37. Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLZ, Cortez BS, Owen LA, Tran NM, Shekhar K, Sanes JR, Stout JT, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Integrated multi-omics single cell atlas of the human retina. bioRxiv [Preprint]. 2023 Nov 17:rs.3.rs-3471275. doi: 10.21203/rs.3.rs-3471275/v1. PMID: 38014002; PMCID: PMC10680922.

36. Hellevik AM, Mardoum P, Hahn J, Kölsch Y, D'Orazi FD, Suzuki SC, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes JR, Baier H, Baden T, Wong RO, Yoshimatsu T. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. bioRxiv [Preprint]. (2023) Sep 13:2023.09.12.557433. doi: 10.1101/2023.09.12.557433. PMID: 37771914; PMCID: PMC10525478.

35. Hahn J, Monavarfeshani A, Qiao M, Kao A, Kölsch Y, Kumar A, Kunze VP, Rasys AM, Richardson R, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, Yan W, Peng YR, Sanes JR‡,, Shekhar K‡,. Evolution of neuronal cell classes and types in the vertebrate retina. bioRxiv [Preprint]. (2023) Apr 8:2023.04.07.536039. doi: 10.1101/2023.04.07.536039. PMID: 37066415; PMCID: PMC10104162. (Nature, in press)

34. Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nature Immunology. (2023) Apr;24(4):700-713. doi: 10.1038/s41590-023-01437-w. Epub 2023 Feb 20. PMID: 36807640. [PDF]

33. Whitney IE, Butrus S, Dyer MA, Rieke F, Sanes JR‡,, Shekhar K‡,. Vision-Dependent and -Independent Molecular Maturation of Mouse Retinal Ganglion Cells. Neuroscience. (2023) Jan 1;508:153-173. doi: 10.1016/j.neuroscience.2022.07.013. Epub 2022 Jul 21. PMID: 35870562. [PDF]

32. Butrus S‡, Sagireddy S, Yan W, and Shekhar K‡ Defining selective neuronal resilience and identifying targets of neuroprotection and axon regeneration using single-cell RNA sequencing – computational approaches, Book Chapter for Methods in Molecular Biology, (2023) 2636:19-41. doi: 10.1007/978-1-0716-3012-9_2. PMID: 36881293

31. Shekhar K‡, Whitney IE, Butrus S, Peng YR, Sanes JR‡. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types. Elife. (2022) Feb 22;11:e73809. doi: 10.7554/eLife.73809. PMID: 35191836; PMCID: PMC8956290. [PDF]

30. Cheng S, Butrus S, Tan L, Xu R, Sagireddy S, Trachtenberg JT, Shekhar K, Zipursky SL. Vision-dependent specification of cell types and function in the developing cortex. Cell. (2022) Jan 20;185(2):311-327.e24. doi: 10.1016/j.cell.2021.12.022. PMID: 35063073; PMCID: PMC8813006. [PDF]

29. Wareham LK, Liddelow SA, Temple S, Benowitz LI, Di Polo A, Wellington C, Goldberg JL, He Z, Duan X, Bu G, Davis AA, Shekhar K, Torre A, Chan DC, Canto-Soler MV, Flanagan JG, Subramanian P, Rossi S, Brunner T, Bovenkamp DE, Calkins DJ. Solving neurodegeneration: common mechanisms and strategies for new treatments. Molecular Neurodegeneration. (2022) Mar 21;17(1):23. doi: 10.1186/s13024-022-00524-0. PMID: 35313950; PMCID: PMC8935795. [PDF]

28. Goetz J, Jessen ZF, Jacobi A, Mani A, Cooler S, Greer D, Kadri S, Segal J, Shekhar K, Sanes JR, Schwartz GW‡. Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression. Cell Reports, (2022) Jul 12;40(2):111040. doi: 10.1016/j.celrep.2022.111040. PMID: 35830791; PMCID: PMC9364428. [PDF]

27. Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, 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 HV, Özata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ÖH‡. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. (2021) Nov 4;28(11):1922-1935.e5. doi: 10.1016/j.stem.2021.08.007. Epub 2021 Sep 15. PMID: 34529935; PMCID: PMC8650761.

