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Article: Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.

Lopatto, David / Silver Key, S Catherine / Van Stry, Melanie / Siders, Jamie / Leung, Wilson / Sandlin, Katie M / Rele, Chinmay P / Reed, Laura K

Journal of microbiology & biology education

2023 Volume 24, Issue 3

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 ...

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
Language	English
Publishing date	2023-09-22
Publishing country	United States
Document type	Journal Article
ISSN	1935-7877
ISSN	1935-7877
DOI	10.1128/jmbe.00039-23
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Article ; Online: Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen.

Liu, Jinjie / Cook, Ron / Danhof, Linda / Lopatto, David / Stoltzfus, Jon R / Benning, Christoph

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

2021 Volume 49, Issue 6, Page(s) 926–934

Abstract: A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered ... ...

Abstract	A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies.
MeSH term(s)	Arabidopsis/genetics ; Biology/education ; Curriculum ; Humans ; Knowledge ; Laboratories ; Molecular Biology/education ; Students
Language	English
Publishing date	2021-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2039717-3
ISSN	1539-3429 ; 1470-8175
ISSN (online)	1539-3429
ISSN	1470-8175
DOI	10.1002/bmb.21579
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Article ; Online: Undergraduate research experiences support science career decisions and active learning.

Lopatto, David

CBE life sciences education

2007 Volume 6, Issue 4, Page(s) 297–306

Abstract: The present study examined the reliability of student evaluations of summer undergraduate research experiences using the SURE (Survey of Undergraduate Research Experiences) and a follow-up survey disseminated 9 mo later. The survey further examines the ... ...

Abstract	The present study examined the reliability of student evaluations of summer undergraduate research experiences using the SURE (Survey of Undergraduate Research Experiences) and a follow-up survey disseminated 9 mo later. The survey further examines the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science careers. Undergraduates participated in an online survey on the benefits of undergraduate research experiences. Participants indicated gains on 20 potential benefits and reported on career plans. Most of the participants began or continued to plan for postgraduate education in the sciences. A small group of students who discontinued their plans for postgraduate science education reported significantly lower gains than continuing students. Women and men reported similar levels of benefits and similar patterns of career plans. Undergraduate researchers from underrepresented groups reported higher learning gains than comparison students. The results replicated previously reported data from this survey. The follow-up survey indicated that students reported gains in independence, intrinsic motivation to learn, and active participation in courses taken after the summer undergraduate research experience.
MeSH term(s)	Career Choice ; Education ; Humans ; Learning ; Program Evaluation ; Research Personnel/education ; Research Personnel/psychology ; Science/education ; Students/psychology ; Teaching/methods ; Universities
Language	English
Publishing date	2007-12-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2465176-X
ISSN	1931-7913 ; 1931-7913
ISSN (online)	1931-7913
ISSN	1931-7913
DOI	10.1187/cbe.07-06-0039
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Article ; Online: Survey of Undergraduate Research Experiences (SURE): first findings.

Lopatto, David

Cell biology education

2004 Volume 3, Issue 4, Page(s) 270–277

Abstract: In this study, I examined the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science ... ...

Abstract	In this study, I examined the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science careers. Undergraduates from 41 institutions participated in an online survey on the benefits of undergraduate research experiences. Participants indicated gains on 20 potential benefits and reported on career plans. Over 83% of 1,135 participants began or continued to plan for postgraduate education in the sciences. A group of 51 students who discontinued their plans for postgraduate science education reported significantly lower gains than continuing students. Women and men reported similar levels of benefits and similar patterns of career plans. Ethnic groups did not significantly differ in reported levels of benefits or plans to continue with postgraduate education.
MeSH term(s)	Career Choice ; Case-Control Studies ; Data Collection ; Education, Graduate ; Ethnic Groups ; Humans ; Learning ; Program Evaluation ; Research Personnel/education ; Research Personnel/psychology ; Science/education ; Sex Factors ; Students/psychology ; Teaching/methods ; Universities
Language	English
Publishing date	2004
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2093782-9
ISSN	1536-7509 ; 1536-7509
ISSN (online)	1536-7509
ISSN	1536-7509
DOI	10.1187/cbe.04-07-0045
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Article ; Online: One-Year Research Experience for Associate's Degree Students Impacts Graduation, STEM Retention, and Transfer Patterns.

