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  1. Thummel R, Li L, Tanase C, Sarras MP Jr, Godwin AR. Differences in expression pattern and function between zebrafish hoxc13 orthologs: recruitment of Hoxc13b into an early embryonic role. Dev Biol. 2004 Oct 15;274(2):318-33. doi: 10.1016/j.ydbio.2004.07.018. PubMed PMID: 15385162.
  2. Bai S, Thummel R, Godwin AR, Nagase H, Itoh Y, Li L, Evans R, McDermott J, Seiki M, Sarras MP Jr. Matrix metalloproteinase expression and function during fin regeneration in zebrafish: analysis of MT1-MMP, MMP2 and TIMP2. Matrix Biol. 2005 Jun;24(4):247-60. doi: 10.1016/j.matbio.2005.03.007. PubMed PMID: 15935631.
  3. Thummel R, Burket CT, Brewer JL, Sarras MP Jr, Li L, Perry M, McDermott JP, Sauer B, Hyde DR, Godwin AR. Cre-mediated site-specific recombination in zebrafish embryos. Dev Dyn. 2005 Aug;233(4):1366-77. doi: 10.1002/dvdy.20475. PubMed PMID: 15977183.
  4. Thummel R, Bai S, Sarras MP Jr, Song P, McDermott J, Brewer J, Perry M, Zhang X, Hyde DR, Godwin AR. Inhibition of zebrafish fin regeneration using in vivo electroporation of morpholinos against fgfr1 and msxb. Dev Dyn. 2006 Feb;235(2):336-46. doi: 10.1002/dvdy.20630. PubMed PMID: 16273523.
  5. Thummel R, Burket CT, Hyde DR. Two different transgenes to study gene silencing and re-expression during zebrafish caudal fin and retinal regeneration. ScientificWorldJournal. 2006 Dec 15;6 Suppl 1:65-81. doi: 10.1100/tsw.2006.328. PubMed PMID: 17205188; PubMed Central PMCID: PMC5917314.
  6. Thummel R, Ju M, Sarras MP Jr, Godwin AR. Both Hoxc13 orthologs are functionally important for zebrafish tail fin regeneration. Dev Genes Evol. 2007 Jun;217(6):413-20. doi: 10.1007/s00427-007-0154-3. Epub 2007 Apr 17. PubMed PMID: 17437127.
  7. Thummel R, Kassen SC, Montgomery JE, Enright JM, Hyde DR. Inhibition of Müller glial cell division blocks regeneration of the light-damaged zebrafish retina. Dev Neurobiol. 2008 Feb 15;68(3):392-408. doi: 10.1002/dneu.20596. PubMed PMID: 18161852; PubMed Central PMCID: PMC3711086.
  8. Yin VP, Thomson JM, Thummel R, Hyde DR, Hammond SM, Poss KD. Fgf-dependent depletion of microRNA-133 promotes appendage regeneration in zebrafish. Genes Dev. 2008 Mar 15;22(6):728-33. doi: 10.1101/gad.1641808. PubMed PMID: 18347091; PubMed Central PMCID: PMC2275425.
  9. Burket CT, Montgomery JE, Thummel R, Kassen SC, LaFave MC, Langenau DM, Zon LI, Hyde DR. Generation and characterization of transgenic zebrafish lines using different ubiquitous promoters. Transgenic Res. 2008 Apr;17(2):265-79. doi: 10.1007/s11248-007-9152-5. Epub 2007 Oct 30. PubMed PMID: 17968670; PubMed Central PMCID: PMC3660017.
  10. Hoptak-Solga AD, Nielsen S, Jain I, Thummel R, Hyde DR, Iovine MK. Connexin43 (GJA1) is required in the population of dividing cells during fin regeneration. Dev Biol. 2008 May 15;317(2):541-8. doi: 10.1016/j.ydbio.2008.02.051. Epub 2008 Mar 12. PubMed PMID: 18406403; PubMed Central PMCID: PMC2429987.
  11. Kassen SC, Thummel R, Burket CT, Campochiaro LA, Harding MJ, Hyde DR. The Tg(ccnb1:EGFP) transgenic zebrafish line labels proliferating cells during retinal development and regeneration. Mol Vis. 2008 May 19;14:951-63. PubMed PMID: 18509551; PubMed Central PMCID: PMC2391084.
