Nae-chyun Chen
Staff Software Engineer, Computational Genomics
San Francisco Bay Area United States
Summary
👤
Senior🎓
Top SchoolNae-chyun Chen is a Staff Software Engineer specializing in computational genomics with a decade of experience building production-ready bioinformatics pipelines for cancer detection and population-aware sequencing analysis. Based in the San Francisco Bay Area, he has transitioned academic innovations—like levioSAM2 and reference-flow methods developed during his PhD at Johns Hopkins—into practical tools used for improving read alignment and lift-over with complete reference genomes. At Exai Bio he progressed from software engineer to staff, developing cfRNA processing methods for a liquid biopsy platform that targets early-stage cancer. His collaborations with NHGRI and Google produced tooling and models (including a population-aware DeepVariant) that measurably reduced variant calling errors and supported the first complete human genome resources. Combining deep algorithmic research with hands-on engineering, he brings both rigorous method development and product-focused implementation to computational genomics challenges. An unusual strength is his cross-disciplinary background spanning IC design, electrical engineering, and economics, which informs pragmatic system design and resource-aware solutions.
10 years of coding experience
2 years of employment as a software developer
Master of Science (M.S.) Integrated Circuit Design, Master of Science (M.S.) Integrated Circuit Design at National Taiwan UniversityJohns Hopkins UniversityNon-degree Electrical and Electronics Engineering, Non-degree Electrical and Electronics Engineering at University of Illinois Urbana-Champaign
English, Chinese
Github Skills (28)
genomes10
lift10
bioinformatics10
package-management9
conda9
genome9
bowtie9
bioconda9
genomics9
workitem8
sarif7
graph7
pathogen7
bcftools6
sequencing6
Programming languages (6)
Github contributions (5)
alshai/levioSAM
Jun 2019 - Apr 2022
Lift-over alignments from variant-aware references
Contributions:7 releases, 1 review, 455 commits in 2 years 9 months
alignmentslift
langmead-lab/reference_flow
Dec 2019 - Dec 2022
Reducing reference bias using multiple population reference genomes
Contributions:3 releases, 115 commits, 4 PRs in 3 years
bioinformaticsgenomesbias
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