Michael Shaffer
Bioinformatics Scientist
Arlington, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolMichael Shaffer is a bioinformatics scientist with 11 years of experience translating multi-omics data into actionable insights for drug discovery and global health. He has led and shipped widely used open-source tools (e.g., DRAM and SCNIC) and built reproducible pipelines that processed thousands of samples, enabling discoveries from vaccine response to microbiome-driven target ID. Comfortable in matrixed pharma and academic settings, he combines systems-biology causal modeling, knowledge-graph integration, and hands-on software engineering (Snakemake, PyPI/bioconda distribution, unit testing) to move projects from data to publication. At the Gates Medical Research Institute he now applies that toolkit to preclinical and clinical studies targeting illnesses in low-and-middle-income countries. An often-overlooked strength is his track record of mentoring and managing cross-disciplinary teams while maintaining sole ownership of complex bioinformatics software.
11 years of coding experience
4 years of employment as a software developer
Doctor of Philosophy (PhD), Computational Bioscience, Doctor of Philosophy (PhD), Computational Bioscience at University of Colorado Anschutz Medical CampusBachelor of Science (BS), Bioinformatics, Bachelor of Science (BS), Bioinformatics at Loyola University of Chicago
Github Skills (31)
sparse10
package-management10
conda10
genomes10
microbiome10
bioconductor10
rna-seq10
bioinformatics10
genomics10
refined10
metagenomics10
network-analysis9
taxonomy9
bioconda9
extensible8
Programming languages (7)
Github contributions (5)
lozuponelab/AMON
Jul 2018 - Dec 2019
Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
Contributions:70 commits, 6 PRs, 38 pushes in 1 year 5 months
microbeshostbioinformaticsmicrobiomemetabolome
WrightonLabCSU/kb_DRAM
May 2020 - Dec 2021
A Kbase app for DRAM
Contributions:134 pushes, 2 branches, 1 comment in 1 year 7 months
kbasedram
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