Publications
Recent microPublication
Since its founding in 2006, the Genomics Education Partnership’s published scholarship has advanced the understanding of genome evolution and effective pedagogical practices in STEM. Through the GEP’s research projects, more than 1,100 students (and counting) have contributed as co-authors on published scientific research papers.
In addition to our traditional publications shown below, GEP students and their faculty mentors are publishing in microPublication.org, which publishes brief articles on research findings presented in a single figure to rapidly disseminate experimentally sound results to the community.
See our microPublications for more information.
Journal of Microbiology & Biology Education. e0017024.
| Publication | Year | Journal | Citation | Topic | |
|---|---|---|---|---|---|
| 19. | Accessible support at a national scale: the use and value of virtual learning assistants across multiple undergraduate institutions | 2025 | Journal of Microbiology and Biology Education | Pribbenow, C. M., Harrington, D., Rele, C. P., Sandlin, K. M., Leung, W., Lopatto, D., & Reed, L. K. (2025). Accessible support at a national scale: the use and value of virtual learning assistants across multiple undergraduate institutions. Journal of Microbiology & Biology Education, e0017024. https://doi.org/10.1128/jmbe.00170-24 | Education |
| 18. | Virtual Engagement in a Hybrid Community of Practice: A Descriptive Study on the Training and Integration of New Members into the Genomics Education Partnership during COVID-19 | 2024 | Journal of STEM Education: Innovations and Research | Gehrke, S., Goodman, A., Ngo, L., Reinke, C., Sandlin, K., & Reed, L. (2024). Virtual engagement in a hybrid community of practice: A descriptive study on the training and integration of new members into the Genomics Education Partnership during COVID-19. Journal of STEM Education: Innovations and Research, 25(2). | Education |
| 17. | Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae | 2023 | Genes, Genomes, Genetics (G3) | Leung, W., Torosin, N., Cao, W., Reed, L. K., Arrigo, C., Elgin, S. C. R., & Ellison, C. E. (2023). Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. G3 (Bethesda, Md.), 13(10), jkad191. https://doi.org/10.1093/g3journal/jkad191 | Science |
| 16. | Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy | 2023 | Journal of Microbiology and Biology Education | Lopatto, D., Silver Key, S. C., Van Stry, M., Siders, J., Leung, W., Sandlin, K. M., Rele, C. P., Genomics Education Partnership, & Reed, L. K. (2023). Supporting the democratization of science during a pandemic: Genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy. Journal of Microbiology & Biology Education, 24(3), e00039-23. https://doi.org/10.1128/jmbe.00039-23 | Education |
| 14. | The Genomics Education Partnership: First Findings on Genomics Research in Community Colleges | 2023 | Scholarship and Practice of Undergraduate Research | Croonquist, P., Falkenberg, V., Minkovsky, N., Sawa, A., Skerritt, M., Sustacek, M., Diotti, R., Aragon, A., Mans, T., Sherr, G., Ward, C., Hall-Woods, M., Goodman, A., Reed, L., & Lopatto, D. (2023). The Genomics Education Partnership: First findings on genomics research in community colleges. Scholarship and Practice of Undergraduate Research, 6(3), 17–28. https://doi.org/10.18833/spur/6/3/1 | Education |
| 15. | Manual annotation of Drosophila genes: a Genomics Education Partnership protocol | 2022 | F1000Research | Rele, C. P., Sandlin, K. M., Leung, W., & Reed, L. K. (2022). Manual annotation of Drosophila genes: A Genomics Education Partnership protocol. F1000Research, 11, 1579. https://doi.org/10.12688/f1000research.126839.3 | Science |
