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Oblique-plane single-molecule localization microscopy for tissues and small intact animals.

Kim J, Wojcik M, Wang Y, Moon S, Zin EA, Marnani N, Newman ZL, Flannery JG, Xu K, Zhang X.

Nat Methods. 2019 Aug 19. doi: 10.1038/s41592-019-0510-z. [Epub ahead of print]


Restoration of high-sensitivity and adapting vision with a cone opsin.

Berry MH, Holt A, Salari A, Veit J, Visel M, Levitz J, Aghi K, Gaub BM, Sivyer B, Flannery JG, Isacoff EY.

Nat Commun. 2019 Mar 15;10(1):1221. doi: 10.1038/s41467-019-09124-x.


Innovative Optogenetic Strategies for Vision Restoration.

Baker CK, Flannery JG.

Front Cell Neurosci. 2018 Sep 21;12:316. doi: 10.3389/fncel.2018.00316. eCollection 2018.


Translational Retinal Research and Therapies.

Hardcastle AJ, Sieving PA, Sahel JA, Jacobson SG, Cideciyan AV, Flannery JG, Beltran WA, Aguirre GD.

Transl Vis Sci Technol. 2018 Sep 13;7(5):8. doi: 10.1167/tvst.7.5.8. eCollection 2018 Sep.


Inherited Retinal Degenerations: Current Landscape and Knowledge Gaps.

Duncan JL, Pierce EA, Laster AM, Daiger SP, Birch DG, Ash JD, Iannaccone A, Flannery JG, Sahel JA, Zack DJ, Zarbin MA; and the Foundation Fighting Blindness Scientific Advisory Board.

Transl Vis Sci Technol. 2018 Jul 18;7(4):6. doi: 10.1167/tvst.7.4.6. eCollection 2018 Jul. No abstract available.


Mutation-Independent Gene Therapies for Rod-Cone Dystrophies.

Fortuny C, Flannery JG.

Adv Exp Med Biol. 2018;1074:75-81. doi: 10.1007/978-3-319-75402-4_10. Review.


Notch Suppression Collaborates with Ascl1 and Lin28 to Unleash a Regenerative Response in Fish Retina, But Not in Mice.

Elsaeidi F, Macpherson P, Mills EA, Jui J, Flannery JG, Goldman D.

J Neurosci. 2018 Feb 28;38(9):2246-2261. doi: 10.1523/JNEUROSCI.2126-17.2018. Epub 2018 Jan 29.


Screening for Neutralizing Antibodies Against Natural and Engineered AAV Capsids in Nonhuman Primate Retinas.

Day TP, Byrne LC, Flannery JG, Schaffer DV.

Methods Mol Biol. 2018;1715:239-249. doi: 10.1007/978-1-4939-7522-8_17.


Optogenetic Retinal Gene Therapy with the Light Gated GPCR Vertebrate Rhodopsin.

Gaub BM, Berry MH, Visel M, Holt A, Isacoff EY, Flannery JG.

Methods Mol Biol. 2018;1715:177-189. doi: 10.1007/978-1-4939-7522-8_12.


Phenotypic characterization of P23H and S334ter rhodopsin transgenic rat models of inherited retinal degeneration.

LaVail MM, Nishikawa S, Steinberg RH, Naash MI, Duncan JL, Trautmann N, Matthes MT, Yasumura D, Lau-Villacorta C, Chen J, Peterson WM, Yang H, Flannery JG.

Exp Eye Res. 2018 Feb;167:56-90. doi: 10.1016/j.exer.2017.10.023. Epub 2017 Nov 6.


Tropism of engineered and evolved recombinant AAV serotypes in the rd1 mouse and ex vivo primate retina.

Hickey DG, Edwards TL, Barnard AR, Singh MS, de Silva SR, McClements ME, Flannery JG, Hankins MW, MacLaren RE.

Gene Ther. 2017 Dec;24(12):787-800. doi: 10.1038/gt.2017.85. Epub 2017 Nov 16.


Wnt Regulates Proliferation and Neurogenic Potential of Müller Glial Cells via a Lin28/let-7 miRNA-Dependent Pathway in Adult Mammalian Retinas.

Yao K, Qiu S, Tian L, Snider WD, Flannery JG, Schaffer DV, Chen B.

