publications

2024

1. Odd Viscodiffusive Fluids

   Alhad Deshpande , Cory Hargus , Karthik Shekhar, and 1 more author

   arXiv preprint arXiv:2411.04309, 2024

   Bib HTML

   

   @article{deshpande2024odd,
     title = {Odd Viscodiffusive Fluids},
     author = {Deshpande, Alhad and Hargus, Cory and Shekhar, Karthik and Mandadapu, Kranthi K},
     journal = {arXiv preprint arXiv:2411.04309},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {4OULZ7Gr8RgC},
   }

2. Transcriptomic changes in retinal ganglion cell types associated with the disruption of cholinergic retinal waves

   Rachana Deven Somaiya , Matthew A Po , Marla B Feller , and 1 more author

   bioRxiv, 2024

   Bib HTML

   

   @article{somaiya2024transcriptomic,
     title = {Transcriptomic changes in retinal ganglion cell types associated with the disruption of cholinergic retinal waves},
     author = {Somaiya, Rachana Deven and Po, Matthew A and Feller, Marla B and Shekhar, Karthik},
     journal = {bioRxiv},
     pages = {2024--12},
     year = {2024},
     publisher = {Cold Spring Harbor Laboratory},
     dimensions = {true},
     google_scholar_id = {f2IySw72cVMC},
   }

3. Comparative transcriptomic insights into the evolutionary origin of the tetrapod double cone

   Dario Tommasini , Takeshi Yoshimatsu , Tom Baden , and 1 more author

   bioRxiv, 2024

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   @article{tommasini2024comparative,
     title = {Comparative transcriptomic insights into the evolutionary origin of the tetrapod double cone},
     author = {Tommasini, Dario and Yoshimatsu, Takeshi and Baden, Tom and Shekhar, Karthik},
     journal = {bioRxiv},
     pages = {2024--11},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {D03iK_w7-QYC},
     publisher = {Cold Spring Harbor Laboratory}
   }

4. Spatial profiling of the interplay between cell type-and vision-dependent transcriptomic programs in the visual cortex

   Fangming Xie , Saumya Jain , Runzhe Xu , and 5 more authors

   bioRxiv, 2024

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   @article{xie2024spatial,
     title = {Spatial profiling of the interplay between cell type-and vision-dependent transcriptomic programs in the visual cortex},
     author = {Xie, Fangming and Jain, Saumya and Xu, Runzhe and Butrus, Salwan and Tan, Zhiqun and Xu, Xiangmin and Shekhar, Karthik and Zipursky, S Lawrence},
     journal = {bioRxiv},
     pages = {2023--12},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {M05iB0D1s5AC},
     publisher = {Cold Spring Harbor Laboratory}
   }

5. Molecular states underlying neuronal cell type development and plasticity in the whisker cortex

   Salwan Butrus , Hannah R Monday , Christopher J Yoo , and 2 more authors

   bioRxiv, 2024

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   @article{butrus2024molecular,
     title = {Molecular states underlying neuronal cell type development and plasticity in the whisker cortex},
     author = {Butrus, Salwan and Monday, Hannah R and Yoo, Christopher J and Feldman, Daniel and Shekhar, Karthik},
     journal = {bioRxiv},
     pages = {2024--10},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {dfsIfKJdRG4C},
     publisher = {Cold Spring Harbor Laboratory}
   }

6. Spatiotemporal dynamics of ionic reorganization near biological membrane interfaces

   Hyeongjoo Row , Joshua B Fernandes , Kranthi K Mandadapu , and 1 more author

   arXiv preprint arXiv:2407.11947, 2024

   Bib HTML

   

   @article{row2024spatiotemporal,
     title = {Spatiotemporal dynamics of ionic reorganization near biological membrane interfaces},
     author = {Row, Hyeongjoo and Fernandes, Joshua B and Mandadapu, Kranthi K and Shekhar, Karthik},
     journal = {arXiv preprint arXiv:2407.11947},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {fPk4N6BV_jEC},
   }

7. The ChAHP chromatin remodelling complex regulates neurodevelopmental disorder risk genes to scale the production of neocortical layers

