Bioinformatic Projects

RishiMasalia_LogoThough my dissertation work is grounded in genetic mapping and water limitation physiology, I have a strong interest and proficiency for bioinformatic projects.

My undergraduate work in Mike Barker’s lab at the University of Arizona, dept. of Ecology and Evolutionary Biology focused on large computational projects. Since graduating the University of Arizona, I still work on bioinformatic “side projects” poised to address broad evolutionary questions.

Projects:

Target Enrichment Bioinformatic Pipeline: I was one of the lead bioinformaticians for the publication, “Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci- An Example from the Compositae” Here, I developed custom perl and R scripts to facilitate bioinformatic methods for those researchers not accustom to programming. my scripts can be found on the Smithsonian github (a collaborator of the project).

Co-expression gene networks: Utilizing custom perl scripts in combination with WGCNA (clustering program), this work looked at the network position of a gene in relation to rates of evolution across plant species. I was a contributing bioinformatician and author for this project.  The publication for this work is still in preparation.

Whole Enchilada Suite: is a series of programs I wrote in collaboration with other members of the Burke and Rieseberg labs, particularly Sariel Hubner. 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 geneic information, enrichment tests, and assessing GxE. This suite is currently proprietary, but when the information is made public will be located on my github page.

Ortholog Divergence among Congeneric Plants and Animals: For my undergraduate thesis, I was the lead bioinformatician in a projected aimed at addressing ortholog divergence across different ranks in the Linnaean system of taxonomy. The publication for this work is still in preparation.

Languages:

  • Perl (fluent)
  • R (fluent)
  • Python (passable)
  • Java (passable)