Professional Education


  • Doctor of Philosophy, Univ of Massachusetts Medical School (2010)

Stanford Advisors


All Publications


  • An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development PLOS GENETICS Benitez, C. M., Qu, K., Sugiyama, T., Pauerstein, P. T., Liu, Y., Tsai, J., Gu, X., Ghodasara, A., Arda, H. E., Zhang, J., Dekker, J. D., Tucker, H. O., Chang, H. Y., Kim, S. K. 2014; 10 (10)
  • An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. PLoS genetics Benitez, C. M., Qu, K., Sugiyama, T., Pauerstein, P. T., Liu, Y., Tsai, J., Gu, X., Ghodasara, A., Arda, H. E., Zhang, J., Dekker, J. D., Tucker, H. O., Chang, H. Y., Kim, S. K. 2014; 10 (10)

    Abstract

    The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus.

    View details for DOI 10.1371/journal.pgen.1004645

    View details for PubMedID 25330008

  • Gene Regulatory Networks Governing Pancreas Development DEVELOPMENTAL CELL Arda, H. E., Benitez, C. M., Kim, S. K. 2013; 25 (1): 5-13

    Abstract

    Elucidation of cellular and gene regulatory networks (GRNs) governing organ development will accelerate progress toward tissue replacement. Here, we have compiled reference GRNs underlying pancreas development from data mining that integrates multiple approaches, including mutant analysis, lineage tracing, cell purification, gene expression and enhancer analysis, and biochemical studies of gene regulation. Using established computational tools, we integrated and represented these networks in frameworks that should enhance understanding of the surging output of genomic-scale genetic and epigenetic studies of pancreas development and diseases such as diabetes and pancreatic cancer. We envision similar approaches would be useful for understanding the development of other organs.

    View details for DOI 10.1016/j.devcel.2013.03.016

    View details for Web of Science ID 000318058400003