My group’s research focuses on the analysis of ‘omics data to understand drug response and improve drug design, for diseases like depression leukemia, and pancreatic cancer. Additionally, I work collaboratively with Dr. Alexandre Erkine to process, analyze and understand high-throughput screeens to elucidate transcriptional regulation mechanisms.
Currently, we are conducting systematic reviews and meta-analyses of publicly available ‘omics data, integrating multiple ‘omics levels to understand why some patients respond better to antidepressants than others. We also continue to develop accessible bioinformatics software, including the NanoTube for easier analysis and visualization of NanoString nCounter data.
Highlighted Projects
A full publication list can be found at Google Scholar.
Research involving Butler Students
- Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses. Cooper DG, Cowden JP, Stanley PA, Karbowski JT, Gaertig VS, Lukan CJ, Vo PM, Worthington AD, Class CA. Manuscript under review. Preprint at bioRxiv: https://doi.org/10.1101/2024.02.19.581045
- Easy NanoString nCounter data analysis with the NanoTube. Class CA, Lukan CJ, Bristow CA, Do KA. Bioinformatics. 2023; 39(1): btac762. DOI: https://doi.org/10.1093/bioinformatics/btac762.
- Faster Assessment of Fluoxetine Response Using Transcriptomics Data. Cowden JP, Worthington AD, Caleb Class. Presented at ASHP Midyear (2021).
- Identifying Early Diagnostic Features of Parkinson’s Disease Using Multi-Omics. Van Ravenswaay L, Retzke K, Class CA. Presented at ASHP Midyear (2021).
Collaborative Research involving Butler Students
- Grammar rules and exceptions for the language of transcriptional activation domains. Cooper DG, Erkina TY, Broyles BK, Class CA, Erkine AM. iScience. 2024. DOI: https://doi.org/10.1016/j.isci.2024.111057
- The enigma of transcriptional activation domains. Erkine AM, Oliveira MA, Class CA. J Mol Bio. 2024; 436(22): 168766. DOI: https://doi.org/10.1016/j.jmb.2024.168766
- Activation of Gene Expression by Protein Domains Acting as Nucleosome Detergents. Broyles BK, Gutierrez AT, Maris TP, Coil DA, Wagner TM, Wang X, Kihara D, Class CA, Erkine AM. iScience. 2021; 24(9). DOI: https://doi.org/10.1016/j.isci.2021.103017.
Other Collaborative Work
- Stem cell-specific survival pathways drive the progression of myelodysplastic syndromes. Ganan-Gomez I, Yang H, Alfonso A, …, Class CA, …, Garcia-Manero G, Colla S. Nature Medicine (2022).
- Activation of Gene Expression by Protein Domains Acting as Nucleosome Detergents. Broyles BK, Gutierrez AT, Maris TP, Coil DA, Wagner TM, Wang X, Kihara D, Class CA, Erkine AM. iScience (2021).
- PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma. Giuliani V, Miller MA, Liu CY, Hartono SR, Class CA, …, Heffernan TP. Nature Communications (2021).
- iDINGO—integrative differential network analysis in genomics with Shiny application. Class CA, Ha MJ, Baladandayuthapani V, Do KA. Bioinformatics (2018). R package available at CRAN, and Shiny application available at GitHub.