  12. Thummel R, Kassen SC, Enright JM, Nelson CM, Montgomery JE, Hyde DR. Characterization of Müller glia and neuronal progenitors during adult zebrafish retinal regeneration. Exp Eye Res. 2008 Nov;87(5):433-44. doi: 10.1016/j.exer.2008.07.009. Epub 2008 Aug 5. PubMed PMID: 18718467; PubMed Central PMCID: PMC2586672.
  13. Kassen SC, Thummel R, Campochiaro LA, Harding MJ, Bennett NA, Hyde DR. CNTF induces photoreceptor neuroprotection and Müller glial cell proliferation through two different signaling pathways in the adult zebrafish retina. Exp Eye Res. 2009 Jun;88(6):1051-64. doi: 10.1016/j.exer.2009.01.007. Epub 2009 Feb 7. PubMed PMID: 19450453.
  14. Thummel R, Enright JM, Kassen SC, Montgomery JE, Bailey TJ, Hyde DR. Pax6a and Pax6b are required at different points in neuronal progenitor cell proliferation during zebrafish photoreceptor regeneration. Exp Eye Res. 2010 May;90(5):572-82. doi: 10.1016/j.exer.2010.02.001. Epub 2010 Feb 10. PubMed PMID: 20152834; PubMed Central PMCID: PMC2856924.
  15. Craig SE, Thummel R, Ahmed H, Vasta GR, Hyde DR, Hitchcock PF. The zebrafish galectin Drgal1-l2 is expressed by proliferating Müller glia and photoreceptor progenitors and regulates the regeneration of rod photoreceptors. Invest Ophthalmol Vis Sci. 2010 Jun;51(6):3244-52. doi: 10.1167/iovs.09-4879. Epub 2010 Jan 13. PubMed PMID: 20071673; PubMed Central PMCID: PMC2891476.
  16. Thomas JL, Vihtelic TS, denDekker AD, Willer G, Luo X, Murphy TR, Gregg RG, Hyde DR, Thummel R. The loss of vacuolar protein sorting 11 (vps11) causes retinal pathogenesis in a vertebrate model of syndromic albinism. Invest Ophthalmol Vis Sci. 2011 May 11;52(6):3119-28. doi: 10.1167/iovs.10-5957. PubMed PMID: 21330665; PubMed Central PMCID: PMC3109019.
  17. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Nov;93(5):726-34. doi: 10.1016/j.exer.2011.09.003. Epub 2011 Sep 17. PubMed PMID: 21945172; PubMed Central PMCID: PMC3243491.
  18. Thummel R, Bailey TJ, Hyde DR. In vivo electroporation of morpholinos into the adult zebrafish retina. J Vis Exp. 2011 Dec 27;(58):e3603. doi: 10.3791/3603. PubMed PMID: 22231802; PubMed Central PMCID: PMC3369653.
  19. Thomas JL, Ochocinska MJ, Hitchcock PF, Thummel R. Using the Tg(nrd:egfp)/albino zebrafish line to characterize in vivo expression of neurod. PLoS One. 2012;7(1):e29128. doi: 10.1371/journal.pone.0029128. Epub 2012 Jan 3. PubMed PMID: 22235264; PubMed Central PMCID: PMC3250405.
  20. Hyde DR, Godwin AR, Thummel R. In vivo electroporation of morpholinos into the regenerating adult zebrafish tail fin. J Vis Exp. 2012 Mar 29;(61). doi: 10.3791/3632. PubMed PMID: 22491016; PubMed Central PMCID: PMC3460582.
  21. Thomas JL, Nelson CM, Luo X, Hyde DR, Thummel R. Characterization of multiple light damage paradigms reveals regional differences in photoreceptor loss. Exp Eye Res. 2012 Apr;97(1):105-16. doi: 10.1016/j.exer.2012.02.004. Epub 2012 Mar 9. PubMed PMID: 22425727; PubMed Central PMCID: PMC3329775.
  22. Lenkowski JR, Qin Z, Sifuentes CJ, Thummel R, Soto CM, Moens CB, Raymond PA. Retinal regeneration in adult zebrafish requires regulation of TGFβ signaling. Glia. 2013 Oct;61(10):1687-97. doi: 10.1002/glia.22549. Epub 2013 Aug 5. PubMed PMID: 23918319; PubMed Central PMCID: PMC4127981.
