A cost-free CURE: Using bioinformatics to identify DNA-binding factors at a specific genomic locus

Schmidt, C. A.; Hodkinson, L. J.; Comstra, H. S.; Rieder, L. E.

doi:10.1101/2022.10.21.513244

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bioRxiv · 10.1101/2022.10.21.513244

A cost-free CURE: Using bioinformatics to identify DNA-binding factors at a specific genomic locus

Schmidt, C. A.·Hodkinson, L. J.·Comstra, H. S.·Rieder, L. E.

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Abstract

Research experiences provide diverse benefits for undergraduates. Many academic institutions have adopted course-based undergraduate research experiences (CUREs) to improve student access to research opportunities. However, potential instructors of a CURE might still face financial or practical hurdles that prevent implementation. Bioinformatics research offers an alternative that is free, safe, compatible with remote learning, and may be more accessible for students with disabilities. Here, we describe a bioinformatics CURE that leverages publicly available datasets to discover novel proteins that target an instructor-determined genomic locus of interest. We use the free, user-friendly bioinformatics platform Galaxy to map ChIP-seq datasets to a genome, which removes the computing burden from students. Both faculty and students directly benefit from this CURE, as faculty can perform candidate screens and publish CURE results. Students gain not only basic bioinformatics knowledge, but also transferable skills, including scientific communication, database navigation, and primary literature experience. The CURE is flexible and can be expanded to analyze different types of high-throughput data or to investigate different genomic loci in any species.

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Schmidt, C. A., Hodkinson, L. J., Comstra, H. S., Rieder, L. E.. 2022-10-24. A cost-free CURE: Using bioinformatics to identify DNA-binding factors at a specific genomic locus. https://doi.org/10.1101/2022.10.21.513244

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