Cassidy RM, Flores EM, Nguyen AT, Cheruvu SS, Uribe RA, Krachler AM and Odem MA. (2023). Systematic analysis of proximal midgut- and anorectal-originating contractions in larval zebrafish using event feature detection and supervised machine learning algorithms. Neurogastroenterology & Motility https://doi.org/10.1111/nmo.14675
Baker PA, Ibarra-García-Padilla R, Venkatesh A, Singleton EW and Uribe RA. (2022). In Toto Imaging of Zebrafish Enteric Nervous System Development Reveals that Gut Colonization is Tied to Proliferation Downstream of Ret. Development. https://doi.org/10.1242/dev.200668
Howard IV AGA and Uribe RA (2022). Hox proteins as regulators of extracellular matrix interactions during neural crest migration. Differentiation. doi.org/10.1016/j.diff.2022.09.003
Wu KL, Moore JM, Miller MD, Chen Y, Lee C, Xu D, Peng Z, Duan Q, Phillips GN^, Uribe RA^ and Xiao H.^ (2022). Expanding the Eukaryotic Genetic Code with a Biosynthesized 21st Amino Acid. Protein Science. http://dx.doi.org/10.1002/pro.4443 ^co-corresponding authors
Howard IV AGA, Nguyen AC, Tworig J, Ravisankar P, Li C, Singleton EW, Kotzur G, Waxman JS and Uribe RA. (2022). Elevated Hoxb5b expands vagal neural crest pool and blocks enteric neuronal development in zebrafish. Frontiers in Cell and Developmental Biology. doi: 10.3389/fcell.2021.803370
Tao L, Moreno-Smith M, Ibarra-García-Padilla R, Milazzo G, Drolet NA, Hernandez BE, Sun Oh Y, Patel I, Kim JJ, Zorman B, Patel T, Kamal AHM, Zhao Y, Hicks J, Vasudevan SA, Putluri N, Coarfa C, Sumazin P, Perini G, Parchem RJ, Uribe RA and Barbieri E. (2021). CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming. Advanced Science, https://doi.org/10.1002/advs.202005047
Ibarra-García-Padilla R, Howard IV AGA, Singleton EW and Uribe RA. (2021). A protocol for Whole-mount Immuno-Coupled Hybridization Chain Reaction (WICHCR) in zebrafish embryos and early larvae. STAR Protocols, Volume 2, Issue 3, 100709,
https://doi.org/10.1016/j.xpro.2021.100709.
Howard IV AGA , Baker PA, Ibarra-García-Padilla R, Moore JA, Rivas LJ, Tallman JJ, Singleton EW, Westheimer JL, Corteguera JA and Uribe RA. (2021). An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. eLife. eLife 2021;10:e60005 doi: 10.7554/eLife.60005
Baker, P.A., Meyer, M.D., Tsang, A. and Uribe, R.A. (2019). Immunohistochemical and ultrastructural analysis of the maturing larval zebrafish enteric nervous system reveals the formation of a neuropil pattern. Scientific Reports, Volume 9, Article number: 6941 www.nature.com/articles/s41598-019-43497-9
Hutchins, E.J., Kunttas, E., Piacentino, M.L., Howard IV, A.G.A., Bronner, M.E. and Uribe, R.A. (2018). Migration and diversification of the vagal neural crest. Developmental Biology, Invited Review article in the Special Edition celebrating the 150th Anniversary of the discovery of Neural Crest doi.org/10.1016/j.ydbio.2018.07.004 PMID: 29981692
Rajan SG, Gallik KL, Monaghan JR, Uribe RA, Bronner ME, Saxena A. (2018). Tracking neural crest cell cycle progression in vivo. Genesis. e23214. In the Special Anniversary Edition celebrating 150 years of Neural Crest Research doi.org/ 10.1002/dvg.23214 PMID: 29956448
Uribe, R.A.*, Hong, S.S. and Bronner, M.E. (2018). Retinoic Acid temporally orchestrates colonization of the gut by vagal neural crest cells. Developmental Biology, Jan 1;433(1):17-32. PMID: 29108781 10.1016/j.ydbio.2017.10.021 *corresponding author
Baker PA, Ibarra-García-Padilla R, Venkatesh A, Singleton EW and Uribe RA. (2022). In Toto Imaging of Zebrafish Enteric Nervous System Development Reveals that Gut Colonization is Tied to Proliferation Downstream of Ret. Development. https://doi.org/10.1242/dev.200668
Howard IV AGA and Uribe RA (2022). Hox proteins as regulators of extracellular matrix interactions during neural crest migration. Differentiation. doi.org/10.1016/j.diff.2022.09.003
Wu KL, Moore JM, Miller MD, Chen Y, Lee C, Xu D, Peng Z, Duan Q, Phillips GN^, Uribe RA^ and Xiao H.^ (2022). Expanding the Eukaryotic Genetic Code with a Biosynthesized 21st Amino Acid. Protein Science. http://dx.doi.org/10.1002/pro.4443 ^co-corresponding authors
Howard IV AGA, Nguyen AC, Tworig J, Ravisankar P, Li C, Singleton EW, Kotzur G, Waxman JS and Uribe RA. (2022). Elevated Hoxb5b expands vagal neural crest pool and blocks enteric neuronal development in zebrafish. Frontiers in Cell and Developmental Biology. doi: 10.3389/fcell.2021.803370
Tao L, Moreno-Smith M, Ibarra-García-Padilla R, Milazzo G, Drolet NA, Hernandez BE, Sun Oh Y, Patel I, Kim JJ, Zorman B, Patel T, Kamal AHM, Zhao Y, Hicks J, Vasudevan SA, Putluri N, Coarfa C, Sumazin P, Perini G, Parchem RJ, Uribe RA and Barbieri E. (2021). CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming. Advanced Science, https://doi.org/10.1002/advs.202005047
Ibarra-García-Padilla R, Howard IV AGA, Singleton EW and Uribe RA. (2021). A protocol for Whole-mount Immuno-Coupled Hybridization Chain Reaction (WICHCR) in zebrafish embryos and early larvae. STAR Protocols, Volume 2, Issue 3, 100709,
https://doi.org/10.1016/j.xpro.2021.100709.