Cell Rep. 2016 Sep 27;17(1):165-178. doi: 10.1016/j.celrep.2016.08.078.


Massively parallel cis-regulatory analysis in the mammalian central nervous system.

Shen SQ, Myers CA, Hughes AE, Byrne LC, Flannery JG, Corbo JC.

Genome Res. 2016 Feb;26(2):238-55. doi: 10.1101/gr.193789.115. Epub 2015 Nov 17.


Neuron-glia signaling in developing retina mediated by neurotransmitter spillover.

Rosa JM, Bos R, Sack GS, Fortuny C, Agarwal A, Bergles DE, Flannery JG, Feller MB.

Elife. 2015 Aug 14;4. doi: 10.7554/eLife.09590.


Optogenetic Vision Restoration Using Rhodopsin for Enhanced Sensitivity.

Gaub BM, Berry MH, Holt AE, Isacoff EY, Flannery JG.

Mol Ther. 2015 Oct;23(10):1562-71. doi: 10.1038/mt.2015.121. Epub 2015 Jul 3.


Adaptive-optics SLO imaging combined with widefield OCT and SLO enables precise 3D localization of fluorescent cells in the mouse retina.

Zawadzki RJ, Zhang P, Zam A, Miller EB, Goswami M, Wang X, Jonnal RS, Lee SH, Kim DY, Flannery JG, Werner JS, Burns ME, Pugh EN Jr.

Biomed Opt Express. 2015 May 21;6(6):2191-210. doi: 10.1364/BOE.6.002191. eCollection 2015 Jun 1.


Gene therapy into photoreceptors and Müller glial cells restores retinal structure and function in CRB1 retinitis pigmentosa mouse models.

Pellissier LP, Quinn PM, Alves CH, Vos RM, Klooster J, Flannery JG, Heimel JA, Wijnholds J.

Hum Mol Genet. 2015 Jun 1;24(11):3104-18. doi: 10.1093/hmg/ddv062. Epub 2015 Feb 20.


Advancing therapeutic strategies for inherited retinal degeneration: recommendations from the Monaciano Symposium.

Thompson DA, Ali RR, Banin E, Branham KE, Flannery JG, Gamm DM, Hauswirth WW, Heckenlively JR, Iannaccone A, Jayasundera KT, Khan NW, Molday RS, Pennesi ME, Reh TA, Weleber RG, Zacks DN; Monaciano Consortium.

Invest Ophthalmol Vis Sci. 2015 Feb 9;56(2):918-31. doi: 10.1167/iovs.14-16049. Review.


CRALBP supports the mammalian retinal visual cycle and cone vision.

Xue Y, Shen SQ, Jui J, Rupp AC, Byrne LC, Hattar S, Flannery JG, Corbo JC, Kefalov VJ.

J Clin Invest. 2015 Feb;125(2):727-38. doi: 10.1172/JCI79651. Epub 2015 Jan 20.


Antibody neutralization poses a barrier to intravitreal adeno-associated viral vector gene delivery to non-human primates.

Kotterman MA, Yin L, Strazzeri JM, Flannery JG, Merigan WH, Schaffer DV.

Gene Ther. 2015 Feb;22(2):116-26. doi: 10.1038/gt.2014.115. Epub 2014 Dec 11.


Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells.

Gaub BM, Berry MH, Holt AE, Reiner A, Kienzler MA, Dolgova N, Nikonov S, Aguirre GD, Beltran WA, Flannery JG, Isacoff EY.

Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5574-83. doi: 10.1073/pnas.1414162111. Epub 2014 Dec 8.


Viral-mediated RdCVF and RdCVFL expression protects cone and rod photoreceptors in retinal degeneration.

Byrne LC, Dalkara D, Luna G, Fisher SK, Clérin E, Sahel JA, Léveillard T, Flannery JG.

J Clin Invest. 2015 Jan;125(1):105-16. doi: 10.1172/JCI65654. Epub 2014 Nov 21.


The expression pattern of systemically injected AAV9 in the developing mouse retina is determined by age.

Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG.

Mol Ther. 2015 Feb;23(2):290-6. doi: 10.1038/mt.2014.181. Epub 2014 Sep 16.


Visual stimulation switches the polarity of excitatory input to starburst amacrine cells.

Vlasits AL, Bos R, Morrie RD, Fortuny C, Flannery JG, Feller MB, Rivlin-Etzion M.