   Samuel Clemot-Dupont , Jose Alex Laurenco Fernandes , Sarah Larrigan , and 8 more authors

   bioRxiv, 2024

   Bib HTML

   

   @article{clemot2024chahp,
     title = {The ChAHP chromatin remodelling complex regulates neurodevelopmental disorder risk genes to scale the production of neocortical layers},
     author = {Clemot-Dupont, Samuel and Fernandes, Jose Alex Laurenco and Larrigan, Sarah and Sun, Xiaoqi and Medisetti, Suma and Stanley, Rory and El Hankouri, Ziyad and Joshi, Shrilaxmi V and Picketts, David J and Shekhar, Karthik and others},
     journal = {bioRxiv},
     pages = {2024--02},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {SeFeTyx0c_EC},
     publisher = {Cold Spring Harbor Laboratory}
   }

8. Ancient origin of the rod bipolar cell pathway in the vertebrate retina

   Ayana M Hellevik , Philip Mardoum , Joshua Hahn , and 8 more authors

   Nature Ecology & Evolution, 2024

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   @article{hellevik2024ancient,
     title = {Ancient origin of the rod bipolar cell pathway in the vertebrate retina},
     author = {Hellevik, Ayana M and Mardoum, Philip and Hahn, Joshua and K{\"o}lsch, Yvonne and D’Orazi, Florence D and Suzuki, Sachihiro C and Godinho, Leanne and Lawrence, Owen and Rieke, Fred and Shekhar, Karthik and others},
     journal = {Nature Ecology \& Evolution},
     pages = {1--15},
     year = {2024},
     dimensions = {true},
     google_scholar_id = {RYcK_YlVTxYC},
     publisher = {Nature Publishing Group UK London}
   }

9. Reconfiguration of the visual code and retinal cell type complement in closely related diurnal and nocturnal mice

   Annette E Allen , Joshua Hahn , Rose Richardson , and 8 more authors

   bioRxiv, 2024

2023

1. Evolution of neuronal cell classes and types in the vertebrate retina

   Joshua Hahn , Aboozar Monavarfeshani , Mu Qiao , and 16 more authors

   Nature, 2023

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   @article{hahn2023evolution,
     title = {Evolution of neuronal cell classes and types in the vertebrate retina},
     author = {Hahn, Joshua and Monavarfeshani, Aboozar and Qiao, Mu and Kao, Allison H and K{\"o}lsch, Yvonne and Kumar, Ayush and Kunze, Vincent P and Rasys, Ashley M and Richardson, Rose and Wekselblatt, Joseph B and Baier, Herwig and Lucas, Robert J and Li, Wei and Meister, Markus and Trachtenberg, Joshua T and Yan, Wenjun and Peng, Yi-Rong and Sanes, Joshua R and Shekhar, Karthik},
     journal = {Nature},
     volume = {624},
     number = {7991},
     pages = {415--424},
     year = {2023},
     dimensions = {true},
     google_scholar_id = {RGFaLdJalmkC},
     publisher = {Nature Publishing Group UK London}
   }

2. Vision-dependent and-independent molecular maturation of mouse retinal ganglion cells

   Irene E Whitney , Salwan Butrus , Michael A Dyer , and 3 more authors

   Neuroscience, 2023

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   @article{whitney2023vision,
     title = {Vision-dependent and-independent molecular maturation of mouse retinal ganglion cells},
     author = {Whitney, Irene E and Butrus, Salwan and Dyer, Michael A and Rieke, Fred and Sanes, Joshua R and Shekhar, Karthik},
     journal = {Neuroscience},
     volume = {508},
     google_scholar_id = {YFjsv_pBGBYC},
     dimensions = {true},
     pages = {153--173},
     year = {2023},
     publisher = {Elsevier}
   }

3. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury

   Inbal Benhar , Jiarui Ding , Wenjun Yan , and 8 more authors

   Nature immunology, 2023

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   @article{benhar2023temporal,
     title = {Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury},
     author = {Benhar, Inbal and Ding, Jiarui and Yan, Wenjun and Whitney, Irene E and Jacobi, Anne and Sud, Malika and Burgin, Grace and Shekhar, Karthik and Tran, Nicholas M and Wang, Chen and others},
     journal = {Nature immunology},
     volume = {24},
     number = {4},
     pages = {700--713},
     year = {2023},
     dimensions = {true},
     google_scholar_id = {GnPB-g6toBAC},
     publisher = {Nature Publishing Group US New York}
   }

4. Defining Selective Neuronal Resilience and Identifying Targets of Neuroprotection and Axon Regeneration Using Single-Cell RNA Sequencing: Computational Approaches

   Salwan Butrus , Srikant Sagireddy , Wenjun Yan , and 1 more author

   In Axon Regeneration: Methods and Protocols , 2023

2022

1. Vision-dependent specification of cell types and function in the developing cortex

   Sarah Cheng , Salwan Butrus , Liming Tan , and 5 more authors

   Cell, 2022

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   @article{cheng2022vision,
     title = {Vision-dependent specification of cell types and function in the developing cortex},
     author = {Cheng, Sarah and Butrus, Salwan and Tan, Liming and Xu, Runzhe and Sagireddy, Srikant and Trachtenberg, Joshua T and Shekhar, Karthik and Zipursky, S Lawrence},
     journal = {Cell},
     volume = {185},
     number = {2},
     pages = {311--327},
     year = {2022},
     dimensions = {true},
     google_scholar_id = {hMod-77fHWUC},
     publisher = {Elsevier}
   }

2. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

   Karthik Shekhar, Irene E Whitney , Salwan Butrus , and 2 more authors

   Elife, 2022

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   @article{shekhar2022diversification,
     title = {Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types},
     author = {Shekhar, Karthik and Whitney, Irene E and Butrus, Salwan and Peng, Yi-Rong and Sanes, Joshua R},
     journal = {Elife},
     volume = {11},
     pages = {e73809},
     google_scholar_id = {k_IJM867U9cC},
     dimensions = {true},
     year = {2022},
     publisher = {eLife Sciences Publications Limited}
   }

3. Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression

   Jillian Goetz , Zachary F Jessen , Anne Jacobi , and 8 more authors

   Cell reports, 2022

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   @article{goetz2022unified,
     title = {Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression},
     author = {Goetz, Jillian and Jessen, Zachary F and Jacobi, Anne and Mani, Adam and Cooler, Sam and Greer, Devon and Kadri, Sabah and Segal, Jeremy and Shekhar, Karthik and Sanes, Joshua R and W, Schwartz Gregory},
     journal = {Cell reports},
     volume = {40},
     number = {2},
     year = {2022},
     google_scholar_id = {j3f4tGmQtD8C},
     dimensions = {true},
     publisher = {Elsevier}
   }

4. Solving neurodegeneration: common mechanisms and strategies for new treatments

   Lauren K Wareham , Shane A Liddelow , Sally Temple , and 8 more authors

   Molecular neurodegeneration, 2022

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   @article{wareham2022solving,
     title = {Solving neurodegeneration: common mechanisms and strategies for new treatments},
     author = {Wareham, Lauren K and Liddelow, Shane A and Temple, Sally and Benowitz, Larry I and Di Polo, Adriana and Wellington, Cheryl and Goldberg, Jeffrey L and He, Zhigang and Duan, Xin and Bu, Guojun and others},
     journal = {Molecular neurodegeneration},
     volume = {17},
     number = {1},
     pages = {23},
     year = {2022},
     google_scholar_id = {NMxIlDl6LWMC},
     dimensions = {true},
     publisher = {Springer}
   }

2021

1. Generating and using transcriptomically based retinal cell atlases

   Karthik Shekhar, and Joshua R Sanes

   Annual Review of Vision Science, 2021

   Bib HTML PDF

   

   @article{shekhar2021generating,
     title = {Generating and using transcriptomically based retinal cell atlases},
     author = {Shekhar, Karthik and Sanes, Joshua R},
     journal = {Annual Review of Vision Science},
     volume = {7},
     pages = {43--72},
     year = {2021},
     google_scholar_id = {r0BpntZqJG4C},
     dimensions = {true},
     publisher = {Annual Reviews}
   }

2. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior

   Yvonne Kölsch , Joshua Hahn , Anna Sappington , and 10 more authors

   Neuron, 2021

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   @article{kolsch2021molecular,
     title = {Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior},
     author = {K{\"o}lsch, Yvonne and Hahn, Joshua and Sappington, Anna and Stemmer, Manuel and Fernandes, Ant{\'o}nio M and Helmbrecht, Thomas O and Lele, Shriya and Butrus, Salwan and Laurell, Eva and Arnold-Ammer, Irene and Shekhar, Karthik and Sanes, Joshua R and Baier, Herwig},
     journal = {Neuron},
     volume = {109},
     number = {4},
     pages = {645--662},
     year = {2021},
     google_scholar_id = {R3hNpaxXUhUC},
     dimensions = {true},
     publisher = {Elsevier}
   }

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

   Semir Beyaz , Charlie Chung , Haiwei Mou , and 8 more authors

   Cell stem cell, 2021

   Bib HTML

   

   @article{beyaz2021dietary,
     title = {Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis},
     author = {Beyaz, Semir and Chung, Charlie and Mou, Haiwei and Bauer-Rowe, Khristian E and Xifaras, Michael E and Ergin, Ilgin and Dohnalova, Lenka and Biton, Moshe and Shekhar, Karthik and Eskiocak, Onur and others},
     journal = {Cell stem cell},
     volume = {28},
     number = {11},
     pages = {1922--1935},
     year = {2021},
     google_scholar_id = {TFP_iSt0sucC},
     dimensions = {true},
     publisher = {Elsevier}
   }

2020

1. Cell atlas of the human fovea and peripheral retina

   Wenjun Yan , Yi-Rong Peng , Tavé Zyl , and 4 more authors

   Scientific reports, 2020
2. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis

   Tavé Zyl , Wenjun Yan , Alexi McAdams , and 5 more authors

   Proceedings of the National Academy of Sciences, 2020

2019

1. Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes

   Nicholas M Tran , Karthik Shekhar, Irene E Whitney , and 8 more authors

   Neuron, 2019

   Bib HTML

   

   @article{tran2019single,
     title = {Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes},
     author = {Tran, Nicholas M and Shekhar, Karthik and Whitney, Irene E and Jacobi, Anne and Benhar, Inbal and Hong, Guosong and Yan, Wenjun and Adiconis, Xian and Arnold, McKinzie E and Lee, Jung Min and others},
     journal = {Neuron},
     volume = {104},
     number = {6},
     pages = {1039--1055},
     year = {2019},
     google_scholar_id = {IWHjjKOFINEC},
     dimensions = {true},
     publisher = {Elsevier}
   }

2. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina

   Yi-Rong Peng , Karthik Shekhar, Wenjun Yan , and 7 more authors

   Cell, 2019

   Bib HTML

   

   @article{peng2019molecular,
     title = {Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina},
     author = {Peng, Yi-Rong and Shekhar, Karthik and Yan, Wenjun and Herrmann, Dustin and Sappington, Anna and Bryman, Gregory S and van Zyl, Tav{\'e} and Do, Michael Tri H and Regev, Aviv and Sanes, Joshua R},
     journal = {Cell},
     volume = {176},
     number = {5},
     pages = {1222--1237},
     year = {2019},
     google_scholar_id = {Wp0gIr-vW9MC},
     dimensions = {true},
     publisher = {Elsevier}
   }

3. Identification of cell types from single-cell transcriptomic data

   Karthik Shekhar, and Vilas Menon

   2019

2018

1. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

   Jeffrey R Moffitt , Dhananjay Bambah-Mukku , Stephen W Eichhorn , and 8 more authors

   Science, 2018
2. Comprehensive identification and spatial mapping of habenular neuronal types using single-cell RNA-seq

   Shristi Pandey , Karthik Shekhar, Aviv Regev , and 1 more author

   Current Biology, 2018
3. T helper cell cytokines modulate intestinal stem cell renewal and differentiation

