Projects:
Target Enrichment For Phylogenetics: In collaboration with the Smithsonian and other academic collaborators, we designed a set of sequence capture probes as a fast and consistent way to target conserved orthologous sequences. We then developed a bioinformatic and phylogenetic workflow to process and analyze the results. The publication can be found here: Mandel et al., (2014)
Co-expression gene networks: Using cluster and network analysis of transcripomic data to look at the network position of a gene in relation to rates of evolution across plant species. The publication can be found here: Masalia RR, Bewick AJ, Burke JM (2017).
Whole Enchilada Suite: A sequential series of programs written in collaboration the Burke and Rieseberg labs, particularly Dr. Sariel Hubner and Dr. Andries Temme. These programs, seven in total, lead researchers through step by step GWAS analysis, including the initial association mapping, capturing the extent of linkage disequilibrium, extracting out genetic information, enrichment tests, and assessing GxE. These scripts can be found on my GitHub Page here.
Gogetter Pipeline: A simple and versitle series of bioinformatic scripts that query GO terms and annotations associated with a FASTA file. This also does data visualization. The publication can be found here: Sessa et al., (2023)
Ortholog Divergence among Congeneric Plants and Animals: The culmination of my undergraduate thesis with Dr. Mike Barker at the University of Arizona. We investigated ortholog divergence across different ranks in the Linnaean system of taxonomy.
Languages:
- Perl (fluent)
- R (fluent)
- Python (fluent)
- Java (passable)
rishimasalia.com 
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