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bioRxiv · 10.1101/2023.11.29.569298

Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics

Plaisier, S. B.·Alarid, D. O.·Brownell, S. E.·Buetow, K.·Cooper, K. M.·Wilson, M. A.
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Abstract

As genomics and information technologies advance, there is a growing demand for research scientists trained in bioinformatics methods to determine gene expression underlying cell biology in health and disease. One approach to increase the number of scientists proficient in bioinformatics is to expand access through online degree programs and remotely-accessible learning materials. Fully-online learners represent a significant and growing community of historically underrepresented students who are frequently excluded from research opportunities that require in-person attendance during standard operational hours. To address this opportunity gap, we developed an asynchronous course-based undergraduate research experience (CURE) for computational genomics specifically for fully-online biology students. We generated custom learning materials and leveraged remotely-accessible resources on a high performance computing cluster to address a novel research question: the effect of changing quality trimming parameters for RNA sequencing reads on the discovery of sex-based differential gene expression in the human placenta. Here we present the process by which the instructional team devised and distributed analysis to address this question over a 7.5-week CURE and provided students with concurrent training in biology, statistics, computer programming, and professional development integral to the successful execution of the project and future publications. Scores from identical learning assessments administered before and after completion of the CURE showed significant learning gains across biology and coding course objectives. Open-response progress reports were submitted weekly and identified self-reported adaptive coping strategies for challenges encountered throughout the course. The instruction team monitored the progress reports to identify problems that could be resolved through collaboration with instructors and peers via messaging platforms and virtual meetings. Analytics from the course messaging platform demonstrated that high posting engagement was strongly correlated to high normalized learning gains, showing that students can effectively use asynchronous communication platforms to facilitate learning. The online genomics CURE resulted in unanticipated positive outcomes, including students voluntarily extending their participation beyond the course duration, presenting their findings at research symposiums, and applying to graduate school. These outcomes underscore the effectiveness of this genomics CURE for training and recruitment purposes and demonstrate that students can be successful in online STEM-based research experiences if given channels for communication, bespoke and accessible learning materials, and the support of experts in the field. Online CUREs can provide valuable research experience to harness the potential of online STEM students towards a more skilled, diverse, and inclusive workforce for the advancement of biomedical science.

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Plaisier, S. B., Alarid, D. O., Brownell, S. E., Buetow, K., Cooper, K. M., Wilson, M. A.. 2023-12-01. Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. https://doi.org/10.1101/2023.11.29.569298

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