The Genomics Education Partnership Provides Undergraduate Research Using Bioinformatics

Inclusion of research experiences in the undergraduate STEM curriculum is a key recommendation by Vision and Change and the 2012 PCAST report. Students who participate in research are more engaged and better prepared to become future scientists or informed citizens. However, availability of research experiences is often limited due to the lack of resources and mentors. The use of bioinformatics provides an outstanding way for students to engage in research in an accessible and cost-effective manner. The Genomics Education Partnership (GEP) is a network of more than 100 colleges and universities annually serving over 1000 undergraduates that uses a central platform at Washington University (WU) in St. Louis to provide course-based research experiences. The curriculum can be adapted to the specific needs of each class and institution type, including large universities, small undergraduate institutions, and community colleges.  GEP focuses on comparative genomics, specifically on the evolution of the Muller F element, a chromatin domain with unique properties in multiple Drosophila species. Students improve the draft genomic sequences and/or carefully annotate these improved sequences. Their findings contribute to student co-authored publications, provide data for elucidating the regulation of chromatin structure and its impact on gene expression, and benefit the scientific community through data submission to public databases. The GEP web framework is managed centrally from WU, with bioinformatics curriculum and tools for faculty and students. New faculty receive hands-on training and effective follow-up support. Sharing of best practices is facilitated online, and in person through annual “alumni” meetings. Pre/Post conceptual knowledge quizzes and post-course surveys demonstrate significant gains in student understanding of genes and genomes, and self-reported gains in understanding the process of science. We find that a computer-based genomics research project can yield gains similar to those obtained through bench research in a traditional summer research program. There is little correlation between institutional characteristics and performance on the quiz or gains in the understanding of science, which argues that all students can benefit from a research-intensive curriculum. GEP is currently looking for faculty interested in implementing the curriculum for beginning (freshman and sophomore) students as a way to teach genetics and genomics, leading to the research experience. No previous training in bioinformatics is required; see http://gep.wustl.edu.