Education
Ph.D., University of Maryland, College Park
B.S., Duke University
Research Interests
The majority of most eukaryotic genomes is comprised of DNA that is annotated as being non-protein-coding in nature. However, much of this non-coding DNA is transcribed into RNA by RNA polymerase II. This genomic “dark matter” typically shows little evidence of selection at the primary sequence level, but there are also striking examples of non-coding RNAs that have evolved to be important and even necessary, like the long non-coding RNAs (lncRNAs) Xist and the roX RNAs. Other genes, like the developmentally critical Tarsal-less/polished rice , generate small peptides from short open reading frames (sORFs) that are missed by traditional gene annotation methods. Though hundreds to thousands of lncRNAs and sORF genes have been annotated in eukaryotic genomes, the vast majority remain uncharacterized. My research is driven by a desire to better understand the roles of these genes and how they are shaped by evolution.
My research has been guided by the following principles:
- I integrate both small-scale and genome-scale approaches and apply evolutionary frameworks in exploring mechanisms.
- I innovate and develop novel methods when necessary to move research forward.
- I strongly emphasize mentorship and professional development in all aspects of my work.
Biography
I earned my B.S. in Biology from Duke University in 2004, studying the evolution of the great white shark using fossil teeth under the instruction of Charles Ciampaglio and Gregory Wray. I then spent two years investigating eukaryotic cell adhesion as a research technician in Richard Fehon’s lab at the University of Chicago, where I was introduced to the model organism Drosophila melanogaster (the fruit fly). I completed my Ph.D. in 2015 under the guidance of Carlos Machado at the University of Maryland, College Park, applying recently developed next-generation sequencing technologies to identify and characterize long non-protein-coding RNAs in Drosophila pseudoobscura . I then worked as a postdoctoral researcher and research associate in the lab of Richard Carthew at Northwestern University, using modern molecular genetic techniques like CRISPR/Cas9 genome modification to functionally characterize non-protein-coding RNAs and cryptic peptides in Drosophila cell biology and development. I joined the Biological Sciences Department at Ohio University in Fall 2025.
Publications
Nyberg, K.G., Navales, F.G., Keles, E., Nguyen, J.Q., Hertz, L.M., and R.W. Carthew. 2024. Robust and heritable knockdown of gene expression using a self-cleaving ribozyme in Drosophila . Genetics . 227(4): iyae067.
Nyberg, K.G.and R.W. Carthew. 2022. CRISPR-/Cas9-Mediated Precise and Efficient Genome Editing in Drosophila . In Drosophila: Methods and Protocols. C. Dahmann, editor. Humana, New York, NY. 135-156.
Nyberg, K.G., Nguyen, J.Q., Kwon, Y., Blythe, S., Beitel, G.J., and R.W. Carthew. 2020. A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila. Fly (Austin). 14(1-4): 34-48.
Stein, J.C. et al. 2018. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics. 50(2):285-296.
Nyberg, K.G.and R.W. Carthew. 2017. Out of the testis: biological impacts of new genes. Genes & Development . 31: 1825-1826.
Nyberg, K.G.and C.A. Machado. 2016. Comparative transcriptomics of long intergenic noncoding RNAs in Drosophila . Genome Biology and Evolution . 8(6): 1839-1858.
Ranz, J.M., Yeh, S.-D., Nyberg, K.G., and C.A. Machado. 2013. Transcriptome profiling of Drosophila interspecific hybrids: insights into mechanisms of regulatory divergence and hybrid dysfunction. In Polyploid and Hybrid Genomics . Z. J. Chen and J. Birchler, editors. John Wiley & Sons, 15-35.
Nyberg, K.G., Conte, M.A., Kostyun, J.L., Forde, A., and A.E. Bely. 2012. Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi , a model for studying the evolution of regeneration. BMC Genomics . 13: 287.
Nilton, A., Oshima, K., Zare, F., Byri, S., Nannmark, U., Nyberg, K.G., Fehon, R.G., and A.E. Uv. 2010. Crooked, Coiled, and Crimpled are three Ly6-like proteins required for proper localization of septate junction components. Development . 137: 2427-37.
Bely, A.E. and K.G. Nyberg. 2010. Evolution of animal regeneration: re-emergence of a field. Trends in Ecology and Evolution. 25(3): 161-170.
Li, Q., Nance, M.R., Kulikauskas, R., Nyberg, K., Fehon, R., Karplus, P.A., Bretscher, A., and J.J. Tesmer. 2007. Self-masking in an intact ERM-merlin protein: an active role for the central a-helical domain. Journal of Molecular Biology. 365(5): 1446-1459.
Nyberg, K.G., Ciampaglio, C.N., and G.A. Wray. 2006. Tracing the ancestry of the great white shark, Carcharodon carcharias , using morphometric analyses of fossil teeth. Journal of Vertebrate Paleontology . 26(4): 806-814.