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The Genomics Education Partnership (GEP; https://thegep.org) began as a consortium of 16 faculty in 2006 with a goal of providing students with Course-based Undergraduate Research Experiences (CUREs) in genomics. Today, GEP has over 200 faculty from more than 180 institutions and engages more than 3,900 undergraduates in authentic genomics research annually. These faculty joined and continued to participate in the GEP for many reasons, including the collaborative nature of the research, the well-established infrastructure, and the supportive network of like-minded colleagues. Faculty implement GEP materials in diverse settings ? ranging from short modules (2-8 weeks) within a course, to a standalone full-semester course, to independent student research. GEP students show significant gains in scientific knowledge and attitudes toward science. In addition to improving their understanding of the research process and how new knowledge is created in the field, GEP students acquire desirable and transferable skills essential for future participation in the workforce, such as problem solving, independence, application of knowledge, team-work, and collaboration. Students also gain competence in the use of computational algorithms to analyze large biological datasets ? thereby preparing students for a growing need of a workforce trained at applying statistics and computational tools to analyze large datasets. In addition, GEP students and their faculty mentors are eligible to be co-authors on the scientific publications that are based on their work. In this workshop, we will provide an overview of the GEP community, a hands-on guided tour of our introductory curriculum aimed to teach gene structure, transcription, translation, and processing, and a step-by-step walkthrough that illustrates the protocol for annotating a protein-coding gene in Drosophila. Participants will receive information on how to join the GEP community and receive training and resources to enable their implementations.
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The Genomics Education Partnership: First Findings on Genomics Research in Community Colleges
The Genomics Education Partnership (GEP), a consortium of diverse colleges and universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with Internet access, may be particularly accessible for two-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, the authors analyzed student knowledge and self-reported outcomes. It was found that CC student gains were comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. The early findings suggest that the GEP model of centralized support with flexible implementation of a course-related undergraduate research experience benefits CC students and may help mitigate barriers to implementing research at CCs.
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- Award ID(s):
- 1915544
- PAR ID:
- 10464163
- Date Published:
- Journal Name:
- Scholarship and Practice of Undergraduate Research
- Page Range / eLocation ID:
- 17 to 28
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/ ) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.more » « less
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Marshall, Pamela Ann (Ed.)ABSTRACT The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org ). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP’s Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020–2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.18833/spur/6/3/1
