With more than 10 years of experience in cell and molecular biology techniques, data analysis, and assay building and optimization, I can help you find, learn, and leverage the latest technologies to their fullest extent.

I have extensively worked and studied molecular biology of eukaryotic cells, primarily focusing on the mutagenesis of embryonic and induced pluripotent stem cells, phenotypic screening analytics, and large-scale -omics data production and analysis.

  • Proficient in assay design, optimization, and analysis of: ChIP (including ChIP-seq), Western Blot, PCR (including RT and q), somatic and stem cell culturing, stem cell differentiation, viral production and transduction, RNA-seq and other NGS and HTS techniques, High Content Screening, and more
  • Multiple NGS data modality analysis using R (bioconductor) and Python including population and single-cell RNA-seq for variant calling, functional genomics, and basic transcriptomics along with data and pipeline QC and results’ integration
  • Mathematica, Python, GoLang, and R programming experience for large-scale bioinformatics data analysis, including taking training courses in Python

Publications

  • He, Y., Duncan, W. D., Cooper, D. J., Hansen, J., Iyengar, R., Ong, E., . . . Diehl, A. D. (2019). OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinformatics, 20(5), 180. doi:10.1186/s12859-019-2723-7
  • Danzi, M. C., Mehta, S. T., Dulla, K., Zunino, G., Cooper, D. J., Bixby, J. L., & Lemmon, V. P. (2018). The effect of Jun dimerization on neurite outgrowth and motif binding. Molecular and cellular neurosciences, 92, 114-127. doi:10.1016/j.mcn.2018.08.001
  • Cooper DJ, Zunino G, Bixby JL, Lemmon VP. Phenotypic screening with primary neurons to identify drug targets for regeneration and degeneration (2017).  Mol Cell Neurosci, 80:161-169
  • Cooper DJ, Chen IC, Hernandez C, Wang Y, Walter CA, McCarrey JR (2017). Pluripotent cells display enhanced resistance to mutagenesis. Stem Cell Research, 19(PA):113-117
  • Cooper DJ, Walter CA, McCarrey JR (2014). Co-regulation of pluripotency and genetic integrity at the genomic level. Stem Cell Research 2014, 13(PA):508–519.

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