Schmidt Casey A, Hodkinson Lauren J, Comstra H Skye, Khan Samia, Torres Henrik, Rieder Leila E
Department of Biology, Emory University, Atlanta, Georgia, USA.
Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA.
J Microbiol Biol Educ. 2023 Oct 24;24(3). doi: 10.1128/jmbe.00120-23. eCollection 2023 Dec.
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.
科研经历为本科生带来诸多益处。许多学术机构采用基于课程的本科科研经历（CUREs）来增加学生获得科研机会的途径。然而，CURE的潜在授课教师可能仍面临财务或实际困难，阻碍其实施。生物信息学研究提供了一种替代方案，它免费、安全，与远程学习兼容，并且对于残疾学生来说可能更容易参与。在此，我们描述一种生物信息学CURE，它利用公开可用的数据集来发现靶向教师确定的感兴趣基因组位点的新蛋白质。我们使用免费、用户友好的生物信息学平台Galaxy将ChIP-seq数据集映射到基因组，从而减轻学生的计算负担。教师和学生都能直接从这个CURE中受益，因为教师可以进行候选筛选并发表CURE结果。学生不仅获得基本的生物信息学知识，还能获得可转移技能，包括科学交流、数据库导航和阅读一手文献的经验。这个CURE很灵活，可以扩展用于分析不同类型的高通量数据，或研究任何物种的不同基因组位点。
