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1. Student Attitudes Contribute to the Effectiveness of a Genomics CURE

Author

David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Stephanie Toering Peters, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Sarah C. R. Elgin, and Laura K. Reed

Subjects
General Immunology and Microbiology, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Education
Abstract

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Published
2021

2. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Author

John M. Braverman, Kenneth Saville, Mollie K. Manier, Katherine C. Teeter, Sarah C. R. Elgin, Rachel Sterne-Marr, Debaditya Mukhopadhyay, Adam Haberman, M. Logan Johnson, Jacob D. Kagey, Emily Furbee, Matthew A. Escobar, Vida Mingo, Stephanie Schroeder, Srebrenka Robic, Anya Goodman, Catherine Reinke, Yuying Gosser, Meg M. Laakso, Mary A. Smith, Daron C. Barnard, Christopher Bazinet, Nathan T. Mortimer, Mary L. Preuss, Cindy Arrigo, Paul J. Overvoorde, Elizabeth Mitchell, Rebecca C. Burgess, Wilson Leung, Diane Sklensky, Laura K. Reed, Lindsey J. Long, Don W. Paetkau, Melissa Kleinschmit, Judith Leatherman, Olga R. Kopp, Janie Brennan, Joyce Stamm, Chunguang Du, Norma A. Velázquez-Ulloa, Thomas C. Giarla, Gerard P. McNeil, Justin Thackeray, Andrew M. Arsham, Jeremy Buhler, Jennifer A. Kennell, Sara J. Anderson, Leming Zhou, Takrima Sadikot, Alexis Nagengast, Susan Parrish, Heather L. Eisler, Dennis Revie, Leocadia V. Paliulis, Chiyedza Small, Anna K. Allen, Amy T. Hark, James E. J. Bedard, Lisa Kadlec, Jeffery S. Thompson, Paula Croonquist, James V. Price, Stephanie Toering Peters, Evan C. Merkhofer, Melanie Van Stry, Matthew Skerritt, Anne G. Rosenwald, Cindy Wolfe, Nicholas Pullen, Nighat P. Kokan, Sondra Dubowsky, Jamie Siders Sanford, Rebecca Spokony, Luis F. Matos, Christopher D. Shaffer, Consuelo J. Alvarez, Justin R. DiAngelo, Jennifer Roecklein-Canfield, Maria Soledad Santisteban, Sheryl T. Smith, Juan Carlos Martínez-Cruzado, Indrani Bose, Christopher J. Jones, Adam Kleinschmit, Brian Yowler, Karim A. Sharif, S. Catherine Silver Key, Amie J. McClellan, Matthew Wawersik, Jennifer C. Jemc, Carina E. Howell, Hemlata Mistry, Rivka L. Glaser, Shan Hays, Kimberly L. Keller, Michael R. Rubin, Martin G. Burg, David Lopatto, Charles R. Hauser, James J. Youngblom, Jennifer Leigh Myka, Michael S. Foulk, and Aparna Sreenivasan

Subjects
QH301-705.5, Process (engineering), media_common.quotation_subject, Frustration, General Biochemistry, Genetics and Molecular Biology, Education, Formative assessment, 03 medical and health sciences, Mathematics education, Biology (General), Set (psychology), lcsh:QH301-705.5, 030304 developmental biology, media_common, lcsh:LC8-6691, 0303 health sciences, LC8-6691, lcsh:Special aspects of education, General Immunology and Microbiology, Research, 4. Education, 05 social sciences, 050301 education, Special aspects of education, Focus group, lcsh:Biology (General), Undergraduate research, General partnership, Working through, General Agricultural and Biological Sciences, Psychology, 0503 education
Abstract

A hallmark of the research experience is encountering experimental difficulty and working through that challenge to reach success. The ability to overcome scientific challenges is essential to being a successful scientist, but replicating these challenges can be difficult in a teaching setting. 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 in this research is continuous and recursive, frequently beginning with frustration but eventually leading to success. In order to explore our “formative frustration” hypothesis, we gathered data about this research experience from faculty via a survey, and from students both via a general survey and a small set of focus groups administered at the end of the GEP CURE. All three datasets contained comments mentioning 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 what we have deemed “formative frustration” is an important aspect for a successful CURE.

Published
2020
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3. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Juan Carlos Martínez-Cruzado, Gary A Kuleck, Shubha Govind, Christopher D. Smith, Judith Leatherman, Jeffrey S. Thompson, Daron C. Barnard, Christopher J. Jones, Paul J. Overvoorde, Matthew Wawersik, Amy Frary, Randall J. DeJong, Dale L. Beach, Todd T. Eckdahl, Laura L. Mays Hoopes, Marian M. Kaehler, David Lopatto, Justin R. DiAngelo, Michael R. Rubin, Mary A. Smith, Carina E. Howell, Donald R. Frohlich, Chunguang Du, Leming Zhou, Eric P. Spana, Stephanie F. Mel, John M. Braverman, Karim A. Sharif, Consuelo J. Alvarez, Gary R. Skuse, Cheryl Bailey, Anya Goodman, Kari Clase, Laura K. Reed, Anne G. Rosenwald, Don W. Paetkau, James E. J. Bedard, Mary L. Preuss, Gerard P. McNeil, Michael J. Wolyniak, Martin G. Burg, Lisa Kadlec, Alexis Nagengast, Susan Parrish, Hemlata Mistry, Hui-Min Chung, Joyce Stamm, April E. Bednarski, Sheryl T. Smith, Aparna Sreenivasan, Paul Szauter, Celeste Peterson, Stephanie Schroeder, Nighat P. Kokan, Satish C. Bhalla, Arlene J. Hoogewerf, Heather L. Eisler, Christy MacKinnon, Mary Spratt, Christopher Bazinet, Amy T. Hark, Wilson Leung, Olga R. Kopp, Diana S Johnson, Elaine R. Mardis, Mary E. Shaw, Catherine Reinke, David Dunbar, Yuying Gosser, Jane Lopilato, Vidya Chandrasekaran, Srebrenka Robic, Sarah C. R. Elgin, Kenneth Saville, Adam Haberman, Dennis Revie, Christopher D. Shaffer, Jennifer Roecklein-Canfield, Julia A. Emerson, Adam Kleinschmit, Jeremy Buhler, Charles R. Hauser, James J. Youngblom, S. Catherine Silver Key, and O'Dowd, Diane K

