Workflow Development

Using computation and wet lab to build characterization workflows

Transcription factor regulation and evolution

Defining the molecular to cellular roles of transcription factors and how they influence gene regulation

induced Pluripotent Stem Cells (iPSCs)

Developing new culture techniques and strategies for understanding gene function

Moving Genomics to Mechanism

The Prokop lab focuses on integrative biosciences for understanding genes and genetic variants, utilizing computational tools to generate testable hypotheses for genomic variants (coding and noncoding) and protein function that are then used to guide wet lab experiments into disease mechanisms and pharmacological intervention. The Prokop lab’s NIH Big Data to Knowledge funded computational tools (BD2K- K01ES025435) focus on deep evolutionary analysis of codon usage combined with protein modeling and molecular dynamic simulations to study the role of genetic variants from whole genome sequencing and GWAS linkage disequilibrium blocks. Variants/proteins are then studied in the lab using a combination of protein biophysics, cell culture (including primary cells and induced pluripotent stem cells), gene regulation, and genomic technologies. The combination of genetic mechanisms for both common and rare disease genetics for a broad spectrum of disorders allows for a more global view of transcriptional regulation involved in disease, gene evolution, disease intersections, a more robust model of genotype-to-phenotype predictions, and hopefully a more patient based treatment strategy. These tools have been successfully applied to genomic insights for chronic kidney disease (PMID: 29476007), mesothelioma (PMID: 29284740), obesity (PMID: 29193816), neurological diseases (PMID: 27830187), cancer metastasis (PMID: 25762439), and genetics of sex differences (PMID: 26848384) to name a few. Additionally, the Prokop lab is interested in the development of educational tools that can be applied to clinical genomics and the creation of research opportunities for students at universities and colleges classically disadvantaged for research experience through the use of cloud based bioinformatics and data basing.

How can we help you

If you would like an assessment of genomic variants, please reach out to our lab to discuss collaborations.