Hi, I'm Sage
I am passionate about public health, bioinformatics, cats, and gnarly bash one-liners. With a BS in Bioinformatics, and a MSc in Bioinformatics and Genomics, I live in Seattle with my family.
I am currently a Senior Bioinformatics Engineer at Theiagen Genomics, where I am a major contributor to our rapidly growing codebase. I've been a part of Theiagen since February 2022.
When not crunching data or writing code, I enjoy spending time with my family, playing the violin, knitting, and reading.
What I do
During my time at Theiagen Genomics, I have led the development of several bioinformatics WDL pipelines and Python tools, including a Mycobacterium tuberculosis antimicrobial resistance interpretation tool (tbp-parser), and a tool that prepares genomic data and metadata for submission to GISAID and NCBI's Sequence Read Archive and BioSample data repositories (Mercury).
As one of the primary contributors to Theiagen's Public Health Bioinformatics codebase, I have mentored junior developers and organized the team to meet deadlines, resolve issues, and add new features in order to develop pipelines for public health surveillance and outbreak response. In addition, I have contributed to several other projects on GitHub, such as the StaPH-B docker builds repository, in order to make bioinformatics tools more accessible to public health professionals.
I am also responsible for innovating the company's use of Google Cloud Platform, primarily using Google Batch and Google Workflows to interact with BigQuery, Looker, and Looker Data Studio, among others.
Not all of my work is code. I have trained public health scientists in Georgia, Ghana, Mozambique, Oman, Ukraine, and the United States to perform bioinformatics analyses on the pathogen data they collect locally. I also provide technical support to our partners when they run into trouble with a pipeline.
How I got here
I spent four years in PhD training at the Penn State College of Medicine, where I worked in three different labs focusing on cancer genomes, with emphasis on structural variant calling, three-dimensional genome architecture, and epigenetics. My dissertation advisor left the university partway through, and I completed my time at Penn State with a master's degree.
In 2021, I became the first bioinformatician hired by the state of Pennsylvania. I was responsible for setting up their bioinformatics infrastructure and establishing industry best practices for the future. Due to the timing of my position, I primarily analyzed SARS-CoV-2 genomes to ensure proper sequencing quality, lineage identification, and phylogenetic tree analysis to help track the evolution of the virus during the pandemic. I have worked in public health genomics ever since.
I continue to publish when the work warrants it, most recently on statewide SARS-CoV-2 genomic surveillance in California. A complete list of my publications is available on Google Scholar and ORCiD.
I am also a member of the PHA4GE Bioinformatics Pipelines and Visualization Working Group. We develop guidance documents for the public health bioinformatics community.
Outside of work
I have played the violin since childhood, and I have continued as an adult by joining community orchestras wherever I have lived.
When I am not playing music, I am usually knitting, reading, or spending time with my family.
If you would like to talk about pipelines, public health genomics, or a bug you cannot reproduce, please send me an email.