Nae-chyun Chen
Head Of Computational Platform
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.
11 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 (26)
genomes10
lift10
bowtie10
bioinformatics10
package-management9
conda9
genomics9
genome8
workitem8
barrage8
sarif8
profiling7
bioconda7
pathogen6
bcftools6
Programming languages (6)
Github contributions (5)
BenLangmead/bowtie-majref
Jan 2020 - Jun 2021
Scripts related to building major-allele references for Bowtie and Bowtie 2
Contributions:1 review, 37 commits, 2 PRs in 1 year 4 months
sarifworkitembowtiebarrageallele
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
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