Nerio, Ron / Webber, Althea / MacLachlan, Effie / Lopatto, David / Caplan, Avrom J

CBE life sciences education

2019 Volume 18, Issue 2, Page(s) ar25

Abstract: The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate's degree students. The program takes place at all 10 associate's degree-granting colleges within the City University of New York system. We ... ...

Abstract	The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate's degree students. The program takes place at all 10 associate's degree-granting colleges within the City University of New York system. We report on a mixed-methods study of 500 students who participated in the program during its initial 3 years. Quantitative longitudinal assessments revealed that students who engaged in CRSP were more likely to be retained in a science, technology, engineering, and mathematics (STEM) discipline or to graduate with a STEM degree than their counterparts in a matched comparison group. Furthermore, students who participated in CRSP demonstrated an increased likelihood of transferring to the more research-intensive 4-year schools within the CUNY system and to R1 universities outside the CUNY system. CRSP students reported an increased sense of belonging in college based on survey data, and focus groups with their mentors provided insight into the factors that led to the gains listed above. These combined results-of student data analysis, student surveys, and mentor focus groups-provide evidence that early research experiences for associate's degree students contribute to their academic success.
MeSH term(s)	Engineering/education ; Ethnic Groups ; Faculty ; Female ; Focus Groups ; Humans ; Male ; Mathematics/education ; Mentors ; Research ; Science/education ; Self Report ; Students ; Surveys and Questionnaires ; Technology/education ; Universities
Language	English
Publishing date	2019-05-31
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2465176-X
ISSN	1931-7913 ; 1931-7913
ISSN (online)	1931-7913
ISSN	1931-7913
DOI	10.1187/cbe.19-02-0042
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Article: The Genomics Education Partnership: First findings on genomics research in community colleges.

Croonquist, Paula / Falkenberg, Virginia / Minkovsky, Natalie / Sawa, Alexa / Skerritt, Matthew / Sustacek, Maire Kate / Diotti, Raffaella / Aragon, Anthony D / Mans, Tamara / Sherr, Goldie L / Ward, Catherine / Hall-Woods, Monica / Goodman, Anya L / Reed, Laura K / Lopatto, David

Scholarship and practice of undergraduate research

2023 Volume 6, Issue 3, Page(s) 17–28

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2023-09-20
Publishing country	United States
Document type	Journal Article
ISSN	2476-101X
ISSN	2476-101X
DOI	10.18833/spur/6/3/1
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Article ; Online: G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.

Sargent, Luke / Liu, Yating / Leung, Wilson / Mortimer, Nathan T / Lopatto, David / Goecks, Jeremy / Elgin, Sarah C R

PLoS computational biology

2020 Volume 16, Issue 6, Page(s) e1007863

Abstract: Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite ... ...

Abstract	Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. This requires access to good genome browsers to enable annotators to visualize and evaluate multiple lines of evidence (e.g., sequence similarity, RNA sequencing [RNA-Seq] results, gene predictions, repeats) and necessitates many volunteers to participate in the work. To address the technical barriers to creating genome browsers, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Genome Browser Assembly Hubs and JBrowse genome browsers. G-OnRamp also converts a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. The genome browsers produced can be transferred to the CyVerse Data Store for long-term access. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research. In the process, students learn about genes/genomes and about how to utilize large datasets. Development of G-OnRamp was guided by extensive user feedback. Sixty-five researchers/educators from >40 institutions participated through in-person workshops, which produced >20 genome browsers now available for research and education. Genome browsers generated for four parasitoid wasp species have been used in a CURE engaging students at 15 colleges and universities. Our assessment results in the classroom demonstrate that the genome browsers produced by G-OnRamp are effective tools for engaging undergraduates in research and in enabling their contributions to the scientific literature in genomics. Expansion of such genomics research/education partnerships will be beneficial to researchers, faculty, and students alike.
MeSH term(s)	Algorithms ; Animals ; Base Sequence ; Computational Biology/education ; Computational Biology/methods ; Computer Graphics ; Databases, Genetic ; Drosophila melanogaster ; Genome ; Genomics/education ; Genomics/methods ; Humans ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; Software ; Students ; User-Computer Interface
Language	English
Publishing date	2020-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1007863
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Article ; Online: Teaching broader impacts of science with undergraduate research.