Neuron. 2014 Sep 3;83(5):1172-84. doi: 10.1016/j.neuron.2014.07.037. Epub 2014 Aug 21.


Imaging light responses of foveal ganglion cells in the living macaque eye.

Yin L, Masella B, Dalkara D, Zhang J, Flannery JG, Schaffer DV, Williams DR, Merigan WH.

J Neurosci. 2014 May 7;34(19):6596-605. doi: 10.1523/JNEUROSCI.4438-13.2014.


Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse.

Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG.

Gene Ther. 2014 Jun;21(6):585-92. doi: 10.1038/gt.2014.31. Epub 2014 Apr 3.


Advances in AAV vector development for gene therapy in the retina.

Day TP, Byrne LC, Schaffer DV, Flannery JG.

Adv Exp Med Biol. 2014;801:687-93. doi: 10.1007/978-1-4614-3209-8_86. Review.


Targeted ablation of Crb2 in photoreceptor cells induces retinitis pigmentosa.

Alves CH, Pellissier LP, Vos RM, Garcia Garrido M, Sothilingam V, Seide C, Beck SC, Klooster J, Furukawa T, Flannery JG, Verhaagen J, Seeliger MW, Wijnholds J.

Hum Mol Genet. 2014 Jul 1;23(13):3384-401. doi: 10.1093/hmg/ddu048. Epub 2014 Feb 2.


AAV-mediated gene delivery in Dp71-null mouse model with compromised barriers.

Vacca O, Darche M, Schaffer DV, Flannery JG, Sahel JA, Rendon A, Dalkara D.

Glia. 2014 Mar;62(3):468-76. doi: 10.1002/glia.22617. Epub 2013 Dec 31.


Specific tools for targeting and expression in Müller glial cells.

Pellissier LP, Hoek RM, Vos RM, Aartsen WM, Klimczak RR, Hoyng SA, Flannery JG, Wijnholds J.

Mol Ther Methods Clin Dev. 2014 Mar 19;1:14009. doi: 10.1038/mtm.2014.9. eCollection 2014.


AAV-mediated, optogenetic ablation of Müller Glia leads to structural and functional changes in the mouse retina.

Byrne LC, Khalid F, Lee T, Zin EA, Greenberg KP, Visel M, Schaffer DV, Flannery JG.

PLoS One. 2013 Sep 27;8(9):e76075. doi: 10.1371/journal.pone.0076075. eCollection 2013.


Misguidance and modulation of axonal regeneration by Stat3 and Rho/ROCK signaling in the transparent optic nerve.

Pernet V, Joly S, Jordi N, Dalkara D, Guzik-Kornacka A, Flannery JG, Schwab ME.

Cell Death Dis. 2013 Jul 18;4:e734. doi: 10.1038/cddis.2013.266.


In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous.

Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV.

Sci Transl Med. 2013 Jun 12;5(189):189ra76. doi: 10.1126/scitranslmed.3005708.


Long-distance axonal regeneration induced by CNTF gene transfer is impaired by axonal misguidance in the injured adult optic nerve.

Pernet V, Joly S, Dalkara D, Jordi N, Schwarz O, Christ F, Schaffer DV, Flannery JG, Schwab ME.

Neurobiol Dis. 2013 Mar;51:202-13. doi: 10.1016/j.nbd.2012.11.011. Epub 2012 Nov 27.


Adeno-associated viral vectors for gene therapy of inherited retinal degenerations.

Flannery JG, Visel M.

Methods Mol Biol. 2013;935:351-69. doi: 10.1007/978-1-62703-080-9_25.


Activation of specific interneurons improves V1 feature selectivity and visual perception.

Lee SH, Kwan AC, Zhang S, Phoumthipphavong V, Flannery JG, Masmanidis SC, Taniguchi H, Huang ZJ, Zhang F, Boyden ES, Deisseroth K, Dan Y.

Nature. 2012 Aug 16;488(7411):379-83. doi: 10.1038/nature11312.


Neuronal Nogo-A upregulation does not contribute to ER stress-associated apoptosis but participates in the regenerative response in the axotomized adult retina.

Pernet V, Joly S, Dalkara D, Schwarz O, Christ F, Schaffer D, Flannery JG, Schwab ME.

