The Genomics Education Partnership: Assessing and Improving a Course‐based Undergraduate Research Experience (CURE)

Abstract

The Genomics Education Partnership (GEP http://gep.wustl.edu ) started in 2006 with 16 member institutions interested in providing genomics research experiences for their upper division students. Over 10 years, GEP has grown to a consortium of faculty from over 100 colleges and universities that provide a course‐based undergraduate research experience (CURE) in genomics and bioinformatics to students at all levels. The GEP CURE is a cutting edge lab experience that can be implemented at any post‐secondary institution, even at schools that have limited laboratory capabilities. The objectives of the Genomics Education Partnership are four‐fold: 1) provide professional development in genomics for college and university faculty, 2) develop genomics curriculum for a variety of educational settings, from small group seminar courses to large introductory courses, 3) assess student gains in knowledge of genomics and attitudes toward research, and 4) accomplish research into genome structure and evolution. The partnership engages approximately 60 faculty and 1000 students per year in the manual sequence improvement and gene annotation of selected genomic regions from different species of fruit flies (Drosophila spp.). Students are guided by their instructors on how to use genomics databases (e.g., FlyBase, NCBI) and bioinformatics tools (e.g., UCSC Genome Browser, BLAST) while learning about gene structure, chromosome organization, evolution, programming, and other topics, depending on the level and the focus of the course. GEP students have improved the quality of the DNA sequence and annotated the genes and other features of interest (e.g., transposons, non‐coding RNAs) from the euchromatic Muller D element and the heterochromatic Muller F element of several Drosophila species. The results of this comparison reveal that F elements have greater transposon density, and their genes have larger coding spans, more coding exons, larger introns, and lower codon bias than the euchromatic reference regions from the D element (Leung et al. 2015 G3 5: 719 and ongoing research). Regardless of the implementation strategy (i.e. short lab modules, stand‐alone research courses, computer science/biology hybrid courses, or independent research projects) the students participating in the GEP show learning gains on attitude and knowledge assessments; these gains correlate with the amount of time invested in the project. Faculty assessment shows that some barriers to the implementation of a research‐based curriculum (e.g., campus acceptance of this pedagogical approach, availability of IT/computer services, faculty expertise) can be alleviated through a central core facility that provides curriculum materials, computational resources, collaborative pedagogy development, and a supportive community. We are currently focused on developing new curriculum for beginning students, including students at community colleges. Small working groups, alumni workshops and webinars keep the momentum going and sustain this large community. The consortium is actively recruiting faculty interested in developing course‐based research experiences for first and second year students.Support or Funding InformationSupport from HHMI grant 52005780 and NSF grant 1431407 to SCRE and from Washington University in St. Louis