Howard IV AGA , Baker PA, Ibarra-García-Padilla R, Moore JA, Rivas LJ, Tallman JJ, Singleton EW, Westheimer JL, Corteguera JA and Uribe RA. (2021). An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. eLife. eLife 2021;10:e60005 doi: 10.7554/eLife.60005
- In this work, the Uribe lab utilizes single-cell transcriptomics to catalogue an atlas of neural crest-derived and other cell types in the developing zebrafish during their late embryonic development.
Baker, P.A., Meyer, M.D., Tsang, A. and Uribe, R.A. (2019). Immunohistochemical and ultrastructural analysis of the maturing larval zebrafish enteric nervous system reveals the formation of a neuropil pattern. Scientific Reports, Volume 9, Article number: 6941 www.nature.com/articles/s41598-019-43497-9
- In this paper, we describe that the zebrafish intestinal wall contains a meshwork of neural tissue, called the myenteric plexus, which matures between 7 and 18 days post fertilization.
Hutchins, E.J., Kunttas, E., Piacentino, M.L., Howard IV, A.G.A., Bronner, M.E. and Uribe, R.A. (2018). Migration and diversification of the vagal neural crest. Developmental Biology, Invited Review article in the Special Edition celebrating the 150th Anniversary of the discovery of Neural Crest doi.org/10.1016/j.ydbio.2018.07.004 PMID: 29981692
- Summarizes current knowledge of vagal neural crest development across vertebrates.
Rajan SG, Gallik KL, Monaghan JR, Uribe RA, Bronner ME, Saxena A. (2018). Tracking neural crest cell cycle progression in vivo. Genesis. e23214. In the Special Anniversary Edition celebrating 150 years of Neural Crest Research doi.org/ 10.1002/dvg.23214 PMID: 29956448
- In this paper, we collaborated with the Saxena lab to create a novel cell cycle occupancy reporter, in neural crest cells.
Uribe, R.A.*, Hong, S.S. and Bronner, M.E. (2018). Retinoic Acid temporally orchestrates colonization of the gut by vagal neural crest cells. Developmental Biology, Jan 1;433(1):17-32. PMID: 29108781 10.1016/j.ydbio.2017.10.021 *corresponding author
- In this study, it was discovered that a very fine window of time is critical for Retinoic Acid to affect vagal neural crest invasion into gut tissue. We also discovered that the transcription factor Meis3 is functionally important downstream of Retinoic Acid, expanding our knowledge of this critical Gene-Environment interaction during development.
Uribe, R.A., Gu, T. and Bronner, M.E. (2016). A novel subset of enteric neurons revealed by ptf1a:GFP during zebrafish enteric nervous system development. Genesis, Mar; 54(3):123-8. doi: 10.1002/dvg.22927. PMID: 26865080
Uribe R.A.*, Buzzi A.L.*, Bronner M.E. and Strobl-Mazzulla, P.H. (2015). Histone demethylase KDM4B regulates otic vesicle invagination via epigenetic control of Dlx3 expression. The Journal of Cell Biology Nov 23; 211(4): 815-27. doi: 10.1083/jcb.201503071. *equal authorship. (Featured in “News: in this Issue”) PMID: 26598618
Uribe, R.A. and Bronner, M.E. (2015). Meis3 is required for neural crest invasion of the gut during zebrafish enteric nervous system development. Molecular Biology of the Cell Nov 1; 26(21): 3728-40 doi:10.1091/mbc.E15-02-0112. PMID: 26354419
Lee J., Cox B.D., Daly C., Lee C., Nuckels R.J., Tittle R.K., Uribe R.A. and Gross J.M. (2012). An ENU mutagenesis screen in zebrafish for visual system mutants identifies a novel splice-acceptor site mutation in patched2 that results in colobomas. Investigative Ophthalmology and Visual Science 53(13): 8214-21. PMID: 23150614
Uribe, R. A., Kwon, T., Marcotte, E.M and Gross, J.M. (2012). Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Developmental Biology 371, 280-292. PMID: 22981606
Luo, J., Uribe, R.A., Hayton, S., Calinescu, A.A., Gross, J.M. and Hitchcock, P.F. (2012). Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina. Neural Development 7(1): 33. PMID: 23111152
Uribe, R.A. and Gross, J.M. (2010). Id2a influences neuron and glia formation in the zebrafish retina by modulating retinoblast cell cycle kinetics. Development 137: 3763-3774. PMID: 20943708
Ng, A., Uribe, R.A., Yieh, L., Nuckels, R. and Gross, J.M. (2009). Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development. Development 136(15): 2601-11. PMID: 19570845
Uribe, R.A. and Gross, J.M. (2007). Immunohistochemistry on Cryosections from Embryonic and Adult Zebrafish Eyes. Cold Spring Harbor Protocols 2007: pdb.prot4779. (Cover photo) PMID: 21357120
- In this study, Dr. Uribe and undergraduate researcher Tiffany Gu characterized the localization of ptf1a:GFP+ cells in the developing enteric plexus in zebrafish fishes.