Cell Death Differ. 2012 Jul;19(7):1096-108. doi: 10.1038/cdd.2011.191. Epub 2011 Dec 23.


Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9.

Dalkara D, Byrne LC, Lee T, Hoffmann NV, Schaffer DV, Flannery JG.

Gene Ther. 2012 Feb;19(2):176-81. doi: 10.1038/gt.2011.163. Epub 2011 Oct 20.


LiGluR restores visual responses in rodent models of inherited blindness.

Caporale N, Kolstad KD, Lee T, Tochitsky I, Dalkara D, Trauner D, Kramer R, Dan Y, Isacoff EY, Flannery JG.

Mol Ther. 2011 Jul;19(7):1212-9. doi: 10.1038/mt.2011.103. Epub 2011 May 24.


AAV mediated GDNF secretion from retinal glia slows down retinal degeneration in a rat model of retinitis pigmentosa.

Dalkara D, Kolstad KD, Guerin KI, Hoffmann NV, Visel M, Klimczak RR, Schaffer DV, Flannery JG.

Mol Ther. 2011 Sep;19(9):1602-8. doi: 10.1038/mt.2011.62. Epub 2011 Apr 26.


Alternative splice variants of the USH3A gene Clarin 1 (CLRN1).

Västinsalo H, Jalkanen R, Dinculescu A, Isosomppi J, Geller S, Flannery JG, Hauswirth WW, Sankila EM.

Eur J Hum Genet. 2011 Jan;19(1):30-5. doi: 10.1038/ejhg.2010.140. Epub 2010 Aug 18.


Changes in adeno-associated virus-mediated gene delivery in retinal degeneration.

Kolstad KD, Dalkara D, Guerin K, Visel M, Hoffmann N, Schaffer DV, Flannery JG.

Hum Gene Ther. 2010 May;21(5):571-8. doi: 10.1089/hum.2009.194.


A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Müller cells.

Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer DV.

PLoS One. 2009 Oct 14;4(10):e7467. doi: 10.1371/journal.pone.0007467.


Müller cell activation, proliferation and migration following laser injury.

Tackenberg MA, Tucker BA, Swift JS, Jiang C, Redenti S, Greenberg KP, Flannery JG, Reichenbach A, Young MJ.

Mol Vis. 2009 Sep 17;15:1886-96.


Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane.

Isosomppi J, Västinsalo H, Geller SF, Heon E, Flannery JG, Sankila EM.

Mol Vis. 2009 Sep 8;15:1806-18.


Severe retinal degeneration caused by a novel rhodopsin mutation.

Liu H, Wang M, Xia CH, Du X, Flannery JG, Ridge KD, Beutler B, Gong X.

Invest Ophthalmol Vis Sci. 2010 Feb;51(2):1059-65. doi: 10.1167/iovs.09-3585. Epub 2009 Sep 9.


CLRN1 is nonessential in the mouse retina but is required for cochlear hair cell development.

Geller SF, Guerin KI, Visel M, Pham A, Lee ES, Dror AA, Avraham KB, Hayashi T, Ray CA, Reh TA, Bermingham-McDonogh O, Triffo WJ, Bao S, Isosomppi J, Västinsalo H, Sankila EM, Flannery JG.

PLoS Genet. 2009 Aug;5(8):e1000607. doi: 10.1371/journal.pgen.1000607. Epub 2009 Aug 14.


Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous.

Dalkara D, Kolstad KD, Caporale N, Visel M, Klimczak RR, Schaffer DV, Flannery JG.

Mol Ther. 2009 Dec;17(12):2096-102. doi: 10.1038/mt.2009.181. Epub 2009 Aug 11.


Molecular evolution of adeno-associated virus for enhanced glial gene delivery.

Koerber JT, Klimczak R, Jang JH, Dalkara D, Flannery JG, Schaffer DV.

Mol Ther. 2009 Dec;17(12):2088-95. doi: 10.1038/mt.2009.184. Epub 2009 Aug 11.


In vivo imaging of microscopic structures in the rat retina.

Geng Y, Greenberg KP, Wolfe R, Gray DC, Hunter JJ, Dubra A, Flannery JG, Williams DR, Porter J.

Invest Ophthalmol Vis Sci. 2009 Dec;50(12):5872-9. doi: 10.1167/iovs.09-3675. Epub 2009 Jul 2.

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