Publications

  1. Nihranz, C. T., Garg, P., Shin, J., Dumas, M., McCalla, S. G., Roy, S., & Casteel, C. L. (2025). Transcriptomic analysis reveals vector attraction to potato virus Y is mediated through temporal regulation of TERPENE SYNTHASE 1 (TPS1). Plant Stress, 16, 100862.
  2. Siahpirani, A. F., McCalla, S. G., Pyne, S., Dillingham, C., Sridharan, R., & Roy, S. (2025). Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation. BioRxiv. † Co-first author, equal contribution with the first-listed author.
  3. McCalla, S. G., Fotuhi Siahpirani, A., Li, J., Pyne, S., Stone, M., Periyasamy, V., Shin, J., & Roy, S. (2023). Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data. G3: Genes, Genomes, Genetics, 13(3), jkad004.
  4. Zhang, S., Pyne, S., Pietrzak, S., Halberg, S., McCalla, S. G., Siahpirani, A. F., Sridharan, R., & Roy, S. (2023). Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nature Communications, 14(1), 3064.
  5. Shin, J., Mueller, K. P., Capowski, E., Pyne, S., McCalla, S. G., Saxena, S., Samimi, K., Nelson, E., Fernandez, M. A., Skala, M., & others. (2023). Single-Cell Transcriptional Analysis of Human In Vitro Platforms to Study Genome Editing Effects in Retinal Tissues. MOLECULAR THERAPY, 31(4), 489–489.
  6. Saha, K., Gimse, K., Shin, J., Wang, Y., Metzger, J. M., Mueller, K., Capowski, E., Pyne, S., McCalla, S. G., Saxena, S., & others. (2022). Profiling Cell Type Specificity and Adverse Events of Genome Editing Nucleases in the Brain and Retina Using Single Cell Transcriptomics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, 63, 63–63.
  7. Iyer, N. R., Shin, J., Cuskey, S., Tian, Y., Nicol, N. R., Doersch, T. E., Seipel, F., McCalla, S. G., Roy, S., & Ashton, R. S. (2022). Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patterns. Science Advances, 8(39), eabn7430.
  8. Ladell, B. A., Walleser, L. R., McCalla, S. G., Erickson, R. A., & Amberg, J. J. (2019). Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA. Conservation Genetics Resources, 11(1), 83–88.
  9. Tran, K. A., Pietrzak, S. J., Zaidan, N. Z., Siahpirani, A. F., McCalla, S. G., Zhou, A. S., Iyer, G., Roy, S., & Sridharan, R. (2019). Defining reprogramming checkpoints from single-cell analyses of induced pluripotency. Cell Reports, 27(6), 1726–1741.
  10. Erickson, R. A., Fienen, M. N., McCalla, S. G., Weiser, E. L., Bower, M. L., Knudson, J. M., & Thain, G. (2018). Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor. PLoS Computational Biology, 14(10), e1006468.
  11. Jackson, C., McCalla, S. G., Amberg, J., Soluk, D., & Britten, H. (2018). The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing. Mitochondrial DNA Part B, 3(2), 562–563.
  12. Larson, J. H., Knights, B. C., McCalla, S. G., Monroe, E., Tuttle-Lau, M., Chapman, D. C., George, A. E., Vallazza, J. M., & Amberg, J. (2017). Evidence of Asian carp spawning upstream of a key choke point in the Mississippi River. North American Journal of Fisheries Management, 37(4), 903–919.
  13. Langseth, M. L., Hsu, L., Amberg, J., Bliss, N., Bock, A. R., Bolus, R. T., Bristol, R. S., Chase, K. J., Crimmins, T. M., Earle, P. S., & others. (2017). Community for Data Integration 2016 annual report. US Geological Survey.
  14. Erickson, R. A., Rees, C. B., Coulter, A. A., Merkes, C. M., McCalla, S. G., Touzinsky, K. F., Walleser, L., Goforth, R. R., & Amberg, J. J. (2016). Detecting the movement and spawning activity of bigheaded carps with environmental DNA. Molecular Ecology Resources, 16(4), 957–965.
  15. Amberg, J. J., McCalla, S. G., Monroe, E., Lance, R., Baerwaldt, K., & Gaikowski, M. P. (2015). Improving efficiency and reliability of environmental DNA analysis for silver carp. Journal of Great Lakes Research, 41(2), 367–373.
  16. Merkes, C. M., McCalla, S. G., Jensen, N. R., Gaikowski, M. P., & Amberg, J. J. (2014). Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS One, 9(11), e113346.
  17. Amberg, J. J., McCalla, S. G., Miller, L., Sorensen, P., & Gaikowski, M. P. (2013). Detection of environmental DNA of Bigheaded Carps in samples collected from selected locations in the St. Croix River and in the Mississippi River. US Geological Survey.
  18. McCalla, S. G. (2010). Patterns of genetic diversity in Diporeia in the Laurentian Great Lakes [Master's thesis]. Purdue University.