Undergraduate research. Genomics Education Partnership.
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ABSTRACT:
SUBMITTER: Lopatto D
PROVIDER: S-EPMC2953277 | biostudies-literature | 2008 Oct
REPOSITORIES: biostudies-literature
Publications
Undergraduate research. Genomics Education Partnership.
Lopatto D D Alvarez C C Barnard D D Chandrasekaran C C Chung H-M HM Du C C Eckdahl T T Goodman A L AL Hauser C C Jones C J CJ Kopp O R OR Kuleck G A GA McNeil G G Morris R R Myka J L JL Nagengast A A Overvoorde P J PJ Poet J L JL Reed K K Regisford G G Revie D D Rosenwald A A Saville K K Shaw M M Skuse G R GR Smith C C Smith M M Spratt M M Stamm J J Thompson J S JS Wilson B A BA Witkowski C C Youngblom J J Leung W W Shaffer C D CD Buhler J J Mardis E E Elgin S C R SC
Science (New York, N.Y.) 20081001 5902
Similar Datasets
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 Genomics Education Partnership (GEP), a consortium of diverse colleges/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 2-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, we analyzed student knowledge and self-reported outcomes. We found that CC student gains are comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. Our early findings suggest that the GEP model of centralized support with flexible CURE implementation benefits CC students and may help mitigate barriers to implementing research at CCs.
| S-EPMC10508916 | biostudies-literature
Project description: Not available
| S-EPMC1868073 | biostudies-literature
Project description: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.
| S-EPMC10579860 | biostudies-literature
Project description:Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.
| S-EPMC4278498 | biostudies-literature
Project description:Over the last two decades, there have been numerous initiatives to improve undergraduate student outcomes in STEM. One model for scalable reform is the inclusive Research Education Community (iREC). In an iREC, STEM faculty from colleges and universities across the nation are supported to adopt and sustainably implement course-based research - a form of science pedagogy that enhances student learning and persistence in science. In this study, we used pathway modelling to develop a qualitative description that explicates the HHMI Science Education Alliance (SEA) iREC as a model for facilitating the successful adoption and continued advancement of new curricular content and pedagogy. In particular, outcomes that faculty realize through their participation in the SEA iREC were identified, organized by time, and functionally linked. The resulting pathway model was then revised and refined based on several rounds of feedback from over 100 faculty members in the SEA iREC who participated in the study. Our results show that in an iREC, STEM faculty organized as a long-standing community of practice leverage one another, outside expertise, and data to adopt, implement, and iteratively advance their pedagogy. The opportunity to collaborate in this manner and, additionally, to be recognized for pedagogical contributions sustainably engages STEM faculty in the advancement of their pedagogy. Here, we present a detailed pathway model of SEA that, together with underpinning features of an iREC identified in this study, offers a framework to facilitate transformations in undergraduate science education.
| S-EPMC11649309 | 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:BackgroundIn a research-based learning environment, students learn how to become critical thinkers and lifelong learners, and to generate discipline-enriching knowledge. Research training is important for all healthcare professionals and the integration of research in education can be one approach to improve evidence-based practice among future professionals. The purpose of this scoping review was to identify studies reporting on research-based education in undergraduate occupational therapy and physiotherapy curricula to document the current state of knowledge and to map factors that reflect and support the implementation of research-based education in undergraduate occupational therapy and physiotherapy programmes.MethodsA scoping review was used to systematically select and summarize existing literature. The search was conducted using a combination of keywords and MeSH terms in the following databases: EBSCO (Academic Search Elite, CINAHL, ERIC), MEDLINE, Embase, Education Source and grey literature. A thematic analysis identified strategies used to implement and promote research-based education in occupational therapy and physiotherapy bachelor programmes.ResultsThe database search identified 3068 records. 75 were eligible for full-text assessment and 27 studies were included. The studies were published between 1999 and 2021 and were conducted in Norway, Canada, South Africa, Australia, the United Kingdom, the United States, New Zealand, Ireland, Taiwan, Italy, and Iran. The study designs were mainly quantitative and qualitative, and studies included primarily occupational therapy and physiotherapy students. We identified the following four strategies: 'student engagement in research', 'curriculum improvement regarding EBP', 'EBP teaching' and 'journal club', where 'EBP teaching' was most frequently identified.ConclusionsFindings from this scoping review suggest that ensuring students' competence in research methods is necessary for students to be able to read and understand research articles, which are important as foundational skills in undergraduate research training. Journal clubs can be a foundation for student engagement with research literature, and students' basic research skills may be facilitated through their involvement in research projects and by conducting systematic reviews. Further, cooperation with clinical practice is important, and the awareness of research-based education should be increased among both faculty members and students.
| S-EPMC9097417 | biostudies-literature
Project description:BackgroundMedical students engage in curricular and extracurricular activities, including undergraduate research (UR). The advantages, difficulties and motivations for medical students pursuing research activities during their studies have rarely been addressed. In Brazil, some medical schools have included undergraduate research into their curriculum. The present study aimed to understand the reality of scientific practice among medical students at a well-established Brazilian medical school, analyzing this context from the students' viewpoint.MethodsA cross-sectional survey based on a questionnaire applied to students from years one to six enrolled in an established Brazilian medical school that currently has no curricular UR program.ResultsThe questionnaire was answered by 415 students, 47.2% of whom were involved in research activities, with greater participation in UR in the second half of the course. Independent of student involvement in research activities, time constraints were cited as the main obstacle to participation. Among students not involved in UR, 91.1% said they favored its inclusion in the curriculum, since this would facilitate the development of such activity. This approach could signify an approximation between the axes of teaching and research. Among students who had completed at least one UR project, 87.7% said they would recommend the activity to students entering the course.ConclusionEven without an undergraduate research program, students of this medical school report strong involvement in research activities, but discussion of the difficulties inherent in its practice is important to future developments.
| S-EPMC4021277 | biostudies-literature
Project description:ObjectiveOpen science (OS) is a global movement focused on improving research equity, reproducibility, and transparency of research outputs in publicly funded research. While OS education in academia is becoming more common, examples of health sciences librarians providing OS training are not. This paper describes how a librarian collaborated with teaching faculty and a research program coordinator to integrate an OS curriculum into an undergraduate professional practice course and assess students' perceptions of OS after participating.MethodsA librarian developed an OS-specific curriculum for an undergraduate professional practice course in Nutrition. This course is part of the First Year Research Experience (FYRE) program, which is integrated into 13-week undergraduate courses to introduce students to core elements of the research process in their first year of study by carrying out a research project. The OS curriculum included an Introduction to OS class, a requirement that students share their research outputs in the Open Science Framework, and an assignment asking students to reflect on their experience learning about and practicing OS. Twenty-one of 30 students consented to having their reflection assignment undergo thematic analysis.ResultsStudents indicated transparency, accountability, accessibility to research outputs, and increased efficiency as positive attributes of OS. The time commitment, fear of being scooped, and concerns over having research be misinterpreted were considered negative attributes. 90% (n=19) of students indicated that they intend to practice OS in the future.ConclusionBased on strong engagement from the students, we believe that this OS curriculum could be adapted to other undergraduate or graduate student contexts where a research project is required.
| S-EPMC10124608 | biostudies-literature