type development and plasticity in the postnatal whisker cortex
    Butrus, S. ; Monday, H. R. ; Yoo, C. J. ; Feldman, D. E.‡ ; Shekhar, K.‡
    PLOS Biology, Feb 2025
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  5. A standardized nomenclature for the rods and cones of the vertebrate retina
    Baden, T.‡ ; Angueyra, J. M. ; Bosten, J. M. ; Collin, S. P. ; Conway, B. R. ; Cortesi, F. ; Dedek, K. ; Euler, T. ; Novales Flamarique, I. ; Franklin, A. ; Haverkamp, S. ; Kelber, A. ; Neuhauss, S. C. F. ; Li, W. ; Lucas, R. J. ; Osorio, D. C. ; Shekhar, K. ; Tommasini, D. ; Yoshimatsu, T. ; Corbo, J. C.
    PLoS Biology, Feb 2025
    citations ...
  6. Comparative transcriptomic insights into the evolution of vertebrate photoreceptor types
    Tommasini, D.‡ ; Yoshimatsu, T.‡ ; Puthussery, T.‡ ; Baden, T.‡ ; Shekhar, K.‡
    Current Biology, Feb 2025
    citations ...
  7. Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex
    Xie, F.‡ ; Jain, S. ; Xu, R. ; Butrus, S. ; Tan, Z. ; Xu, X. ; Shekhar, K.‡ ; Zipursky, S. L.‡
    Proceedings of the National Academy of Sciences, Feb 2025
    citations ...
  8. Spatiotemporal dynamics of ionic reorganization near biological membrane interfaces
    Row, H. ; Fernandes, J. B. ; Mandadapu, K. K.‡ ; Shekhar, K.‡
    Physical Review Research, Feb 2025
    citations ...
  9. Altered proportions of retinal cell types and distinct visual codes in rodents occupying divergent ecological niches
    Allen, A. E.‡ ; Hahn, J. ; Richardson, R. ; Pantiru, A. ; Mouland, J. ; Babu, A. ; Baño-Otalora, B. ; Monavarfeshani, A. ; Yan, W. ; Williams, C. ; Wynne, J. ; Rodgers, J. ; Milosavljevic, N. ; Orlowska-Feuer, P. ; Storchi, R. ; Sanes, J. R. ; Shekhar, K. ; Lucas, R. J.
    Current Biology, Feb 2025
    citations ...
  10. The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis
    Clémot-Dupont, S. ; Lourenço Fernandes, J. A. ; Larrigan, S. ; Sun, X. ; Medisetti, S. ; Stanley, R. ; El Hankouri, Z. ; Joshi, S. V. ; Picketts, D. J. ; Shekhar, K. ; Mattar, P.‡
    Proceedings of the National Academy of Sciences, Feb 2025
    citations ...

2024

  1. Odd Viscodiffusive Fluids
    Deshpande, A. ; Hargus, C. ; Shekhar, K.‡ ; Mandadapu, K. K.‡
    arXiv preprint arXiv:2411.04309, Feb 2024
    arXiv: 2411.04309 - arXiv preprint
    citations ...
  2. Ancient origin of the rod bipolar cell pathway in the vertebrate retina
    Hellevik, A. M. ; Mardoum, P. ; Hahn, J. ; Kölsch, Y. ; D’Orazi, F. D. ; Suzuki, S. C. ; Godinho, L. ; Lawrence, O. ; Rieke, F. ; Shekhar, K. ; Sanes, J. R. ; Baier, H. ; Baden, T. ; Wong, R. O. ; Yoshimatsu, T.‡
    Nature Ecology & Evolution, Feb 2024
    citations ...

2023

  1. Evolution of neuronal cell classes and types in the vertebrate retina
    Hahn, J. ; Monavarfeshani, A. ; Qiao, M. ; Kao, A. H. ; Kölsch, Y. ; Kumar, A. ; Kunze, V. P. ; Rasys, A. M. ; Richardson, R. ; Wekselblatt, J. B. ; Baier, H. ; Lucas, R. J. ; Li, W. ; Meister, M. ; Trachtenberg, J. T. ; Yan, W. ; Peng, Y. R. ; Sanes, J. R.‡ ; Shekhar, K.‡
    Nature, Feb 2023
    PDF citations ...
  2. Vision-dependent and-independent molecular maturation of mouse retinal ganglion cells
    Whitney, I. E. ; Butrus, S. ; Dyer, M. A. ; Rieke, F. ; Sanes, J. R.‡ ; Shekhar, K.‡
    Neuroscience, Feb 2023
    PDF citations ...
  3. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury
    Benhar, I.‡ ; Ding, J. ; Yan, W. ; Whitney, I. E. ; Jacobi, A. ; Sud, M. ; Burgin, G. ; Shekhar, K. ; Tran, N. M. ; Wang, C. ; He, Z. ; Sanes, J. R. ; Regev, A.‡
    Nature immunology, Feb 2023
    PDF citations ...
  4. Defining Selective Neuronal Resilience and Identifying Targets of Neuroprotection and Axon Regeneration Using Single-Cell RNA Sequencing: Computational Approaches
    Butrus, S.‡ ; Sagireddy, S. ; Yan, W. ; Shekhar, K.‡
    In Axon Regeneration: Methods and Protocols , Feb 2023
    citations ...

