Gigabases to Gigabytes

Personal website by an aspiring quantitative geneticist

I'm a member of both the Ernst Lab and the QuantGen Group at Michigan State University. I've been trained in various aspects spanning computational genome science (software and pipeline creation) and quantitative genetics. I'm largely interested in understanding the genetic architecture of complex traits through improved GWAS and genomic prediction methods.

My hobbies and skills

Many of which I've developed during my time as a PhD student

  • Linear models
  • Statistical genetics
  • Exploratory genomic data analysis
  • Literate programming for research
  • Software development with R & C++
  • Coding with my cat, Duchess

Highlighted code and academic accomplishments

editTools

editTools is a fast R package designed using compiled code meant for the anlaysis of RNA editing from whole genome sequencing and RNAseq data. It is used to generate results for the manuscript Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements.

spin

spin is a simple R/Bash solution for easy submission of R scripts on PBS resource managers. Designed with literate programming and file organization in mind.

breedTools

breedTools is an R package that uses simple and fast methods to estimate breed or subpopulation composition. It is used to generate results for the manuscript Estimation of genome-wide and locus-specific breed composition in pigs.

My ePoster at the 2016 ISAG conference

An interactive ePoster showcasing swine editome patterns and its association with PRE-1 retrotransposons. During presentation, the ePoster was in presentation mode with click to advance set to off. Navigation is done using interactive ePoster elements.

BMC Genomics publication

Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements

T.A.S. publication

Estimation of genome-wide and locus-specific breed composition in pigs