26. Shekhar K‡ and Sanes JR‡. Generating and using transcriptomically based retinal cell atlases. Annual Review of Vision Science, (2021) [PDF]

25. Kölsch Y, Hahn J, Sappington A, Stemmer M, Fernandes AM,  Helmbrecht TO, Lele S, Butrus S, Laurell E, Arnold-Ammer I, Shekhar K‡, Sanes JR‡, and Baier H‡.  "Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior". Neuron, 109(4) (2021) [PDF] (bioRxiv preprint)

24. Yan W*, Peng Y*, van Zyl T*, Regev A, Shekhar K, Juric D, and Sanes JR.  "Cell Atlas of the Human Fovea and Peripheral Retina". Scientific Reports, 10(9802), (2020) [PDF]

23. van Zyl T*, Yan W*, McAdams A, Peng YR, Shekhar K, Regev A, Juric D, and Sanes JR‡. "Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis". PNAS, 117(19):10339-10349 (2020) [PDF]

22. Tran NM*, Shekhar K*, Whitney IE*, Jacobi A*, Benhar I, Hong G, Yan W, ..., Regev A, He Z, and Sanes JR‡. "Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes". Neuron, 104(6):1039-55 (2019) [PDF]

21. Yirong  Peng*, Karthik Shekhar*, Wenjun Yan, Dustin  Herrmann,  Anna Sappington, Greg Bryman, Tavé van Zyl,  Aviv Regev, Michael T. Do and Joshua R. Sanes‡, “Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina”, Cell, 176(5),1222-1237,(2019) [PDF]

20 Karthik Shekhar‡ and Vilas Menon‡, “Identification of Cell Types from Single-Cell Transcriptomic Data”, Computational Methods for Single-Cell Data Analysis: pp. 45-77, G. C. Yuan (ed), 2019 [PDF]

19. Jeffrey R. Moffitt, Dhananjay Bambah-Mukku, Stephen W. Eichorn, Eric, Vaughn, Karthik Shekhar, Julio D. Perez, Nimrod D. Rubenstein, Junjie Hao, Aviv Regev, Catherine Dulac and Xiaowei Zhuang, “Molecular, Spatial and Functional Single-Cell Profiling of the Hypothalamic Preoptic Region”, Science, 362(6416)(2018)

[PDF]

18. Moshe Biton*, Adam L. Haber*, Noga Rogel*, Grace Burgin, Semir Beyaz, Alexandra Schnell, Orr Ashenberg, Chien-Wen Su, Christopher Smillie, Karthik Shekhar, Zuojia Chen, Chuan Wu, ...,  Omer  Yilmaz, Aviv  Regev  and Ramnik  J.  Xavier, “T helper cells modulate intestinal stem cell renewal and differentiation.” Cell, 175(5), 1307-1320 (2018) [PDF]

17. Jeffrey A. Farrell, Yiqun Wang, Samantha J. Riesenfeld, Karthik Shekhar, Aviv Regev and Alexander F. Schier, “Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis”, Science, 360(6392) (2018) [PDF]

16. Shristi Pandey, Karthik Shekhar, Aviv Regev and Alexander F. Schier, “Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-cell RNA-seq.”, Current Biology, 28(7),1052-1065,(2018) [PDF]

15. Kevin J. Kaczorowski, Karthik Shekhar, Dieudonné Nkulikiyimfura, Cornelia L. Dekker, Holden Maecker, Mark M. Davis, Arup K. Chakraborty and Petter Brodin, “Continuous Immunotypes describe human immune variation and predict diverse responses.”, Proc. Natl. Acad. Sci., 114(30), E6097-E6106, (2018) [PDF]

14. Adam L. Haber, Moshe Biton, Noga Rogel, Rebecca H. Herbst, Karthik Shekhar, Christopher Smillie, Grace Burgin, Toni M. Delorey, Michael R. Howitt, Yarden Katz, Itay Tirosh, Semir Beyaz, Danielle Dionne, Mei Zhang, Raktima Raychowdhury, Wendy S. Garrett, Orit Rozenblatt-Rosen, Hai Ning Shi, Omer Yilmaz, Ramnik J. Xavier and Aviv Regev, “A single-cell survey of the small intestinal epithelium.”, Nature, 551(7680), 333, (2017) [PDF]

13. Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R. Choudhury, Francois Aguet , Ellen Gelfand, Kristin Ardlie, David A Weitz, Orit Rozenblatt-Rosen, Feng Zhang and Aviv Regev, “Massively parallel single-nucleus RNA-seq with DroNc-seq.”, Nature Methods, 14(10), 955, (2017) [PDF]

12. Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, ..., Orit Rozenblatt-Rosen, Andrew A. Lane, Muzlifah Haniffa, Aviv Regev, and Nir Hacohen, “Single-cell RNA- seq reveals new types of human blood dendritic cells, monocytes and progenitors.”, Science, 356 (6335), eaah4573, (2017) [PDF]

11. Christopher A. Werley, Miao-Ping Chien, Jellert Gaublomme, Karthik Shekhar, B. Alexander Yi, Joel Kralj, William Bloxham, Aviv Regev and Adam E. Cohen “Geometry-dependent maturation of iPSC-derived cardiomyocytes probed by simultaneous voltage and calcium imaging with genetically encoded fluorescent sensors.”, PloS one, 12(3), e0172671, (2017) [PDF]

10. Alexandra-Chloé Villani‡ and Karthik Shekhar‡, “Single-cell RNA Sequencing of Human T cells”, T-Cell Differentiation: Methods and Protocols: 203-209, Enrico Lugli (ed), (2017) [PDF]

9. Karthik Shekhar*, Sylvain W. Lapan*, Irene E. Whitney*, Nicholas M. Tran, Evan Z. Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z. Levin, James T. Nemesh, Melissa Goldman, Steven A. McCarroll, Constance L. Cepko, Aviv Regev and Joshua R. Sanes, “Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics”, Cell, 166(5), 1308-1323, (2016) [PDF]

8. Brian D. Stadinski, Karthik Shekhar, Iria Gomez-Tourino, Jonathan Jung, Katsuhiro Sasaki, Andrew K. Sewell, Mark Peaman, Arup K Chakraborty and Eric S Huseby,  “Hydrophobic CDR3 residues promote the development of self-reactive T cells”, Nature Immunology,17(8), 946, (2016)

7. Zaza Ndhlovu, Philomena Kamya, Nikoshia Mewalal, Henrik Kloverpris, Thandeka Nkosi, Karyn Pretorius, Faatima Laher, Funsho Ogunshola, Denis Chopera, Karthik Shekhar, Nasreen Ismail,..., Arup Chakraborty, Krista Dong, Thumbi Ndung’u and Bruce D Walker, “Magnitude and kinetics of CD8+ T cell activation in hyperacute HIV infection impact viral set point”, Immunity, 43(3), 591-604 (2015)

6. Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, ..., David A. Weitz, Joshua R. Sanes, Alex H. Shalek, Aviv Regev, and Steven A. McCarroll “Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets”, Cell,161(5), 1202-1214 (2015) [PDF]

5. Ahmed A. Quadeer, Raymond H Louie, Karthik Shekhar, Arup K Chakraborty, I-Ming Hsing and Matthew McKay, “Statistical Linkage of Mutations in the Non-Structural Proteins of Hepatitis C Virus Exposes Vulnerable Regions for Potent Vaccine Design”, Journal of Virology, 88(13), 7628-7644 (2014)

4. Karthik Shekhar*, Petter Brodin*, Mark M Davis and Arup K Chakraborty, “Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)”, Proc. Natl. Acad. Sci., 111(1), 202-207, (2014)

3. Karthik Shekhar, Claire F Ruberman, Andrew L Ferguson, Mehran Kardar and Arup K Chakraborty, “Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes”, Phys. Rev. E., 88(6), 062705 (2013)

2. Dan H Barouch, James B Whitney, Brian Moldt, Florian Klein, Thiago Y Oliveira, Jinyan Liu, Kathryn E Stephenson, Hui-Wen Chang, Karthik Shekhar, Sanjana Gupta, ..., Arup K. Chakraborty, Pascal Poignard, Michel C. Nussenzweig and Dennis R. Burton, “Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys”, Nature, 503(7475), 224-228 (2013)

1. Vincent Dahirel*, Karthik Shekhar*, Florencia Pereyra, Toshiyuki Miura, Mikita Artyomov, Shiv Talsania, Todd M Allen, Marcus Altfeld, Mary Carrington, Darrell J Irvine, Bruce D Walker and Arup K. Chakraborty, “Coordinated linkage of HIV evolution reveals regions of immunological vulnerability”, Proc. Natl. Acad. Sci.,108(28),11530-11535 (2011)