Publications
2022
- Dingus, JG, Tang, JCY, Amamoto, R, Wallick, GK, Cepko, CL (2022) A general approach for stabilizing nanobodies for intracellular expression. Elife 11
- Kishi, JY, Liu, N, West, ER, Sheng, K, Jordanides, JJ, Serrata, M, Cepko, CL, Saka, SK, Yin, P (2022) Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. Nat Methods 19 : 1393-1402
- Amamoto, R, Wallick, GK, Cepko, CL (2022) Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration. Elife 11
- Wang, SK, Cepko, CL (2022) Targeting Microglia to Treat Degenerative Eye Diseases. Front Immunol 13 : 843558
- Goz Ayturk, D, You, W, Cepko, CL (2022) Mouse Lines with Cre-Mediated Recombination in Retinal Amacrine Cells.
eNeuro 9
- West, ER, Lapan, SW, Lee, C, Kajderowicz, KM, Li, X, Cepko, CL (2022) Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity. Cell Rep 38 :110191
- West, ER, Cepko, CL (2022) Development and diversification of bipolar interneurons in the mammalian retina. Dev Biol 481 : 30-42
2021
- Wang, SK, Xue, Y, Cepko, CL (2021) Augmentation of CD47/SIRPalpha signaling protects cones in genetic models of retinal degeneration. JCI Insight 6
- Xue, Y, Wang, SK, Rana, P, West, ER, Hong, CM, Feng, H, Wu, DM, Cepko, CL (2021) AAV-Txnip prolongs cone survival and vision in mouse models of retinitis pigmentosa. Elife 10
- Chan, YK, Wang, SK, Chu, CJ, Copland, DA, Letizia, AJ, Costa Verdera, H, Chiang, JJ, Sethi, M, Wang, MK, Neidermyer, WJ, Jr., Chan, Y, Lim, ET, Graveline, AR, Sanchez, M, Boyd, RF, Vihtelic, TS, Inciong, R, Slain, JM, Alphonse, PJ, Xue, Y, Robinson-McCarthy, LR, Tam, JM, Jabbar, MH, Sahu, B, Adeniran, JF, Muhuri, M, Tai, PWL, Xie, J, Krause, TB, Vernet, A, Pezone, M, Xiao, R, Liu, T, Wang, W, Kaplan, HJ, Gao, G, Dick, AD, Mingozzi, F, McCall, MA, Cepko, CL, Church, GM (2021) Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses. Sci Transl Med 13
- Anahtar, MN, McGrath, GEG, Rabe, BA, Tanner, NA, White, BA, Lennerz, JKM, Branda, JA, Cepko, CL, Rosenberg, ES (2021) Clinical Assessment and Validation of a Rapid and Sensitive SARS-CoV-2 Test Using Reverse Transcription Loop-Mediated Isothermal Amplification Without the Need for RNA Extraction. Open Forum Infect Dis 8 : ofaa631
2020
- Wu, DM, Ji, X, Ivanchenko, MV, Chung, M, Piper, M, Rana, P, Wang, SK, Xue, Y, West, E, Zhao, SR, Xu, H, Cicconet, M, Xiong, W, Cepko, CL (2021) Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa. JCI Insight 6
- Wang, SK, Lapan, SW, Hong, CM, Krause, TB, Cepko, CL (2020) In Situ Detection of Adeno-associated Viral Vector Genomes with SABER-FISH. Mol Ther Methods Clin Dev 19 : 376-386
- Rabe, BA, Cepko, C (2020) SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification. Proc Natl Acad Sci U S A 117 39: 24450-24458
- Chan, CSY, Lonfat, N, Zhao, R, Davis, AE, Li, L, Wu, MR, Lin, CH, Ji, Z, Cepko, CL, Wang, S (2020) Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina. Development 147 14
- Wang, SK, Xue, Y, Cepko, CL (2020) Microglia modulation by TGF-β1 protects cones in mouse models of retinal degeneration. J Clin Invest 130 8: 4360-4369