Uribe R.A.*, Buzzi A.L.*, Bronner M.E. and Strobl-Mazzulla, P.H. (2015). Histone demethylase KDM4B regulates otic vesicle invagination via epigenetic control of Dlx3 expression. The Journal of Cell Biology Nov 23; 211(4): 815-27. doi: 10.1083/jcb.201503071. *equal authorship. (Featured in “News: in this Issue”) PMID: 26598618
- In this collaborative work, Dr. Uribe worked with graduate student Ailin Buzzi and Dr. Pablo Strobl-Mazzulla while in the Bronner lab to discover that the epigenetic factor KDM4B functions to regulate otic vesicle invagination and epithelial polarization in chick.
Uribe, R.A. and Bronner, M.E. (2015). Meis3 is required for neural crest invasion of the gut during zebrafish enteric nervous system development. Molecular Biology of the Cell Nov 1; 26(21): 3728-40 doi:10.1091/mbc.E15-02-0112. PMID: 26354419
- In this investigative work, Dr. Uribe discovered that the transcription factor Meis3 functions to promote vagal neural crest migration into the primitive gut tube in zebrafish embryos.
Lee J., Cox B.D., Daly C., Lee C., Nuckels R.J., Tittle R.K., Uribe R.A. and Gross J.M. (2012). An ENU mutagenesis screen in zebrafish for visual system mutants identifies a novel splice-acceptor site mutation in patched2 that results in colobomas. Investigative Ophthalmology and Visual Science 53(13): 8214-21. PMID: 23150614
- In this team project while a graduate student in the Gross lab, Dr. Uribe helped to screen through a family of zebrafish mutants for defects in eye formation during development. Of 18 recessive mutants discovered, this paper focuses description of the mutant phenotype called coloboma caused by a mutation in the patched2 gene.
Uribe, R. A., Kwon, T., Marcotte, E.M and Gross, J.M. (2012). Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Developmental Biology 371, 280-292. PMID: 22981606
- This study found that the protein Id2a functions upstream of the Notch pathway to regulate cell cycle exit of retinal progenitors and their ability to undergo neuronal differentiation. This study was one of the first in the zebrafish eye community to leverage RNA-sequencing and bioinformatic analysis of isolated retinal tissue.
Luo, J., Uribe, R.A., Hayton, S., Calinescu, A.A., Gross, J.M. and Hitchcock, P.F. (2012). Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina. Neural Development 7(1): 33. PMID: 23111152
- This collaborative work with the Hitchcock lab found that the secreted factor Midkine-A influences the expression of Id2a in order to impact the cell cycle state of retinal progenitor cells.
Uribe, R.A. and Gross, J.M. (2010). Id2a influences neuron and glia formation in the zebrafish retina by modulating retinoblast cell cycle kinetics. Development 137: 3763-3774. PMID: 20943708
- In this comprehensive work while a graduate student in the Gross lab, Dr. Uribe discovered that Id2a levels influence the cell cycle state of retinal progenitor cells and their ability to undergo neurogenesis during retinal development in zebrafish. This was the first study to implicate Id genes in retinal growth control to affect neural development.
Ng, A., Uribe, R.A., Yieh, L., Nuckels, R. and Gross, J.M. (2009). Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development. Development 136(15): 2601-11. PMID: 19570845
- In this Gross lab paper, mutations in the genes gart and paics were discovered to affect pigmentation and eye growth during zebrafish development.
Uribe, R.A. and Gross, J.M. (2007). Immunohistochemistry on Cryosections from Embryonic and Adult Zebrafish Eyes. Cold Spring Harbor Protocols 2007: pdb.prot4779. (Cover photo) PMID: 21357120
- In this protocol paper, a method to prepare, section and perform immunohistochemistry on tissues from eyes is described in zebrafish.
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