   Moshe Biton , Adam L Haber , Noga Rogel , and 8 more authors

   Cell, 2018
4. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

   Jeffrey A Farrell , Yiqun Wang , Samantha J Riesenfeld , and 3 more authors

   Science, 2018

2017

1. Massively parallel single-nucleus RNA-seq with DroNc-seq

   Naomi Habib , Inbal Avraham-Davidi , Anindita Basu , and 8 more authors

   Nature methods, 2017
2. Continuous immunotypes describe human immune variation and predict diverse responses

   Kevin J Kaczorowski , Karthik Shekhar, Dieudonné Nkulikiyimfura , and 5 more authors

   Proceedings of the National Academy of Sciences, 2017
3. Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing

   Christopher A Werley , Miao-Ping Chien , Jellert Gaublomme , and 8 more authors

   PloS one, 2017
4. Single-cell RNA sequencing of human T cells

   Alexandra-Chloé Villani , and Karthik Shekhar

   2017
5. A single-cell survey of the small intestinal epithelium

   Adam L Haber , Moshe Biton , Noga Rogel , and 8 more authors

   Nature, 2017
6. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

   Alexandra-Chloé Villani , Rahul Satija , Gary Reynolds , and 8 more authors

   Science, 2017

2016

1. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics

   Karthik Shekhar, Sylvain W Lapan , Irene E Whitney , and 8 more authors

   Cell, 2016

   Bib HTML

   

   @article{shekhar2016comprehensive,
     title = {Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics},
     author = {Shekhar, Karthik and Lapan, Sylvain W and Whitney, Irene E and Tran, Nicholas M and Macosko, Evan Z and Kowalczyk, Monika and Adiconis, Xian and Levin, Joshua Z and Nemesh, James and Goldman, Melissa and others},
     journal = {Cell},
     volume = {166},
     number = {5},
     pages = {1308--1323},
     year = {2016},
     google_scholar_id = {Se3iqnhoufwC},
     dimensions = {true},
     publisher = {Elsevier}
   }

2. Hydrophobic CDR3 residues promote the development of self-reactive T cells

   Brian D Stadinski , Karthik Shekhar, Iria Gómez-Touriño , and 6 more authors

   Nature immunology, 2016

   Bib

   @article{stadinski2016hydrophobic,
     title = {Hydrophobic CDR3 residues promote the development of self-reactive T cells},
     author = {Stadinski, Brian D and Shekhar, Karthik and G{\'o}mez-Touri{\~n}o, Iria and Jung, Jonathan and Sasaki, Katsuhiro and Sewell, Andrew K and Peakman, Mark and Chakraborty, Arup K and Huseby, Eric S},
     journal = {Nature immunology},
     volume = {17},
     number = {8},
     pages = {946--955},
     year = {2016},
     dimensions = {true},
     publisher = {Nature Publishing Group US New York}
   }

2015

1. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

   Evan Z Macosko , Anindita Basu , Rahul Satija , and 8 more authors

   Cell, 2015
2. Magnitude and kinetics of CD8+ T cell activation during hyperacute HIV infection impact viral set point

   Zaza M Ndhlovu , Philomena Kamya , Nikoshia Mewalal , and 8 more authors

   Immunity, 2015

2014

1. Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE)

   Karthik Shekhar, Petter Brodin , Mark M Davis , and 1 more author

   Proceedings of the National Academy of Sciences, 2014
2. Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design

   Ahmed A Quadeer , Raymond HY Louie , Karthik Shekhar, and 3 more authors

   Journal of Virology, 2014

2013

1. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

   Karthik Shekhar, Claire F Ruberman , Andrew L Ferguson , and 3 more authors

   Physical review E, 2013
2. Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys

   Dan H Barouch , James B Whitney , Brian Moldt , and 8 more authors

   Nature, 2013

2011

1. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

   Vincent Dahirel , Karthik Shekhar, Florencia Pereyra , and 8 more authors

   Proceedings of the National Academy of Sciences, 2011