# Nae-Chyun Chen

> Software + genomics | Exai Bio

Location: San Francisco Bay Area, United States
Profile: https://flows.cv/naechyun

I build computational solutions for biohealth problems, including cancer detection and fundamental genomics research.

I currently work at Exai Bio to build our computational platform. Our team develops scalable, robust and accurate approaches for early-cancer detection using cell-free RNAs and generative AI.

Prior to Exai Bio, I designed computational methods to account for genomic reference biases. My work includes sequence alignment , lift-over, and variant calling. I was fortunate to contribute a little bit to the first complete human genome.

I believe the integration of biological and computational knowledge is the key to drive innovation and make progress on biohealth problems. Happy to connect and chat ☕️!

## Work Experience
### Staff Software Engineer, Computational Genomics @ Exai Bio
Jan 2024 – Present | California, United States
- Develop computational methods to process cell-free RNA (cfRNA) data for Exai Bio's liquid biopsy platform.
- The methods include sequence alignment, trimming, deduplication, sequence quantification and variant calling.
- Evaluate machine learning model performance to support model development and decision making.

### Senior Software Engineer, Computational Genomics @ Exai Bio
Jan 2023 – Jan 2024 | California, United States
- Co-led the software development life cycle management of the bioinformatics engineering platform.
- Aggregated, cleaned and managed datasets to facilitate machine learning model development.

### Software Engineer, Computational Genomics @ Exai Bio
Jan 2022 – Jan 2023 | California, United States
- Developed and optimized the core R&D bioinformatics pipeline to process 100+k samples.

### Doctoral Student @ The Johns Hopkins University
Jan 2018 – Jan 2022 | Baltimore, Maryland, United States
* Advised by Dr. Ben Langmead
* Developed the "levioSAM2" software to improve alignment using a complete reference genome and lift-over (Nature Methods 2023)
* Developed computational methods to improve alignment using population genomic information ("reference flow", Genome Biology 2021; "levioSAM", Bioinformatics 2021)
* Analyzed the HLA allele typing performance of a graph-based sequence alignment method ("FORGe", Genome Biology 2018)

### Teaching Assistant @ The Johns Hopkins University
Jan 2021 – Jan 2021 | Baltimore, Maryland, United States
Sketching and Indexing (Dr. Ben Langmead), Department of Computer Science

### Project Student @ National Human Genome Research Institute (NHGRI)
Jan 2021 – Jan 2022 | remote
* Advised by Dr. Adam Phillippy and Dr. Sergey Koren
* Generated lift-over and browser resources for the first complete human genome (Science 2022, Nature 2023)
* Developed the "levioSAM2" software to improve alignment using a complete reference genome and lift-over (Nature Methods 2023)
* Developed the "chaintools" toolkit to process chain files describing whole-genome maps

### Student Researcher @ Google
Jan 2020 – Jan 2020 | remote
* Developed a population-aware DeepVariant model that reduced SNP errors by 5% (BMC Bioinformatics 2023)
* Poster presentation at Biological Data Science, CSHL, 2020

### Research Intern @ Google
Jan 2020 – Jan 2020 | remote
DeepVariant team, Google Health

### Teaching Assistant @ National Taiwan University
Jan 2015 – Jan 2017 | Taipei City, Taiwan
Computer Architecture, 2016 Fall
Computer Architecture, 2016 Spring
Data Compression, 2015 Fall

### Research Intern @ Synopsys Inc
Jan 2016 – Jan 2016 | Sunnyvale, California
Developed a toolkit to evaluate the correlation between two routing stages in IC Compiler II.


## Education
### Doctor of Philosophy - PhD in Computer Science
The Johns Hopkins University

### Master of Science (M.S.) in Integrated Circuit Design
National Taiwan University

### Bachelor of Science - BS in Electrical Engineering
National Taiwan University

### Bachelor of Arts - BA in Economics
National Taiwan University

### Non-degree in Electrical and Electronics Engineering
University of Illinois Urbana-Champaign


## Contact & Social
- LinkedIn: https://linkedin.com/in/ncchen
- Portfolio: http://naechyun.github.io/

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Source: https://flows.cv/naechyun
JSON Resume: https://flows.cv/naechyun/resume.json
Last updated: 2026-03-29