Sean Simmons
Cambridge, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolSean Simmons is a Principal Scientist and computational biologist with 11+ years of experience translating complex genomics data into biological insight, particularly in single-cell, spatial, and multimodal RNA/ATAC studies. At the Broad Institute he led large-scale analyses—from million-cell Perturb-seq experiments to allele-specific expression studies validating Parkinson’s GWAS hits—and built production pipelines and tools in Java, nextflow, Python/pysam and R. He combines a strong math background (PhD in Applied Mathematics from MIT) with hands-on wet-lab collaboration to benchmark new technologies and guide therapeutic target decisions. Sean has a track record of creating privacy-aware algorithms for genomic studies earlier in his career, and he mentors junior scientists while bridging methods development and production bioinformatics. Now based in Cambridge, MA, he brings both deep statistical rigor and pragmatic engineering to complex translational genomics problems.
11 years of coding experience
3 years of employment as a software developer
Doctor of Philosophy (Ph.D.) Applied Mathematics (Focus on Computational Biology), Doctor of Philosophy (Ph.D.) Applied Mathematics (Focus on Computational Biology) at Massachusetts Institute of TechnologyBachelor of Science (BS) Mathematics, Bachelor of Science (BS) Mathematics at The University of Texas at Austin
Github Skills (33)
seq9
rna-seq8
bioinformatics7
sequencing7
python-bindings7
genomics7
hierarchical4
bayesian3
decomposition3
r-package3
structural-variation2
sampling2
single-cell-genomics2
poisson2
modeling2
Programming languages (6)
Github contributions (5)
seanken/CellTypeComp
Oct 2020 - Dec 2021
Contributions:5 commits, 7 pushes in 1 year 1 month
klarman-cell-observatory/ivPerturbSeq
Sep 2019 - Jan 2021
Contributions:14 pushes, 1 branch, 2 comments in 1 year 4 months
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