| 13. | Student Attitudes Contribute to the Effectiveness of a Genomics CURE | 2022 | Journal of Microbiology and Biology Education | Lopatto, D., Rosenwald, A. G., Burgess, R. C., Silver Key, C., Van Stry, M., Wawersik, M., DiAngelo, J. R., Hark, A. T., Skerritt, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., … Reed, L. K. (2022). Student attitudes contribute to the effectiveness of a genomics CURE. Journal of Microbiology & Biology Education, 23(2), e00208-21. https://doi.org/10.1128/jmbe.00208-21 | Education |
| 12. | Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience | 2020 | Journal of Microbiology and Biology Education | Lopatto, D., Rosenwald, A. G., DiAngelo, J. R., Hark, A. T., Skerritt, M., Wawersik, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bazinet, C., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., Burgess, R. C., Croonquist, P., … Elgin, S. C. R. (2020). Facilitating growth through frustration: Using genomics research in a Course-Based Undergraduate Research Experience. Journal of Microbiology & Biology Education, 21(1), 21.1.6. https://doi.org/10.1128/jmbe.v21i1.2005 | Education |
| 11. | Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element | 2017 | Genes, Genomes, Genetics (G3) | Leung, W., Shaffer, C. D., Chen, E. J., Quisenberry, T. J., Ko, K., Braverman, J. M., Giarla, T. C., Mortimer, N. T., Reed, L. K., Smith, S. T., Robic, S., McCartha, S. R., Perry, D. R., Prescod, L. M., Sheppard, Z. A., Saville, K. J., McClish, A., Morlock, E. A., Sochor, V. R., … Elgin, S. C. R. (2017). Retrotransposons are the major contributors to the expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda, Md.), 7(8), 2439–2460. https://doi.org/10.1534/g3.117.040907 | Science |
| 10. | An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure | 2017 | CourseSource | Laakso, M. M., Paliulis, L. V., Croonquist, P., Derr, B., Gracheva, E., Hauser, C., Howell, C., Jones, C., Kagey, J. D., Kennell, J., Silver Key, S. C., Mistry, H., Robic, S., Sanford, J., Santisteban, M., Small, C., Spokony, R., Stamm, J., Van Stry, M., … Elgin, S. C. R. (2017). An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure. CourseSource, 4. https://doi.org/10.24918/cs.2017.13 | Education |
| 9. | The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates | 2017 | Trends in Genetics | Elgin, S. C. R., Hauser, C., Holzen, T. M., Jones, C., Kleinschmit, A., Leatherman, J., & Genomics Education Partnership. (2017). The GEP: Crowd-sourcing big data analysis with undergraduates. Trends in Genetics: TIG, 33(2), 81–85. https://doi.org/10.1016/j.tig.2016.11.004 | Education |
| 8. | A Hands-on Introduction to Hidden Markov Models | 2016 | CourseSource | Weisstein, A. E., Gracheva, E., Goodwin, Z., Qi, Z., Leung, W., Shaffer, C. D., & Elgin, S. C. R. (2016). A Hands-on introduction to hidden Markov models. CourseSource, 3. https://doi.org/10.24918/cs.2016.8 | Education |
| 7. | Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution | 2015 | Genes, Genomes, Genetics (G3) | Leung, W., Shaffer, C. D., Reed, L. K., Smith, S. T., Barshop, W., Dirkes, W., Dothager, M., Lee, P., Wong, J., Xiong, D., Yuan, H., Bedard, J. E. J., Machone, J. F., Patterson, S. D., Price, A. L., Turner, B. A., Robic, S., Luippold, E. K., McCartha, S. R., … Elgin, S. C. R. (2015). Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda, Md.), 5(5), 719–740. https://doi.org/10.1534/g3.114.015966 | Science |
