Current Projects

1. Bulk RNASeq with multiple batch variables to detect gene signature of disease
2. Intronic alternative poly-A site identification from Bulk RNASeq

Completed RI-Bioinformatics Projects

1. Bulk RNASeq and DNA methylation arrays, and comparison between these data types
   • ​multiple time points, treatments, and batch variables
2. Maximum-depth sequencing analysis to find rare variants
   • ​including cross-pipeline comparisons

Other expertise

1. Barcode sequencing analysis, specifically random-barcoded transposon sequencing
2. Metabolic modeling using flux-balance analysis and derivatives thereof
   1. including COMETS software development and integration of signaling
3. Semi-automated image analysis of microscopy and Petri dish images and time series
   1. including spatial analyses
4. Computational modeling
   1. ordinary differential equations
   2. partial differential equations (ODEs in space)
   3. stochastic population genetics simulations
   4. diffusion and force-based stochastic simulations
5. Statistics
   1. Regression of many types, including GLMs and mixed-effect models
   2. bootstrapping / re-sampling
6. Experimental design
   1. Appropriate blocking
   2. Power analysis

Software

1. languages: R, python, bash, Java, Matlab
2. scripting, version control, package development
3. interactive report generation using RMarkdown, javascript packages, and shiny