Academic Publications

Community Tools

Frequently, it is my role to streamline analyses for a community, either by linking tools together or by hiding endless command line behind wrappers and Shiny Apps. Below is a recent project to build genomic resources for a new model.

New Genome

Bioinformatic Analysis

As a bioinformatician, I often collaborate on analyses of genomic data, which also requires contribution to manuscripts.

Biofilm RNA

Developmental Editing

I have mentored many students, leading to coauthored conference papers. These are often the first papers students have written, requiring a lot of developmental, line, and even copy editing.

Frog Calls with AI

Shiny DGE

Peer Reviewed Conference and Journal Articles

Amiri, E. E., Tenger-Trolander, A., Li, M., Julian, A. T., Kasan, K., Sanders, S. A., Blythe, S., & Schmidt-Ott, U. (2025). Breaking anterior-posterior symmetry in the moth fly Clogmia albipunctata [Preprint]. bioRxiv. https://doi.org/10.1101/2025.01.13.632851

Lomheim, H. J., Reyes Rodas, L., Price, D., Sarbu, S. M., Băncilă, R. I., Carroll, C., Freeborn, L., Sanders, S., & Protas, M. (2025). Comparative embryology and transcriptomics of Asellus infernus, an isopod crustacean from sulfidic groundwater. Evolution and Development, 27(3), e70014. https://doi.org/10.1111/ede.70014

McManus, W. R., Mulvey, K., Brooks, E. M., Sanders, S. A., & Schorey, J. S. (2025). Growth in biofilms prepares Mycobacterium avium subsp. hominissuis for the macrophage microenvironment. Frontiers in Microbiology, 16, 1709239. https://doi.org/10.3389/fmicb.2025.1709239

Tenger-Trolander, A., Amiri, E., Gantz, V., Kwan, C. W., Yadav, H., Sanders, S. A., & Schmidt-Ott, U. (2025). Genomic resources for the scuttle fly Megaselia abdita: A model organism for comparative developmental studies in flies. Development, 152(22), dev204732. https://doi.org/10.1242/dev.204732

Wenninger, A., Knopp, J., Frye, S., Weaver, A., McAdams, N., Miller, S., Nomura, T., Whitlark, A., Swantkowski, J., Noble, A., Lavender, C., Nam, S., MacKenzie, C., Wiebelt‑Smith, I., Sander, C., Hutson, K., Bergqvist‑Patzke, J., Sanders, S., Haldar, K., Contractor, A., & Patzke, C. (2024). Human neuron and mouse models reveal synaptic imbalance in Kabuki syndrome [Preprint]. bioRxiv. https://doi.org/10.1101/2024.10.04.616738v4

Brooks, E. M., Sanders, S. A., & Pfrender, M. E. (2024). freeCount: A coding free framework for guided count data visualization and analysis. In Practice and Experience in Advanced Research Computing (PEARC ’24) (pp. 1–4). Association for Computing Machinery. https://doi.org/10.1145/3626203.3670605

Lomheim, H. J., Reyes Rodas, L., Mulla, L., Freeborn, L., Sun, D. A., Sanders, S. A., Protas, M. E. (2023). Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution. EvoDevo, 14(1), 9. https://doi.org/10.1186/s13227-023-00213-z

Petek, M., Zagorščak, M., Ramšak, Z., Sanders, S., Tomaž, S., Tseng, E., Zouine, M., Coll, A., & Gruden, K. (2020). Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato. Scientific Data. doi: https://doi.org/10.1101/845818

Foran, E. G., Suggs, E. D., Underwood, T. A., Snapp-Childs, W., & Sanders, S. A. (2019). ‘Automatic recognition of frog calls’. doi: 10.5967/PS4S-D421

Ropelewski, A., Blood, P.M., Madrid, M., Doak, T., Ganote, C., Sanders, S., & Papudeshi, B. (2018). Hackathon: Developing and applying best practice protocols for running applications and software on HPC systems, In PEARC18 Conference Proceedings, Pittsburgh, PA. Retrieved from https://pearc18.conference-program.com/?page_id=10&id=spec112&sess=sess132

Guido, E., Anderson, J., Slayton, T., Sanders, S., & Walker, T. (2018). Harvesting Field Station Data; Sensors to Jetstream. Practice and Experience in Advanced Research Computing (PEARC) 2018, Pittsburgh, PA.

Ganote. C, Sanders, S., Blood, P., & Doak, T. (2017). A Voice for Bioinformatics. Practice and Experience in Advanced Research Computing (PEARC) 2017, New Orleans, LA.

Yang, T., Fang, L., Sanders, S., Jayanthi, S., Rajan, G., Podicheti, R., Kumar, T.S., Mockaitis, K., & Medina-Bolivar, F. (2017). Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. Journal of Biological Chemistry. 293: 28-46.

Doak, T, Blood, P., Sanders, S., & Stewart, S. (2017). National Center for Genome Analysis Support: Providing National Cyberinfrastructure to Biologists, with a Focus on Genomics. Practice and Experience in Advanced Research Computing (PEARC) 2017, New Orleans, LA.

Klegarth, A.R., Sanders, S., Gloss, A., Lane, K.E., Fuentes, A., & Hollocher, H. (2017). Investigating biogeographic boundaries of the Sunda Shelf: A Phylogenetic analysis of two island populations of Macaca fascicularis. American Journal of Physical Anthropology. 163(1).

Sanders, S., Coleman, J.L, & Placyk, J.S. (2010). Graptemys ouachitensis sabinensis (Sabine Map Turtle) coloration. Herpetological Review. 41 (2): 214.

Sanders, S. & Harding, J. (2007). "Crotalus unicolor" (On-line), Animal Diversity Web.

Lundrigan, B. & Sanders, S. (2005). "Oryx gazella" (On-line), Animal Diversity Web.