| 6. | A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics | 2014 | CBE-Life Sciences Education | Lopatto, D., Hauser, C., Jones, C. J., Paetkau, D., Chandrasekaran, V., Dunbar, D., MacKinnon, C., Stamm, J., Alvarez, C., Barnard, D., Bedard, J. E. J., Bednarski, A. E., Bhalla, S., Braverman, J. M., Burg, M., Chung, H.-M., DeJong, R. J., DiAngelo, J. R., Du, C., … Elgin, S. C. R. (2014). A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics. CBE Life Sciences Education, 13(4), 711–723. https://doi.org/10.1187/cbe.13-10-0200 | Education |
| 5. | A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time | 2014 | CBE-Life Sciences Education | Shaffer, C. D., Alvarez, C. J., Bednarski, A. E., Dunbar, D., Goodman, A. L., Reinke, C., Rosenwald, A. G., Wolyniak, M. J., Bailey, C., Barnard, D., Bazinet, C., Beach, D. L., Bedard, J. E. J., Bhalla, S., Braverman, J., Burg, M., Chandrasekaran, V., Chung, H.-M., Clase, K., … Elgin, S. C. R. (2014). A course-based research experience: How benefits change with increased investment in instructional time. CBE Life Sciences Education, 13(1), 111–130. https://doi.org/10.1187/cbe-13-08-0152 | Education |
| 4. | Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in D. melanogaster and D. virilis | 2010 | Genetics | Leung, W., Shaffer, C. D., Cordonnier, T., Wong, J., Itano, M. S., Slawson Tempel, E. E., Kellmann, E., Desruisseau, D. M., Cain, C., Carrasquillo, R., Chusak, T. M., Falkowska, K., Grim, K. D., Guan, R., Honeybourne, J., Khan, S., Lo, L., McGaha, R., Plunkett, J., … Elgin, S. C. R. (2010). Evolution of a distinct genomic domain in Drosophila: Comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics, 185(4), 1519–1534. https://doi.org/10.1534/genetics.110.116129 | Science |
| 3. | The Genomics Education Partnership: Successful Integration of Research Into Laboratory Classes at a Diverse Group of Undergraduate Institutions | 2010 | CBE-Life Sciences Education | Shaffer, C. D., Alvarez, C., Bailey, C., Barnard, D., Bhalla, S., Chandrasekaran, C., Chandrasekaran, V., Chung, H.-M., Dorer, D. R., Du, C., Eckdahl, T. T., Poet, J. L., Frohlich, D., Goodman, A. L., Gosser, Y., Hauser, C., Hoopes, L. L. M., Johnson, D., Jones, C. J., … Elgin, S. C. R. (2010). The Genomics Education Partnership: Successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sciences Education, 9(1), 55–69. https://doi.org/10.1187/09-11-0087 | Education |
| 2. | Undergraduate Research: Genomics Education Partnership | 2008 | Science | Lopatto, D., Alvarez, C., Barnard, D., Chandrasekaran, C., Chung, H.-M., Du, C., Eckdahl, T., Goodman, A. L., Hauser, C., Jones, C. J., Kopp, O. R., Kuleck, G. A., McNeil, G., Morris, R., Myka, J. L., Nagengast, A., Overvoorde, P. J., Poet, J. L., Reed, K., … Elgin, S. C. R. (2008). Undergraduate research. Genomics Education Partnership. Science (New York, N.Y.), 322(5902), 684–685. https://doi.org/10.1126/science.1165351 | Education |
| 1. | Comparison of Dot Chromosome Sequences from D. melanogaster and D. virilis Reveals an Enrichment of DNA Transposon Sequences in Heterochromatic Domains | 2006 | Genome Biology | Slawson, E. E., Shaffer, C. D., Malone, C. D., Leung, W., Kellmann, E., Shevchek, R. B., Craig, C. A., Bloom, S. M., Bogenpohl, J., Dee, J., Morimoto, E. T. A., Myoung, J., Nett, A. S., Ozsolak, F., Tittiger, M. E., Zeug, A., Pardue, M.-L., Buhler, J., Mardis, E. R., & Elgin, S. C. R. (2006). Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biology, 7(2), R15. https://doi.org/10.1186/gb-2006-7-2-r15 | Science |
- Page Last Updated: March 12, 2025