Who is John?

I’m a bioinformatics scientist with a passion for building and studying resilient systems.

Questions that interest me:

• How do biological systems respond to stress?
• How do we infer causality in high-dimensional and compositional biological datasets (-omics data)?
• How should we collect and efficiently process terabytes of relevant genetic sequencing data on a regular basis?

Fields/tools I like to draw from:

• causal inference
• protein language modeling
• ontologies and knowledge graphs
• statistical ecology and genetics
• stress physiology

What I do:

I build software for efficient bioinformatic processing and biologically-inspired statistical modeling of high-dimensional and compositional “-omics” data (e.g., metagenomics, metatranscriptomics, metabolomics).

This currently supports making custom gene/protein engineering and custom synthetic biology product quality control at Integrated DNA Technologies.

During my PhD, I focused on ecology of the gut microbiome, host-microbe interactions and the gut-brain axis. I utilize causal inference techniques and machine learning.

I gravitate toward collaborative projects (where I can help someone else develop the best tools to answer their biological questions) and mentoring/teaching, as I see these as two of the most direct ways I can do good.

In other contexts:

From a non-professional perspective, I like to explore the areas around me, particularly via ultra-distance trail running, cycling, and climbing. Music is a large part of my life, as I have played a variety of instruments for many years, with a focus on Appalachian folk on the banjo and jazz trombone.

Site contents

Using the navbar at the top of this page, you can see my resume, academic CV, educational resources, and personal writing (race reports). The GitHub icon on the top right will take you to my GitHub.