LRLoop: A method to predict feedback loops in cell-cell communication

Cell fate, Development, Neural development, Neurogenesis, Retina, scRNA-Seq, , , , ,

Xin, Y., Lyu, P., Jiang, J., Zhou, F., Wang, J., Blackshaw, S., & Qian, J. (2022). LRLoop: A method to predict feedback loops in cell-cell communication. Bioinformatics (Oxford, England), 38(17), 4117–4126. Advance online publication. https://doi.org/10.1093/bioinformatics/btac447

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Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy

Muller glia, Neurodegeneration, Neurogenesis, Notch/Delta, Photoreceptor, Retina, scRNA-Seq, , , , , ,

Fogerty, J., Song, P., Boyd, P., Grabinski, S. E., Hoang, T., Reich, A., Cianciolo, L. T., Blackshaw, S., Mumm, J. S., Hyde, D. R., & Perkins, B. D. (2022). Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy. The Journal of neuroscience : the official journal of the Society for Neuroscience, 42(26), 5144–5158. https://doi.org/10.1523/JNEUROSCI.0244-22.2022

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Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina

Cell lineage analysis, Muller glia, Neurogenesis, Retina, RNA binding proteins, , , ,

Hoang, T., Kim, D. W., Appel, H., Pannullo, N. A., Leavey, P., Ozawa, M., Zheng, S., Yu, M., Peachey, N. S., & Blackshaw, S. (2022). Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina. Cell reports, 39(11), 110849. https://doi.org/10.1016/j.celrep.2022.110849

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In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration

Neurodegeneration, Photoreceptor, Retina, scRNA-Seq, , ,

Choi, E. H., Suh, S., Foik, A. T., Leinonen, H., Newby, G. A., Gao, X. D., Banskota, S., Hoang, T., Du, S. W., Dong, Z., Raguram, A., Kohli, S., Blackshaw, S., Lyon, D. C., Liu, D. R., & Palczewski, K. (2022). In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration. Nature communications, 13(1), 1830. https://doi.org/10.1038/s41467-022-29490-3

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Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids

Retina, scRNA-Seq,

Thomas, E. D., Timms, A. E., Giles, S., Harkins-Perry, S., Lyu, P., Hoang, T., Qian, J., Jackson, V. E., Bahlo, M., Blackshaw, S., Friedlander, M., Eade, K., & Cherry, T. J. (2022). Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids. Developmental cell, 57(6), 820–836.e6. https://doi.org/10.1016/j.devcel.2022.02.018

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Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration

Neurodegeneration, Retina,

Shah, S. H., Schiapparelli, L. M., Ma, Y., Yokota, S., Atkins, M., Xia, X., Cameron, E. G., Huang, T., Saturday, S., Sun, C. B., Knasel, C., Blackshaw, S., Yates, J. R., Cline, H. T., & Goldberg, J. L. (2022). Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. eLife, 11, e68148. https://doi.org/10.7554/eLife.68148

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Cross-species transcriptomic and epigenomic analysis reveals key regulators of injury response and neuronal regeneration in vertebrate retinas

Neural development, Neurodegeneration, Neurogenesis, Retina, scRNA-Seq, Transcriptomics

Hoang TV, Wang J, Boyd P, Wang F, Santiago C, Jiang L, Lahne M, Todd LJ, Saez C, Yoo S, Keuthan C, Palazzo I, Squires N, Campbell WA, Jia M, Rajaii F, Parayil T, Wang G, Ash J, Fischer AJ, Hyde DR, Qian J, Blackshaw S.

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