Clarence Mah
Computational Biologist II
San Diego, California, United States
Summary
👤
Senior🎓
Top SchoolClarence Mah is a computational biologist with 11 years of experience building open-source software and machine learning tools to extract subcellular insights from spatial omics and RNA biology. He developed bento-tools, a widely used Python framework for subcellular spatial transcriptomics analysis (part of the Scverse ecosystem) and applied deep learning, computer vision, and probabilistic models to decode MERFISH and in situ sequencing data. His work spans academia and industry—from a Genome Biology–published PhD and UCSD postdoc to roles at Singular Genomics and Stellaromics—bringing production-focused engineering practices (CI, unit testing, Nextflow pipelines) to high-content imaging and omics workflows. Comfortable with GPUs, HPC, and large public datasets (ENCODE, TCGA, GTEx), he blends rigorous biology with software craftsmanship to turn complex imaging and sequencing data into actionable biological hypotheses.
11 years of coding experience
6 years of employment as a software developer
Bachelor of Science (B.S.), Bioinformatics, Bachelor of Science (B.S.), Bioinformatics at University of California, San DiegoDoctor of Philosophy - PhD, Bioinformatics and Systems Biology, Doctor of Philosophy - PhD, Bioinformatics and Systems Biology at University of California San DiegoHigh School, High School at Lynbrook High School
English, Chinese
Github Skills (88)
spatial-transcriptomics10
seq10
transcriptomics10
gene-expression10
spatial10
single-cell-analysis10
bioinformatics10
dimensionality-reduction9
rna-seq9
python9
clustering9
genomics9
tsne9
kebab-case9
jupyterlab-extension9
Programming languages (8)
Github contributions (5)
SEARCH-Alliance/inspect
Apr 2020 - May 2020
covid qPCR test app
Contributions:91 commits, 13 PRs, 33 pushes in 1 month
qpcrtest-app
YeoLab/bento-tools
Mar 2020 - Jan 2023
A Python toolkit for subcellular analysis of spatial transcriptomics data
Contributions:12 releases, 29 reviews, 373 commits in 2 years 10 months
pythonspatial-transcriptomicsspatialbioinformaticspython-toolkit
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