Keiler, Kenneth C / Jackson, Kathy L / Jaworski, Leslie / Lopatto, David / Ades, Sarah E

PLoS biology

2017 Volume 15, Issue 3, Page(s) e2001318

Abstract: Science plays an important role in most aspects of society, and scientists face ethical decisions as a routine part of their work, but science education frequently omits or segregates content related to ethics and broader impacts of science. ... ...

Abstract	Science plays an important role in most aspects of society, and scientists face ethical decisions as a routine part of their work, but science education frequently omits or segregates content related to ethics and broader impacts of science. Undergraduate research experiences have the potential to bridge traditional divides in education and provide a holistic view of science. In practice, these experiences can be inconsistent and may not provide the optimal learning environment. We developed a course that combines seminar and independent research elements to support student learning during undergraduate research, makes ethical and societal impacts of science clear by relating them to the students' own research projects, and develops students' ethical decision-making skills. Here, we describe the course and provide resources for developing a similar course.
MeSH term(s)	Curriculum ; Ethics, Research/education ; Universities
Language	English
Publishing date	2017-03-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.2001318
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Article: Broadening the voice of science: Promoting scientific communication in the undergraduate classroom.

Cirino, Lauren A / Emberts, Zachary / Joseph, Paul N / Allen, Pablo E / Lopatto, David / Miller, Christine W

Ecology and evolution

2017 Volume 7, Issue 23, Page(s) 10124–10130

Abstract: Effective and accurate communication of scientific findings is essential. Unfortunately, scientists are not always well trained in how to best communicate their results with other scientists nor do all appreciate the importance of speaking with the ... ...

Abstract	Effective and accurate communication of scientific findings is essential. Unfortunately, scientists are not always well trained in how to best communicate their results with other scientists nor do all appreciate the importance of speaking with the public. Here, we provide an example of how the development of oral communication skills can be integrated with research experiences at the undergraduate level. We describe our experiences developing, running, and evaluating a course for undergraduates that complemented their existing undergraduate research experiences with instruction on the nature of science and intensive training on the development of science communication skills. Students delivered science talks, research monologues, and poster presentations about the ecological and evolutionary research in which they were involved. We evaluated the effectiveness of our approach using the CURE survey and a focus group. As expected, undergraduates reported strong benefits to communication skills and confidence. We provide guidance for college researchers, instructors, and administrators interested in motivating and equipping the next generation of scientists to be excellent science communicators.
Language	English
Publishing date	2017-10-24
Publishing country	England
Document type	Journal Article
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.3501
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Article ; Online: Situating Second-Year Success: Understanding Second-Year STEM Experiences at a Liberal Arts College.

Gregg-Jolly, Leslie / Swartz, Jim / Iverson, Ellen / Stern, Joyce / Brown, Narren / Lopatto, David

CBE life sciences education

2016 Volume 15, Issue 3

Abstract: Challenges particular to second-year students have been identified that can impact persistence in science, technology, engineering, and mathematics (STEM) fields. We implemented a program to improve student success in intermediate-level science courses ... ...

Abstract	Challenges particular to second-year students have been identified that can impact persistence in science, technology, engineering, and mathematics (STEM) fields. We implemented a program to improve student success in intermediate-level science courses by helping students to feel they belonged and could succeed in STEM. We used survey measures of perceptions and attitudes and then qualitative measures to characterize the impact of support strategies, including peer mentoring, a second-year science student retreat, learning and advising support resources, and department-specific activities. Analysis of registration and transcript information revealed underperformance by students of color (SOC) and first-generation (FG) students in 200-level science courses. Comparison of these data before and during programming revealed significant improvement in success rates of these students in 200-level biology and chemistry courses, but success rates of SOC and FG students remain lower than the overall rate for 200-level science courses. Contemporaneous with the program, qualitative and quantitative measures of student attitudes revealed a high level of belongingness and support. The results suggest that a focus on students' metacognition about their own abilities and strategic knowledge of how to succeed may be a fruitful direction for future research.
MeSH term(s)	Art ; Attitude ; Curriculum ; Engineering/education ; Humans ; Mathematics/education ; Science/education ; Students/statistics & numerical data ; Surveys and Questionnaires ; Technology/education ; Universities
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2465176-X
ISSN	1931-7913 ; 1931-7913
ISSN (online)	1931-7913
ISSN	1931-7913
DOI	10.1187/cbe.16-01-0044
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