- Perez-Cervantes, C, Smith, LA, Nadadur, RD, Hughes, AEO, Wang, S, Corbo, JC, Cepko, C, Lonfat, N, Moskowitz, IP (2020) Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development 147 3
2019
- Amamoto, R, Garcia, MD, West, ER, Choi, J, Lapan, SW, Lane, EA, Perrimon, N, Cepko, CL (2019) Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation. Elife 8
- Kishi, JY, Lapan, SW, Beliveau, BJ, West, ER, Zhu, A, Sasaki, HM, Saka, SK, Wang, Y, Cepko, CL, Yin, P (2019) SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat. Methods 16 6: 533-544
- Wang, SK, Xue, Y, Rana, P, Hong, CM, Cepko, CL (2019) Soluble CX3CL1 gene therapy improves cone survival and function in mouse models of retinitis pigmentosa. Proc. Natl. Acad. Sci. U.S.A. 116 20: 10140-10149
- Xiong, W, Wu, DM, Xue, Y, Wang, SK, Chung, MJ, Ji, X, Rana, P, Zhao, SR, Mai, S, Cepko, CL (2019) AAV cis-regulatory sequences are correlated with ocular toxicity. Proc. Natl. Acad. Sci. U.S.A. 116 12: 5785-5794
2017
- Tang, JCY, Rudolph, S, Cepko, CL (2017) Viral Delivery of GFP-Dependent Recombinases to the Mouse Brain. Methods Mol. Biol. 1642 : 109-126
- da Silva, S, Cepko, CL (2017) Fgf8 Expression and Degradation of Retinoic Acid Are Required for Patterning a High-Acuity Area in the Retina. Dev. Cell 42 1: 68-81.e6
- Chinchore, Y, Begaj, T, Wu, D, Drokhlyansky, E, Cepko, CL (2017) Glycolytic reliance promotes anabolism in photoreceptors. Elife 6
- Lonfat, N, Cepko, C (2017) Epigenomics of Retinal Development in Mice and Humans. Neuron 94 3: 420-423
- Drokhlyansky, E, Göz Aytürk, D, Soh, TK, Chrenek, R, O’Loughlin, E, Madore, C, Butovsky, O, Cepko, CL (2017) The brain parenchyma has a type I interferon response that can limit virus spread. Proc. Natl. Acad. Sci. U.S.A. 114 1: E95-E104
2016
- Shekhar, K, Lapan, SW, Whitney, IE, Tran, NM, Macosko, EZ, Kowalczyk, M, Adiconis, X, Levin, JZ, Nemesh, J, Goldman, M, McCarroll, SA, Cepko, CL, Regev, A, Sanes, JR (2016) Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell166 5: 1308-1323.e30
- Tang, JC, Drokhlyansky, E, Etemad, B, Rudolph, S, Guo, B, Wang, S, Ellis, EG, Li, JZ, Cepko, CL (2016) Detection and manipulation of live antigen-expressing cells using conditionally stable nanobodies. Elife 5
- Wang, S, Cepko, CL (2016) Photoreceptor Fate Determination in the Vertebrate Retina. Invest. Ophthalmol. Vis. Sci. 57 5: ORSFe1-6
- Beier, KT, Mundell, NA, Pan, YA, Cepko, CL (2016) Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors. Curr Protoc Neurosci 74 : 1.26.1-27
- Xiong, W, Cepko, C (2016) Distinct Expression Patterns of AAV8 Vectors with Broadly Active Promoters from Subretinal Injections of Neonatal Mouse Eyes at Two Different Ages. Adv. Exp. Med. Biol. 854 : 501-7
2015
- Cepko, CL (2015) The Determination of Rod and Cone Photoreceptor Fate. Annu Rev Vis Sci 1 : 211-234
- Drokhlyansky, E, Soh, TK, Cepko, CL (2015) Preferential Budding of Vesicular Stomatitis Virus from the Basolateral Surface of Polarized Epithelial Cells Is Not Solely Directed by Matrix Protein or Glycoprotein. J. Virol. 89 22: 11718-22
- Tang, JC, Rudolph, S, Dhande, OS, Abraira, VE, Choi, S, Lapan, SW, Drew, IR, Drokhlyansky, E, Huberman, AD, Regehr, WG, Cepko, CL (2015) Cell type-specific manipulation with GFP-dependent Cre recombinase. Nat. Neurosci. 18 9: 1334-41
