Gregg Thomas
Senior Bioinformatics Scientist
Northwest Labs B227.65
With a background in bioinformatics and evolutionary biology, Gregg joined the group in July of 2021 from a postdoctoral position at the University of Montana in Jeff Good's lab . Previously he studied at Indiana University with Matt Hahn .
Gregg is excited to understand the processes and patterns of molecular evolution by using genomics and phylogenetics, and working through some of the problems that vast amounts of genomic data has presented. To this end, he has worked on modeling mutation rate variation in mammals, detecting convergent evolution on genomic data, and analyzing gene family evolution in a number of species.
He contributes to and develops software to facilitate research in comparative genomics. He contributed to CAFE to account for error in gene family analysis, and developed the program GRAMPA to study polyploidy in the context of gene tree topologies. He now develops and maintains PhyloAcc to identify substitution rate shifts in phylogenetic trees.
To foster best practices and reproducibility in computational biology he also teaches workshops, with subjects ranging from basic computational, programming, and data science skills to more advanced topics like genome assembly and phylogenetics. In the past, he has taught at the Conservation Genetics workshop (ConGen) and he helps teach a variety of subjects in our group.
Outside of the lab, he has a passion for dogs and animals in general. He also enjoys being active and doing puzzles with his partner!
See Gregg's website for his CV, publication list, and software.
Links:
Pages authored by Gregg
- [Tutorial] Intro to conda/mamba
- [Tutorial] Add outgroup to HAL file
- [Tutorial] Cactus whole genome alignment
- [Tutorial] Pangenomes with Minigraph-Cactus
- [Tutorial] Replace a genome in a HAL file
- [Tutorial] Add new genome to HAL file
- [Workshop] Biotips Day 4: Shell scripting
- [Workshop] Unix tips and tricks for bioinformatics
- [Workshop] Biotips Day 1: Bioinformatics command line tools and file formats
- [Workshop] Biotips Day 3: Interval files and shell scripting
- [Workshop] Biotips Day 2: Bioinformatics command line tools and file formats
- [Short Training] R tidyverse
- [Short Training] Plotting in R with ggplot
- [Workshop] Introduction to R Part 1: R Basics
- [Workshop] Introduction to R Part 3: ggplot
- [Workshop] Introduction to R
- [Workshop] Introduction to R Part 2: tidyverse
- [Workshop] Introduction to Python for Data Science
- [Workshop] Healthy habits for data science 2
- [Workshop] Healthy habits for data science
- [Maintainer] Computing glossary
- [Maintainer] Biotips - Local setup
- [Maintainer] Biotips - Cannon setup
- [Maintainer] Software