2022

  1. Vision-dependent specification of cell types and function in the developing cortex
    Cheng, S. ; Butrus, S. ; Tan, L. ; Xu, R. ; Sagireddy, S. ; Trachtenberg, J. T. ; Shekhar, K.‡ ; Zipursky, S. L.‡
    Cell, Feb 2022
    PDF citations ...
  2. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
    Shekhar, K.‡ ; Whitney, I. E. ; Butrus, S. ; Peng, Y. R. ; Sanes, J. R.‡
    Elife, Feb 2022
    PDF citations ...
  3. Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression
    Goetz, J. ; Jessen, Z. F. ; Jacobi, A. ; Mani, A. ; Cooler, S. ; Greer, D. ; Kadri, S. ; Segal, J. ; Shekhar, K. ; Sanes, J. R. ; Schwartz, G. W.‡
    Cell reports, Feb 2022
    PDF citations ...
  4. Solving neurodegeneration: common mechanisms and strategies for new treatments
    Wareham, L. K.‡ ; Liddelow, S. A. ; Temple, S. ; Benowitz, L. I. ; Di Polo, A. ; Wellington, C. ; Goldberg, J. L. ; He, Z. ; Duan, X. ; Bu, G. ; Davis, A. A. ; Shekhar, K. ; La Torre, A. ; Chan, D. C. ; Canto-Soler, M. V. ; Flanagan, J. G. ; Subramanian, P. ; Rossi, S. ; Brunner, T. ; Bovenkamp, D. E. ; Calkins, D. J.‡
    Molecular neurodegeneration, Feb 2022
    PDF citations ...

2021

  1. Generating and using transcriptomically based retinal cell atlases
    Shekhar, K.‡ ; Sanes, J. R.‡
    Annual Review of Vision Science, Feb 2021
    PDF citations ...
  2. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior
    Kölsch, Y. ; Hahn, J. ; Sappington, A. ; Stemmer, M. ; Fernandes, A. M. ; Helmbrecht, T. O. ; Lele, S. ; Butrus, S. ; Laurell, E. ; Arnold-Ammer, I. ; Shekhar, K.‡ ; Sanes, J. R.‡ ; Baier, H.‡
    Neuron, Feb 2021
    PDF citations ...
  3. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis
    Beyaz, S.‡ ; Chung, C. ; Mou, H. ; Bauer-Rowe, K. E. ; Xifaras, M. E. ; Ergin, I. ; Dohnalova, L. ; Biton, M. ; Shekhar, K. ; Eskiocak, O. ; Papciak, K. ; Ozler, K. ; Almeqdadi, M. ; Yueh, B. ; Fein, M. ; Annamalai, D. ; Valle-Encinas, E. ; Erdemir, A. ; Dogum, K. ; Shah, V. ; Alici-Garipcan, A. ; Meyer, H. V. ; Ozata, D. M. ; Elinav, E. ; Kucukural, A. ; Kumar, P. ; McAleer, J. P. ; Fox, J. G. ; Thaiss, C. A. ; Regev, A. ; Roper, J. ; Orkin, S. H.‡ ; Yilmaz, Ö. H.‡
    Cell stem cell, Feb 2021
    citations ...

2020

  1. Cell atlas of the human fovea and peripheral retina
    Yan, W. ; Peng, Y. R. ; Zyl, T. ; Regev, A. ; Shekhar, K. ; Juric, D. ; Sanes, J. R.‡
    Scientific reports, Feb 2020
    citations ...
  2. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis
    Zyl, T.‡ ; Yan, W. ; McAdams, A. ; Peng, Y. R. ; Shekhar, K. ; Regev, A. ; Juric, D. ; Sanes, J. R.‡
    Proceedings of the National Academy of Sciences, Feb 2020
    citations ...

