Biomedical Data

One of the Calit2’s original interdisciplinary themes was “Digitally Enabled Genomic Medicine,” which envisioned a future in which both the human genomics and wireless sensor “read outs” of individuals would be routine. I decided that to better understand these evolving trends I should try to live as a Future Patient in what Lee Hood has termed Predictive, Preventive, Personalized and Participatory (P4) Medicine. I had my full human genome sequenced and began quantifying the state of my body, creating multi-year time-series of biomarkers from my blood and from my stool. By 2011, using these time series, I discovered that I was chronically inflamed, caused by a colonic autoimmune disease that both my doctors and I were unaware I had. The progression of the disease caused massive dysbiosis in my gut microbiome and eventually a stricture in my sigmoid colon. My Calit2@UCSD software development team developed interactive 3D visualizations of individual‘s MRI/CAT scans to personalize pre-planning of robotically-assisted surgery, which I was able to help prototype with a sigmoid resection in November 2016. I had been fortunate to have Carl Woese, the Father of the microbial Tree of Life, as a mentor on microbes at UIUC in the 1990s. In 2005, the Gordon and Betty Moore Foundation funded me and the J. Craig Venter Institute to create the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA), housed in Calit2’s Qualcomm Institute. By 2013 CAMERA had become a global repository for microbiome ecology datasets, serving over 5000 remote users in 90 countries. As part of my Future Patient project I have worked for a decade with UCSD Professor Rob Knight’s team to genomically analyze my gut microbiome time-series, which now includes over 700 daily stool samples.

Focus areas

Quantifying My Body

The Future Patient project — genomics, longitudinal blood biomarkers, self-tracking, and 3D surgical visualization.

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Microbial Communities

CAMERA, microbiome time series, and gut microbial ecology — from Woese-era microbial trees to daily stool sampling.

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