  23. Thomas JL, Thummel R. A novel light damage paradigm for use in retinal regeneration studies in adult zebrafish. J Vis Exp. 2013 Oct 24;(80):e51017. doi: 10.3791/51017. PubMed PMID: 24192580; PubMed Central PMCID: PMC3960977.
  24. Gramage E, D'Cruz T, Taylor S, Thummel R, Hitchcock PF. Midkine-a protein localization in the developing and adult retina of the zebrafish and its function during photoreceptor regeneration. PLoS One. 2015;10(3):e0121789. doi: 10.1371/journal.pone.0121789. eCollection 2015. PubMed PMID: 25803551; PubMed Central PMCID: PMC4372396.
  25. Taylor SM, Alvarez-Delfin K, Saade CJ, Thomas JL, Thummel R, Fadool JM, Hitchcock PF. The bHLH Transcription Factor NeuroD Governs Photoreceptor Genesis and Regeneration Through Delta-Notch Signaling. Invest Ophthalmol Vis Sci. 2015 Nov;56(12):7496-515. doi: 10.1167/iovs.15-17616. PubMed PMID: 26580854; PubMed Central PMCID: PMC4654396.
  26. Thomas JL, Ranski AH, Morgan GW, Thummel R. Reactive gliosis in the adult zebrafish retina. Exp Eye Res. 2016 Feb;143:98-109. doi: 10.1016/j.exer.2015.09.017. Epub 2015 Oct 19. PubMed PMID: 26492821.
  27. Zhang J, Lachance V, Schaffner A, Li X, Fedick A, Kaye LE, Liao J, Rosenfeld J, Yachelevich N, Chu ML, Mitchell WG, Boles RG, Moran E, Tokita M, Gorman E, Bagley K, Zhang W, Xia F, Leduc M, Yang Y, Eng C, Wong LJ, Schiffmann R, Diaz GA, Kornreich R, Thummel R, Wasserstein M, Yue Z, Edelmann L. A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects. PLoS Genet. 2016 Apr;12(4):e1005848. doi: 10.1371/journal.pgen.1005848. eCollection 2016 Apr. PubMed PMID: 27120463; PubMed Central PMCID: PMC4847778.
  28. Thummel R, Kathryn Iovine M. Using Morpholinos to Examine Gene Function During Fin Regeneration. Methods Mol Biol. 2017;1565:79-85. doi: 10.1007/978-1-4939-6817-6_7. PubMed PMID: 28364235.
  29. Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT. Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. Epub 2017 Jan 17. PubMed PMID: 28096348; PubMed Central PMCID: PMC5293114.
  30. Granneman JG, Kimler VA, Zhang H, Ye X, Luo X, Postlethwait JH, Thummel R. Lipid droplet biology and evolution illuminated by the characterization of a novel perilipin in teleost fish. Elife. 2017 Feb 28;6. doi: 10.7554/eLife.21771. PubMed PMID: 28244868; PubMed Central PMCID: PMC5342826.
  31. Kroeger PT Jr, Drummond BE, Miceli R, McKernan M, Gerlach GF, Marra AN, Fox A, McCampbell KK, Leshchiner I, Rodriguez-Mari A, BreMiller R, Thummel R, Davidson AJ, Postlethwait J, Goessling W, Wingert RA. The zebrafish kidney mutant zeppelin reveals that brca2/fancd1 is essential for pronephros development. Dev Biol. 2017 Aug 1;428(1):148-163. doi: 10.1016/j.ydbio.2017.05.025. Epub 2017 Jun 1. PubMed PMID: 28579318; PubMed Central PMCID: PMC5571230.
  32. Thomas JL, Morgan GW, Dolinski KM, Thummel R. Characterization of the pleiotropic roles of Sonic Hedgehog during retinal regeneration in adult zebrafish. Exp Eye Res. 2018 Jan;166:106-115. doi: 10.1016/j.exer.2017.10.003. Epub 2017 Oct 10. PubMed PMID: 29030175; PubMed Central PMCID: PMC5756498.
  33. Ranski AH, Kramer AC, Morgan GW, Perez JL, Thummel R. Characterization of retinal regeneration in adult zebrafish following multiple rounds of phototoxic lesion. PeerJ. 2018;6:e5646. doi: 10.7717/peerj.5646. eCollection 2018. PubMed PMID: 30258730; PubMed Central PMCID: PMC6151257.
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