2019

  1. Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes
    Tran, N. M.* ; Shekhar, K.* ; Whitney, I. E.* ; Jacobi, A. ; Benhar, I. ; Hong, G. ; Yan, W. ; Adiconis, X. ; Arnold, M. E. ; Lee, J. M. ; Levin, J. Z. ; Lin, D. ; Wang, C. ; Lieber, C. M. ; Regev, A. ; He, Z. ; Sanes, J. R.‡
    Neuron, Feb 2019
    citations ...
  2. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina
    Peng, Y. R.* ; Shekhar, K.* ; Yan, W. ; Herrmann, D. ; Sappington, A. ; Bryman, G. S. ; Zyl, T. ; Do, M. T. H. ; Regev, A. ; Sanes, J. R.‡
    Cell, Feb 2019
    citations ...
  3. Identification of cell types from single-cell transcriptomic data
    Shekhar, K.‡ ; Menon, V.‡
    Feb 2019
    citations ...

2018

  1. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region
    Moffitt, J. R. ; Bambah-Mukku, D. ; Eichhorn, S. W. ; Vaughn, E. ; Shekhar, K. ; Perez, J. D. ; Rubinstein, N. D. ; Hao, J. ; Regev, A. ; Dulac, C.‡ ; Zhuang, X.‡
    Science, Feb 2018
    citations ...
  2. Comprehensive identification and spatial mapping of habenular neuronal types using single-cell RNA-seq
    Pandey, S.‡ ; Shekhar, K. ; Regev, A. ; Schier, A. F.‡
    Current Biology, Feb 2018
    citations ...
  3. T helper cell cytokines modulate intestinal stem cell renewal and differentiation
    Biton, M. ; Haber, A. L. ; Rogel, N. ; Burgin, G. ; Beyaz, S. ; Schnell, A. ; Ashenberg, O. ; Su, C. W. ; Smillie, C. ; Shekhar, K. ; Chen, Z. ; Wu, C. ; Ordovas-Montanes, J. ; Alvarez, D. ; Herbst, R. ; Zhang, M. ; Tirosh, I. ; Dionne, D. ; Nguyen, L. ; Xifaras, M. ; Shalek, A. ; Andrian, U. ; Graham, D. ; Rozenblatt-Rosen, O. ; Shi, H. ; Kuchroo, V. ; Yilmaz, Ö. ; Regev, A.‡ ; Xavier, R.‡
    Cell, Feb 2018
    citations ...
  4. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
    Farrell, J. A. ; Wang, Y. ; Riesenfeld, S. J. ; Shekhar, K. ; Regev, A.‡ ; Schier, A. F.‡
    Science, Feb 2018
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2017

  1. Massively parallel single-nucleus RNA-seq with DroNc-seq
    Habib, N. ; Avraham-Davidi, I. ; Basu, A. ; Burks, T. ; Shekhar, K. ; Hofree, M. ; Choudhury, S. ; Aguet, F. ; Gelfand, E. ; Ardlie, K. ; Weitz, D. ; Rozenblatt-Rosen, O. ; Zhang, F. ; Regev, A.‡
    Nature methods, Feb 2017
    citations ...
  2. Continuous immunotypes describe human immune variation and predict diverse responses
    Kaczorowski, K. J. ; Shekhar, K. ; Nkulikiyimfura, D. ; Dekker, C. L. ; Maecker, H. ; Davis, M. M. ; Chakraborty, A. K.‡ ; Brodin, P.‡
    Proceedings of the National Academy of Sciences, Feb 2017
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  3. Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing
    Werley, C. A. ; Chien, M. P. ; Gaublomme, J. ; Shekhar, K. ; Butty, V. ; Yi, B. A. ; Kralj, J. ; Bloxham, W. ; Boyer, L. ; Regev, A. ; Cohen, A.‡
    PloS one, Feb 2017
    citations ...
  4. Single-cell RNA sequencing of human T cells
    Villani, A. C.‡ ; Shekhar, K.‡
    Feb 2017
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  5. A single-cell survey of the small intestinal epithelium
    Haber, A. L. ; Biton, M. ; Rogel, N. ; Herbst, R. H. ; Shekhar, K. ; Smillie, C. ; Burgin, G. ; Delorey, T. M. ; Howitt, M. R. ; Katz, Y. ; Tirosh, I. ; Beyaz, S. ; Dionne, D. ; Zhang, M. ; Raychowdhury, R. ; Garrett, W. ; Rozenblatt-Rosen, O. ; Shi, H. ; Yilmaz, O. ; Xavier, R.‡ ; Regev, A.‡
    Nature, Feb 2017
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  6. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
    Villani, A. C. ; Satija, R. ; Reynolds, G. ; Sarkizova, S. ; Shekhar, K. ; Fletcher, J. ; Griesbeck, M. ; Butler, A. ; Zheng, S. ; Lazo, S. ; Jardine, L. ; Dixon, D. ; Stephenson, E. ; Nilsson, E. ; Grundberg, I. ; McDonald, D. ; Filby, A. ; Li, W. ; De Jager, P. L. ; Rozenblatt-Rosen, O. ; Lane, A. A. ; Haniffa, M. ; Regev, A.‡ ; Hacohen, N.‡
    Science, Feb 2017
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2016

