Nae-Chyun Chen

Resume (PDF), CV (PDF), updated: May 15th, 2022

Research Interests

I work on computational genomics, primarily sequence data processing methods. These include sequence alignment and variant calling. One of my main focuses is to reduce reference bias due to assembly artifacts and lack of genetic diversity. I'm also experienced in processing immunogenomics data, such as HLA, TCR, and BCR. Before my PhD work, I designed hardware architectures on FPGA and ASIC to accelerate computing.

#computational_genomics      #sequence_alignment      #variant calling      #lift-over      #pangenomics

Skills

  • Languages: Mandarin (traditional), English, Taiwanese
  • Progamming languages: Python, R, C++, C, Rust
  • Hardware description language: Verilog
  • Tools: git, Latex, Bash, Snakemake, unittest, Docker, make, cmake

Education

  • PhD in Computer Science (2018-expected 2022)
    Johns Hopkins Unversity, with Dr. Ben Langmead
  • MS in Electronics Engineering (2015-2017)
    BS in Electrical Engineering and BA in Economics (2010-2015)
    National Taiwan University (NTU), MS with Dr. Yi-Chang Lu
  • Exchange student (2014)
    University of Illinois at Urbana-Champaign

Working

  • Research Intern & Student Researcher (2020)
    Google, Remote, USA
    DeepVariant Team (Brain Genomics), Google Health
  • Technical Intern (2016)
    Synopsys, Sunnyvale, California, USA
    IC Compiler II (ICC2) Team

Teaching

  • Undergraduate Researcher Mentor (2022)
    Advised Steven Solar (senior undergrad at JHU) to develop a data-driven model to predict sequence mapping quality.
  • Internship Mentor (2019)
    Advised Sheila Iyer (high-school intern) to study the reference bias of genomic sequence alignment. The work became part of a research paper and won regional science fair.
  • Teaching Assistant
    JHU: Sketching and Indexing (2021)
    NTU: Data Compression (2015) (grad-level), Computer Architecture (2016, 2017) (upper undergrad)

Volunteer

I served as a volunteer with the Children of Sea club at NTU. I helped to organize four summer/winter camps for local kids in 2011-2013 at Penghu — a distant island of Taiwan. We also worked closely with local communities to held annual events and visited elder people whose children were working out of town. This experience has become a big part of me. I went back to Penghu to serve one year in Wen-Ao Elementary School in 2018.

Podcast

I co-host the "生技來一刻" podcast (in Mandarin) to interview experts in biotech to discuss career and technological advancements.