Michael Shaffer

About Me

I grew up with a passion for science. I was priviledged to have parents who indulged me in this by taking me to museums and helping me constantly learn more about how the world works around me. In the thrid grade I remember hearing about the human genome project for the first time and I think from that moment I was hooked on biology and, even though I didn't know it yet, bioinformatics. I went on to pursue my undergraduate degree in bioinformatics which is where I got my first research experience. After that I got my PhD in computational bioscience where I studied 'omics data integration focusing on 16S rRNA amplicon sequencing and untargeted LC/MS metabolomics. I then started my postdoc where I have delved into metagenomics, metatranscriptomics and metaproteomics. Here I have been able to apply myself to both software development projects as well as applied multi-omics integration work.

But my dream in science is to create systems which allow for the rational design of pre- and probiotics. We know that the microbiome is important and that metabolism is one of the key drivers of microbial community assembly. We can harness the information contained within microbial genomes along with measurements of their activity to predict if a new microbe could stably join a community or how the addition of a compound would shift community activity and abundance. Once we can do this we will be able to make personalized, percision microbiome medicine possible and manipulate human microbial communities to increase human health.

If you want to see a big list of everything I've done in my career then you can click here to check out my full CV.

Contact Information

Email me at shaffer.michael.t at gmail.com
Follow me on Twitter @mikerobiome
Check out my GitHub @shafferm

My Academic History

BS Bioinformatics and Molecular Biology, Loyola University Chicago -> PhD Computational Bioscience University of Colorado Anschutz Medical Campus -> Postdoc Wrighton Lab at Colorado State University
Click here to see my full CV.

My Interests

I have a steady flow of hobbies and interests that keep me plenty busy outside of work. I love the outdoors. In the winter I enjoy skiing and the rest of the year I can frequently be found hiking, road cycling and mountain biking. The picture above is from the Snowy Range in Wyoming near Medicine Bow Peak. I translate my interest in microbiology to home brewing and beer drinking (especially sour beers). I also have been trying to learn to play music on both mandolin and guitar.