  1. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics
    Shekhar, K.* ; Lapan, S. W.* ; Whitney, I. E.* ; Tran, N. M. ; Macosko, E. Z. ; Kowalczyk, M. ; Adiconis, X. ; Levin, J. Z. ; Nemesh, J. ; Goldman, M. ; McCarroll, S. ; Cepko, C.‡ ; Regev, A.‡ ; Sanes, J. R.‡
    Cell, Feb 2016
    citations ...
  2. Hydrophobic CDR3 residues promote the development of self-reactive T cells
    Stadinski, B. D. ; Shekhar, K. ; Gómez-Touriño, I. ; Jung, J. ; Sasaki, K. ; Sewell, A. K. ; Peakman, M. ; Chakraborty, A. K. ; Huseby, E. S.‡
    Nature immunology, Feb 2016
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2015

  1. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
    Macosko, E. Z. ; Basu, A. ; Satija, R. ; Nemesh, J. ; Shekhar, K. ; Goldman, M. ; Tirosh, I. ; Bialas, A. ; Kamitaki, N. ; Martersteck, E. ; Trombetta, J. ; Weitz, D. ; Sanes, J. ; Shalek, A. ; Regev, A. ; McCarroll, S.‡
    Cell, Feb 2015
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  2. Magnitude and kinetics of CD8+ T cell activation during hyperacute HIV infection impact viral set point
    Ndhlovu, Z. M. ; Kamya, P. ; Mewalal, N. ; Kløverpris, H. N. ; Nkosi, T. ; Pretorius, K. ; Laher, F. ; Ogunshola, F. ; Chopera, D. ; Shekhar, K. ; Ghebremichael, M. ; Ismail, N. ; Moodley, A. ; Malik, A. ; Leslie, A. ; Goulder, P. J. R. ; Buus, S. ; Chakraborty, A. ; Dong, K. ; Ndung’u, T. ; Walker, B. D.‡
    Immunity, Feb 2015
    citations ...

2014

  1. Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE)
    Shekhar, K.* ; Brodin, P.* ; Davis, M. M.‡ ; Chakraborty, A. K.‡
    Proceedings of the National Academy of Sciences, Feb 2014
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  2. Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design
    Quadeer, A. A. ; Louie, R. H. ; Shekhar, K. ; Chakraborty, A. K.‡ ; Hsing, I. M. ; McKay, M. R.‡
    Journal of Virology, Feb 2014
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2013

  1. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes
    Shekhar, K. ; Ruberman, C. F. ; Ferguson, A. L. ; Barton, J. P. ; Kardar, M. ; Chakraborty, A. K.‡
    Physical review E, Feb 2013
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  2. Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys
    Barouch, D. H.‡ ; Whitney, J. B. ; Moldt, B. ; Klein, F. ; Oliveira, T. Y. ; Liu, J. ; Stephenson, K. E. ; Chang, H. W. ; Shekhar, K. ; Gupta, S. ; Nkolola, J. P. ; Seaman, M. S. ; Smith, K. M. ; Borducchi, E. N. ; Cabral, C. ; Smith, J. Y. ; Blackmore, S. ; Sanisetty, S. ; Perry, J. R. ; Beck, M. ; Lewis, M. G. ; Rinaldi, W. ; Chakraborty, A. K. ; Poignard, P. ; Nussenzweig, M. C. ; Burton, D. R.
    Nature, Feb 2013
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2011

  1. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability
    Dahirel, V.* ; Shekhar, K.* ; Pereyra, F. ; Miura, T. ; Artyomov, M. ; Talsania, S. ; Allen, T. M. ; Altfeld, M. ; Carrington, M. ; Irvine, D. J. ; Walker, B. D. ; Chakraborty, A. K.‡
    Proceedings of the National Academy of Sciences, Feb 2011
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* co-first author

‡ corresponding author