Subjects
Value (ethics), Program evaluation, Time Factors, General Biochemistry, Genetics and Molecular Biology, Information science, Education, Surveys and Questionnaires, Mathematics education, ComputingMilieux_COMPUTERSANDEDUCATION, Humans, Learning, Cooperative Behavior, Curriculum, Biology, Mathematics, Data collection, Genome, Data Collection, Research, Molecular Sequence Annotation, Articles, Genomics, Investment (macroeconomics), Faculty, Research Personnel, Variety (cybernetics), Knowledge, Undergraduate research, Attitude, Self Report, Curriculum and Pedagogy, Program Evaluation
Abstract

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students., There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014
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4. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Author

E. Gloria C. Regisford, Jeremy Buhler, Christopher D. Smith, Cheryl Bailey, Laura L. Mays Hoopes, Marian M. Kaehler, Anne G. Rosenwald, Elizabeth Shoop, Satish C. Bhalla, Yuying Gosser, Mary Shaw, Donald R. Frohlich, Gary A Kuleck, Gerard P. McNeil, Barbara A. Wilson, Joyce Stamm, Daron C. Barnard, Alexis Nagengast, Susan Parrish, Stephanie Schroeder, Jeffrey S. Thompson, Jennifer Leigh Myka, Consuelo J. Alvarez, Chitra Chandrasekaran, Christopher D. Shaffer, Robert W. Morris, Jim Youngblom, Paul J. Overvoorde, Mary Spratt, Diana L. E. Johnson, Todd T. Eckdahl, Charles R. Hauser, Vidya Chandrasekaran, Christopher J. Jones, David Lopatto, Kelynne E. Reed, Mary A. Smith, Robert Moss, Gary R. Skuse, Anya Goodman, Sarah C. R. Elgin, Wilson Leung, Olga R. Kopp, Nighat P. Kokan, Chunguang Du, Jeff L Poet, Elaine R. Mardis, Dennis Revie, Matthew Wawersik, Ken Saville, Douglas R Dorer, Hui-Min Chung, and Eric P. Spana

Subjects
Genetic Research, Universities, Genomics, Science education, General Biochemistry, Genetics and Molecular Biology, Education, 03 medical and health sciences, Annotation, Pedagogy, ComputingMilieux_COMPUTERSANDEDUCATION, Animals, Students, Curriculum, 030304 developmental biology, 0303 health sciences, Medical education, 4. Education, 05 social sciences, Educational technology, 050301 education, Articles, Faculty, ComputingMethodologies_PATTERNRECOGNITION, Undergraduate research, General partnership, Active learning, Laboratories, 0503 education
Abstract

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.

Published
2010

5. A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

Author

Lisa Kadlec, Vidya Chandrasekaran, Michael R. Rubin, Aparna Sreenivasan, Srebrenka Robic, David Dunbar, Christopher D. Shaffer, Amy Frary, Sarah C. R. Elgin, Charles R. Hauser, Gerard P. McNeil, Michael J. Wolyniak, Jane Lopilato, Shubha Govind, Chunguang Du, Gary A Kuleck, Martin G. Burg, Justin R. DiAngelo, Julia A. Emerson, Jennifer A Roecklien-Canfield, Kenneth Saville, Adam Haberman, Alexis Nagengast, Susan Parrish, David Lopatto, James J. Youngblom, Wilson Leung, Laura D Reed, Nighat P. Kokan, Olga R. Kopp, Amy T. Hark, Arlene J. Hoogewerf, Mary Spratt, Yuying Gosser, Elaine R. Mardis, James E. J. Bedard, John M. Braverman, April E. Bednarski, Christy MacKinnon, Karim A. Sharif, Christopher D. Smith, Diana L. E. Johnson, Satish C. Bhalla, Marian M. Kaehler, Daron C. Barnard, Jeremy Buhler, Donald R. Frohlich, S. Catherine Silver Key, Randall J. DeJong, Stephanie F. Mel, Paul J. Overvoorde, Consuelo J. Alvarez, Jeffrey S. Thompson, Don W. Paetkau, Dennis Revie, Mary A. Smith, Mary Shaw, Todd T. Eckdahl, Joyce Stamm, Hui-Min Chung, Juan Carlos Martínez-Cruzado, Christopher J. Jones, Gary R. Skuse, Anya Goodman, Mary L. Preuss, Leming Zhou, Eric P. Spana, Anne G. Rosenwald, Matthew Wawersik, Jennifer Mary Threlfall, Stephanie Schroeder, Sheryl T. Smith, E. Gloria C. Regisford, and Dolan, Erin

Subjects
Value (ethics), Models, Educational, Universities, Genomics, Articles, General Biochemistry, Genetics and Molecular Biology, United States, Education, Incentive, Undergraduate research, Models, Clinical Research, General partnership, Pedagogy, Sustainability, ComputingMilieux_COMPUTERSANDEDUCATION, Curriculum development, Engineering ethics, Educational, Curriculum, Program Development, Curriculum and Pedagogy
Abstract

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles., 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.

Published
2014
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