The undergraduate genomics research initiative.
Ontology highlight
ABSTRACT:
SUBMITTER: Kerfeld CA
PROVIDER: S-EPMC1868073 | biostudies-literature | 2007 May
REPOSITORIES: biostudies-literature
Publications
The undergraduate genomics research initiative.
Kerfeld Cheryl A CA Simons Robert W RW
PLoS biology 20070501 5
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Project description: Not available
| S-EPMC2953277 | biostudies-literature
Project description:A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.
| S-EPMC7048401 | biostudies-literature
Project description:I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically. There are 1,437 enzyme activities for which Enzyme Commission (EC) numbers have been assigned but no sequence can be found in public protein-sequence databases.
| S-EPMC507876 | biostudies-other
Project description:UnlabelledEngaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.ImportanceEngagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.
| S-EPMC3950523 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-06-27 | GSE76311 | GEO
Project description:Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.
| S-EPMC2830162 | biostudies-literature
Project description:The University of British Columbia has developed a course-based undergraduate research experience (CURE) that engages students in authentic molecular microbiology research. This capstone course is uniquely built around an open-access online undergraduate research journal entitled Undergraduate Journal of Experimental Microbiology and Immunology (UJEMI). Students work in teams to derive an original research question, formulate a testable hypothesis, draft a research proposal, carry out experiments in the laboratory, and publish their results in UJEMI. The CURE operates in a feed forward manner whereby student-authored UJEMI publications drive research questions in subsequent terms of the course. Progress toward submission of an original manuscript is scaffolded using a series of communication assignments which facilitate formative development. We present a periodic model of our CURE that guides students through a research cycle. We review two ongoing course-based projects to highlight how UJEMI publications prime new research questions in the course. A journal-driven CURE represents a broadly applicable pedagogical tool that immerses students in the process of doing science.
| S-EPMC7719674 | biostudies-literature
Project description:In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.
| S-EPMC4255357 | biostudies-literature
Project description:We present an exploratory study of how undergraduates' involvement in research influences postgraduates (i.e., graduate and postdoctoral researchers) and faculty. We used a qualitative approach to examine the relationships among undergraduates, postgraduates, and the faculty head in a research group. In this group, undergraduates viewed postgraduates as more approachable than the faculty head both literally and figuratively. Mentorship by postgraduates presented unique challenges for undergraduates, including unrealistic expectations and varying abilities to mentor. The postgraduates and faculty head concurred that undergraduates contributed to the group's success and served as a source of frustration. Postgraduates appreciated the opportunity to observe multiple approaches to mentoring as they saw the faculty head and other postgraduates interact with undergraduates. The faculty head viewed undergraduate research as important for propagating the research community and for gaining insights into undergraduates and their postgraduate mentors. These results highlight how the involvement of undergraduates and postgraduates in research can limit and enhance the research experiences of members of the undergraduate-postgraduate-faculty triad. A number of tensions emerge that we hypothesize are intrinsic to undergraduate research experiences at research universities. Future studies can focus on determining the generalizability of these findings to other groups and disciplines.
| S-EPMC2995772 | biostudies-literature
Project description:Background To support diversity in biomedical science, the American Heart Association launched the Supporting Undergraduate Research Experiences for undergraduate students from underrepresented backgrounds to provide mentorship and high-level exposure at 5 leading medical institutions. Here we describe the initial formation of the partnership and the alteration made in response to the program to accommodate COVID-19 safety precautions. Methods and Results We outline how programming shifted from local, in-person programming in the summer of 2019 to a collaborative, mainly virtual curriculum in 2020 using students' self-reported before and after surveys from both 2019 (n=33) and 2020 (n=42). Students from both in-person (2019) and virtual programs (2020) self-reported significant gains in scientific proficiency. A qualitative-directed content analysis of student open-response questions was performed. Students reported extensive benefits from the 2020 virtual training, including Personal Gains, Research Skills, Thinking and Working Like a Scientist, and Attitudes and Behaviors. Notedly, we observed increases in the Attitudes and Behaviors category. We outline the pros and cons of in-person and virtual programming and make recommendations moving forward in a postpandemic world with hybrid work and learning systems. Conclusions Our effort informs the development of future undergraduate research training programs, significantly maximizing a hybrid training modality. The American Heart Association Supporting Undergraduate Research Experiences serves as a model for building multi-institutional partnerships and providing research experiences that overcome institutional barriers and support students' interests, commitment, and ability to persist in science, technology, engineering, and math fields.
| S-EPMC9238450 | biostudies-literature