Who is John?
I’m a community-oriented, interdisciplinary scientist with a passion for studying and building 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:
- statistical ecology and genetics
- causal inference
- stress physiology
- ontologies and knowledge graphs
- machine learning
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).
These projects often focus on ecology of the gut microbiome, host-microbe interactions and the gut-brain axis. I utilize causal inference techniques and machine learning, where I prioritize analysis transparency way for actionable insights.
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. I’m passionate about building community and support networks for myself and those around me, which I often find myself doing through cooking, music, and sport.
Professional activities
I’m a PhD candidate in the Interdisciplinary Quantitative Biology program at the University of Colorado Boulder, housed by the Department of Integrative Physiology. I’m co-advised by Cathy Lozupone and Chris Lowry.
My dissertation has involved development and validation of data analysis pipelines for novel approaches to studying how mammals and their gut microbiomes communicate molecularly.
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.