- Cepko, C, Punzo, C (2015) Cell metabolism: Sugar for sight. Nature 522 7557: 428-9
- Xiong, W, MacColl Garfinkel, AE, Li, Y, Benowitz, LI, Cepko, CL (2015) NRF2 promotes neuronal survival in neurodegeneration and acute nerve damage. J. Clin. Invest. 125 4: 1433-45
- Mundell, NA, Beier, KT, Pan, YA, Lapan, SW, Göz Aytürk, D, Berezovskii, VK, Wark, AR, Drokhlyansky, E, Bielecki, J, Born, RT, Schier, AF, Cepko, CL (2015) Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms. J. Comp. Neurol.523 11: 1639-63
2014
2013
- Tang, JC, Szikra, T, Kozorovitskiy, Y, Teixiera, M, Sabatini, BL, Roska, B, Cepko, CL (2013) A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation. Cell 154: 928-39
- Emerson, MM, Surzenko, N, Goetz, JJ, Trimarchi, J, Cepko, CL (2013) Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors. Dev. Cell 26: 59-72
- Mizeracka, K, DeMaso, CR, Cepko, CL (2013) Notch1 is required in newly postmitotic cells to inhibit the rod photoreceptor fate. Development 140: 3188-97
- Mizeracka, K, Trimarchi, JM, Stadler, MB, Cepko, CL (2013) Analysis of gene expression in wild-type and Notch1 mutant retinal cells by single cell profiling. Dev. Dyn. 242: 1147-59
- Cepko, CL, Vandenberghe, LH (2013) Retinal gene therapy coming of age. Hum. Gene Ther. 24: 242-4
- Beier, KT, Saunders, AB, Oldenburg, IA, Sabatini, BL, Cepko, CL (2013) Vesicular stomatitis virus with the rabies virus glycoprotein directs retrograde transsynaptic transport among neurons in vivo. Front Neural Circuits 7: 11
- Whited, JL, Tsai, SL, Beier, KT, White, JN, Piekarski, N, Hanken, J, Cepko, CL, Tabin, CJ (2013) Pseudotyped retroviruses for infecting axolotl in vivo and in vitro. Development 140: 1137-46
- Beier, KT, Borghuis, BG, El-Danaf, RN, Huberman, AD, Demb, JB, Cepko, CL (2013) Transsynaptic tracing with vesicular stomatitis virus reveals novel retinal circuitry. J. Neurosci. 33: 35-51
2012
- Beier, K, Cepko, C (2012) Viral tracing of genetically defined neural circuitry. J Vis Exp :
- Roesch, K, Stadler, MB, Cepko, CL (2012) Gene expression changes within Müller glial cells in retinitis pigmentosa. Mol. Vis. 18: 1197-214
- Cepko, CL (2012) Emerging gene therapies for retinal degenerations. J. Neurosci. 32: 6415-20
- Hafler, BP, Surzenko, N, Beier, KT, Punzo, C, Trimarchi, JM, Kong, JH, Cepko, CL (2012) Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates. Proc. Natl. Acad. Sci. U.S.A. 109: 7882-7
- Punzo, C, Xiong, W, Cepko, CL (2012) Loss of daylight vision in retinal degeneration: are oxidative stress and metabolic dysregulation to blame? J. Biol. Chem. 287: 1642-8
2011
- Emerson, MM, Cepko, CL (2011) Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors. Dev. Biol. 360: 241-55
- Beier, KT, Saunders, A, Oldenburg, IA, Miyamichi, K, Akhtar, N, Luo, L, Whelan, SP, Sabatini, B, Cepko, CL (2011) Anterograde or retrograde transsynaptic labeling of CNS neurons with vesicular stomatitis virus vectors. Proc. Natl. Acad. Sci. U.S.A. 108: 15414-9
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