Brian Clark

Assistant Professor of Ophthalmology and Visual Sciences, Assistant Professor of Developmental Biology

    • 1159 Citations

    Research output per year

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    Personal profile

    Research interests

    The goal of my research program is to identify the mechanisms by which a common retinal progenitor is intrinsically instructed to generate a temporally regulated program of retinal cell type specification. We aim to understand how a progenitor cell is selected to (A) undergo a neurogenic division, (B) specify as as a retinal neuron or glia, and (C) how these mechanisms change across development and correspond to changes in cell type identity. Using single cell RNA-sequencing on the developing mouse retina (Clark and Stein-O`Brien, et al, BioRxiv), we are beginning to understand the transcriptional signature of retinal progenitors across development and during the process of retinal neurogenesis. We have identified numerous genes with unknown retinal function that display both dynamic and temporally restricted expression patterns that we hypothesize to be important in the regulation of retinal development. Using a suite of moderate to high-throughput techniques, we aim to identify the mechanisms by which these genes function to control retinal neurogenesis and cell fate specification. Current efforts are focused on examining similarities and differences in retinal neurogenesis and cell type specification across vertebrate species. While many of the candidate genes encode for proteins, the lab is also focused on understanding the roles of long, non-protein coding RNAs (lncRNAs) during retinal development and the mechanisms by which these unique biomolecules function. Combined, we anticipate these studies to expand our understanding on the mechanisms governing transcriptional regulation and cell fate specification.

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    Research Output

    • 1159 Citations
    • 21 Article
    • 1 Chapter
    • 1 Review article

    ASCOT identifies key regulators of neuronal subtype-specific splicing

    Ling, J. P., Wilks, C., Charles, R., Leavey, P. J., Ghosh, D., Jiang, L., Santiago, C. P., Pang, B., Venkataraman, A., Clark, B. S., Nellore, A., Langmead, B. & Blackshaw, S., Dec 1 2020, In : Nature communications. 11, 1, 137.

    Research output: Contribution to journalArticle

    Open Access
  • Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

    Ray, T. A., Cochran, K., Kozlowski, C., Wang, J., Alexander, G., Cady, M. A., Spencer, W. J., Ruzycki, P., Clark, B. S., Laeremans, A., He, M. X., Wang, X., Park, E., Hao, Y., Iannaccone, A., Hu, G., Fedrigo, O., Skiba, N. P., Arshavsky, V. Y. & Kay, J. N., Dec 1 2020, In : Nature communications. 11, 1, 3328.

    Research output: Contribution to journalArticle

    Open Access
  • 2 Scopus citations

    Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development

    Lu, Y., Shiau, F., Yi, W., Lu, S., Wu, Q., Pearson, J. D., Kallman, A., Zhong, S., Hoang, T., Zuo, Z., Zhao, F., Zhang, M., Tsai, N., Zhuo, Y., He, S., Zhang, J., Stein-O'Brien, G. L., Sherman, T. D., Duan, X., Fertig, E. J. & 8 others, Goff, L. A., Zack, D. J., Handa, J. T., Xue, T., Bremner, R., Blackshaw, S., Wang, X. & Clark, B. S., May 18 2020, In : Developmental cell. 53, 4, p. 473-491.e9

    Research output: Contribution to journalArticle

  • 4 Scopus citations

    Zeb2 regulates the balance between retinal interneurons and Müller glia by inhibition of BMP–Smad signaling

    Menuchin-Lasowski, Y., Dagan, B., Conidi, A., Cohen-Gulkar, M., David, A., Ehrlich, M., Giladi, P. O., Clark, B. S., Blackshaw, S., Shapira, K., Huylebroeck, D., Henis, Y. I. & Ashery-Padan, R., Dec 1 2020, In : Developmental Biology. 468, 1-2, p. 80-92 13 p.

    Research output: Contribution to journalArticle

  • Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species

    Stein-O'Brien, G. L., Clark, B. S., Sherman, T., Zibetti, C., Hu, Q., Sealfon, R., Liu, S., Qian, J., Colantuoni, C., Blackshaw, S., Goff, L. A. & Fertig, E. J., May 22 2019, In : Cell Systems. 8, 5, p. 395-411.e8

    Research output: Contribution to journalArticle

    Open Access
  • 20 Scopus citations