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Recent microPublication

(A) Synteny of genomic neighborhood of Myc in D. melanogaster and D. eugracilis. Gene arrows pointing in the same direction as target gene in both D. eugracilis and D. melanogaster are on the same strand as the target gene; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Myc and the downstream genes are on the + strand; the arrow pointing to the left indicates that the upstream genes are on the – strand in D. eugracilis. White arrows in D. eugracilis indicate the locus ID and the orthology to the corresponding gene in D. melanogaster, and gray arrows indicate that the orthologous genes upstream of Myc in D. melanogaster are found on a different scaffold in D. eugracilis than Myc. The brackets beneath the local synteny diagram for D. eugracilis show which scaffold each gene is found on. The gene names given in the D. eugracilis gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. eugracilis. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. eugracilis (black), Spaln of D. melanogaster Proteins (purple, alignment of RefSeq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of RefSeq genes for D. eugracilis), RNA-seq from female (red), male (blue), and mixed embryos (purple) (alignment of Illumina RNA-seq reads from D. eugracilis), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. eugracilis RNA-seq (Chen et al., 2014; PRJNA63469). Note that there is no measured expression of the first CDS of Myc (Flybase ID: 1_12880_0) in females (Flybase IDs from FB2022_03; Larkin et al., 2021). Splice junctions shown have a minimum read-depth of 702 with 500-999 and >1000 supporting reads in brown and red respectively. The custom gene model (User Supplied Track) is indicated in black with CDSs depicted by boxes and introns by narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Myc-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. eugracilis (y-axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. The gaps in the dot plot indicate regions with low sequence similarity. The region within the black box (box a) contains a tandem repeat in CDS 2 that is conserved across both D. melanogaster and D. eugracilis. The green box (box b) highlights low sequence similarity in CDS one (D) Idiosyncrasies in the protein alignment. CDS one, which is boxed in green (box b), has many segments with low amino acid sequence similarity between D. melanogaster and D. eugracilis. The black box (box a) indicates a tandem repeat in the second CDS.
Gene model for the ortholog of Myc in Drosophila eugracilis
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.

GEP New Publication Alert

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. Vol. 25 No. 2 (2024).
PublicationYearJournalCitationTopic
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-192024Journal of STEM Education: Innovations and ResearchGehrke, 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 ananassae2023Genes, Genomes, Genetics (G3)Leung W, Torosin N, Cao W, et al. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. G3 (Bethesda). 2023;13(10):jkad191. doi:10.1093/g3journal/jkad191Science
16.Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy2023Journal of Microbiology and Biology EducationLopatto D, Silver Key SC, Van Stry M, Siders J, Leung W, Sandlin KM, Rele CP, , Reed LK. 2023. Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy. J Microbiol Biol Educ. 24:e00039-23.
https://doi.org/10.1128/jmbe.00039-23 		Education
15.Manual annotation of Drosophila genes: a Genomics Education Partnership protocol2023F1000ResearchRele CP, Sandlin KM, Leung W and Reed LK. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol [version 3; peer review: 2 approved]. F1000Research 2023, 11:1579 (https://doi.org/10.12688/f1000research.126839.3) Science
14.The Genomics Education Partnership: First Findings on Genomics Research in Community Colleges2023Scholarship and Practice of Undergraduate ResearchCroonquist, P., Falkenberg, V., Minkovsky, N., Sawa, A., Skerritt, M., Sustacek, M. K., ... & Lopatto, D. (2023). The Genomics Education Partnership: First findings on genomics research in community colleges. Scholarship and practice of undergraduate research, 6(3), 17.Education
13.Student Attitudes Contribute to the Effectiveness of a Genomics CURE2022Journal of Microbiology and Biology EducationLopatto, D., Rosenwald, A. G., Burgess, R. C., Silver Key, C., Van Stry, M., Wawersik, M., ... & Reed, L. K. (2022). Student attitudes contribute to the effectiveness of a genomics CURE. Journal of Microbiology & Biology Education, 23(2), e00208-21.Education
12.Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience 2020Journal of Microbiology and Biology EducationLopatto, D., Rosenwald, A. G., DiAngelo, J. R., Hark, A. T., Skerritt, M., Wawersik, M., ... & Elgin, S. C. (2020). Facilitating growth through frustration: using genomics research in a course-based undergraduate research experience. Journal of microbiology & biology education, 21(1), 10-1128.Education
11.Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element2017Genes, Genomes, Genetics (G3)Leung W, Shaffer CD, Chen EJ, et al. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda). 2017;7(8):2439-2460. Published 2017 Aug 7. doi:10.1534/g3.117.040907Science
10.An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure2017CourseSourceLaakso, M. M., Paliulis, L. V., Croonquist, P., Derr, B., Gracheva, E., Hauser, C., ... & Elgin, S. C. (2021). An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure.Education
9.The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates2017Trends in GeneticsElgin SCR, Hauser C, Holzen TM, et al. The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates. Trends Genet. 2017;33(2):81-85. doi:10.1016/j.tig.2016.11.004Education
8.A Hands-on Introduction to Hidden Markov Models2016CourseSourceWeisstein, A. E., Gracheva, E., Goodwin, Z., Qi, Z., Leung, W., Shaffer, C. D., & Elgin, S. C. (2021). A Hands-on Introduction to Hidden Markov Models.Education
7.Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution2015Genes, Genomes, Genetics (G3)Leung W, Shaffer CD, Reed LK, et al. Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda). 2015;5(5):719-740. Published 2015 Mar 4. doi:10.1534/g3.114.015966Science
6.A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics 2014CBE-Life Sciences EducationLopatto, D., Hauser, C., Jones, C. J., Paetkau, D., Chandrasekaran, V., Dunbar, D., ... & Elgin, S. C. (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.Education
5. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time2014CBE-Life Sciences EducationShaffer CD, Alvarez CJ, Bednarski AE, et al. A course-based research experience: how benefits change with increased investment in instructional time. CBE Life Sci Educ. 2014;13(1):111-130. doi:10.1187/cbe-13-08-0152Education
4.Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in D. melanogaster and D. virilis2010GeneticsLeung W, Shaffer CD, Cordonnier T, et al. Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics. 2010;185(4):1519-1534. doi:10.1534/genetics.110.116129Science
3.The Genomics Education Partnership: Successful Integration of Research Into Laboratory Classes at a Diverse Group of Undergraduate Institutions2010CBE-Life Sciences EducationShaffer CD, Alvarez C, Bailey C, et al. The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sci Educ. 2010;9(1):55-69. doi:10.1187/09-11-0087Education
2.Undergraduate Research: Genomics Education Partnership2008ScienceLopatto D, Alvarez C, Barnard D, et al. Undergraduate research. Genomics Education Partnership. Science. 2008;322(5902):684-685. doi:10.1126/science.1165351Education
1.Comparison of Dot Chromosome Sequences from D. melanogaster and D. virilis Reveals an Enrichment of DNA Transposon Sequences in Heterochromatic Domains2006Genome BiologySlawson EE, Shaffer CD, Malone CD, et al. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol. 2006;7(2):R15. doi:10.1186/gb-2006-7-2-r15Science
  • Page Last Updated: September 7, 2024