Amanda Birmingham
Senior Bioinformatics Programmer
California, United States
Summary
👤
Senior🎓
Top SchoolAmanda Birmingham is a Senior Bioinformatics Programmer based in California with two decades of experience in computational biology and over 30 publications totaling 6,000+ citations. Currently at UC San Diego Health, she focuses on SARS-CoV-2 variant identification across clinical and wastewater surveillance, translating sequencing data into actionable public health insights. With deep expertise in statistical methods and biological data synthesis, she bridges research and operational pipelines to deliver reproducible, production-ready analyses. Her long career combines academic rigor from an Amherst College BA with practical impact in clinical genomics, and she is known for applying creative bioinformatics solutions to real-world surveillance challenges.
11 years of coding experience
Bachelor of Arts (B.A.), Bachelor of Arts (B.A.) at Amherst College
Github Skills (57)
bam10
autoencoder10
microbiome10
sequencing10
binder10
fasta10
jupyter9
meta9
hosts9
matrix9
removal9
mass-spectrometry9
bioinformatics9
throughput9
jupyter-widget9
Programming languages (4)
Github contributions (5)
ucsd-ccbb/mali-dual-crispr-pipeline
Mar 2017 - Oct 2017
Contributions:10 releases, 192 commits, 62 pushes in 7 months
ucsd-ccbb/C-VIEW
Feb 2021 - Jan 2023
This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
Contributions:20 releases, 1 review, 557 commits in 1 year 11 months
viral-genomicsprocessing-pipelinebioinformaticssars-cov-2bam
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