PNNL

Abby received her BS in mathematics with a minor in biology from the University of Washington in Bothell. There she worked with Jesse Zaneveld using the QIIME2 microbiome tool to quantify the change in a community's gut microbiome before and after the introduction of vegetables into their diet. She also worked with Taran Gujral at Fred Hutchinson Cancer Research Center implementing elastic net regression in R to predict kinase and kinase inhibitor interactions. 

She worked on a variety of projects during her role as a post-bachelors research associate in the Earth and Biological Sciences Directorate's Systems Biology team at Pacific Northwest National Laboratory (PNNL). She developed a pipeline in R that webscrapes, cleans, and filters RB-TnSeq fitness data, contributed to the development of the amino acid encoded kmer analysis Python package Snekmer, and then turned Snekmer into an app on KBase, a large-scale online data science platform. In this role, she also got experience cleaning and analyzing MiSeq and HiSeq bacterial growth data, submitting genomes to Integrated Microbial Genomes, and automating the population of a postgreSQL open source database with genome sequences pulled from National Center for Biotechnology Information.

Her current data scientist role is in the Computing, Analytics, and Modeling group within the Environmental Molecular Sciences Laboratory on the PNNL campus. 

• Bioinformatics
• Computational Biology
• Systems Modeling
• Python
• R

• BS in mathematics, University of Washington

Chang et al. 2023. "Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding." Bioinformatics Advances 3 (1) DOI: 10.1093/bioadv/vbad005