Research
I am interested in how the genetic relationships between hosts and their associated microbiomes change across different environments.
I investigate topics related to:
- Host-microbe-environment interactions
- Host genetic influence on microbiome composition
- Conservation in microbial niche space
- Microbial functional redundancy across environments
- Host evolutionary responses to microbes (and vice versa)
Skills & Experience
- Ph.D. in Bioinformatics and Genomics from Penn State University
- Proficient programming skills in Python, R, and UNIX/bash environments
- Demonstrated experience in modeling and analysis of genomic and microbial sequence data
- Excellent knowledge of biological/statistical data analysis methods
- Familiarity with Linux/Unix command line and high-performance computing environments
- Excellent communication, teamwork, and organizational skills
- Background in population/comparative genomics and microbial ecology
Software
- Package Environments: Rstudio, conda, pip, jupyter-notebooks
- Genome analysis/variant calling: vcftools, bcftools, IGV
- Genome-wide association studies (GWAS): sommer, rrBLUP, statgenGWAS
- Microbiome compositon analysis: phyloseq, microbiome
- Microbiome sequence analysis: dada2, mothur, Qiime2
- Modeling: base-r, sommer, sJSDM, Scikit-Learn, keras, scipy, pytorch, tensorflow
- Phylogenetics: ape, phytools, phylogram, decipher,
- Raw data processing: base-r, pandas, numpy, cutadapt, FastQC, dplyr, tidyr
- Sequence alignment: BLAST, clustalx, muscle
- Statistics, base-r, vegan
- Visualizations: Matplotlib, ggplot, seaborn