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
- 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
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
- Wang, S, Sengel, C, Emerson, MM, Cepko, CL (2014) A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. Dev. Cell 30: 513-27 (PDF)
- Cepko, C (2014) Intrinsically different retinal progenitor cells produce specific types of progeny. Nat. Rev. Neurosci. 15: 615-27 (PDF)
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 (PDF)
- 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 (PDF)
- Mizeracka, K, DeMaso, CR, Cepko, CL (2013) Notch1 is required in newly postmitotic cells to inhibit the rod photoreceptor fate. Development 140: 3188-97 (PDF)
- 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 (PDF)
- Cepko, CL, Vandenberghe, LH (2013) Retinal gene therapy coming of age. Hum. Gene Ther. 24: 242-4 (PDF)
- 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 (PDF)
- 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 (PDF)
- 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 (PDF)
2012
- Beier, K, Cepko, C (2012) Viral tracing of genetically defined neural circuitry. J Vis Exp : (PDF)
- Roesch, K, Stadler, MB, Cepko, CL (2012) Gene expression changes within Müller glial cells in retinitis pigmentosa. Mol. Vis. 18: 1197-214 (PDF)
- Cepko, CL (2012) Emerging gene therapies for retinal degenerations. J. Neurosci. 32: 6415-20 (PDF)
- 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 (PDF)
- 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 (PDF)
2011
- Emerson, MM, Cepko, CL (2011) Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors. Dev. Biol. 360: 241-55 (PDF)
- 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 (PDF)