Kuan-hao Chao
Senior Deep Learning Engineer at Illumina
California, United States
Summary
🤩
Rockstar🎓
Top SchoolKuan-hao Chao is a Senior Deep Learning Engineer at Illumina AI Lab with nine years of experience bridging deep learning and genomics, holding a Ph.D. in Computer Science from Johns Hopkins University. His work spans sequence-to-function modeling, DNA language models, splice-site prediction with dilated residual CNNs, and producing the first gapless Southern Chinese Han genome assembly. He developed Shorkie, a masked-DNA language model pretrained on 165 fungal genomes and fine-tuned on high-resolution yeast TF induction RNA‑seq, and has applied SMT solvers and novel heuristics to make Wheeler graph problems tractable for pangenome indexing. An advocate of open source, he combines rigorous academic research with production-focused engineering to translate complex genomic signals into practical models and tools. Based in California, he welcomes collaborations that push the frontier of AI-driven biology.
9 years of coding experience
Australian National UniversityBachelor of Engineering - BE, Electrical and Electronics Engineering, Bachelor of Engineering - BE, Electrical and Electronics Engineering at National Taiwan UniversityJohns Hopkins UniversityHigh School Diploma - Math and Science Honor, High School Diploma - Math and Science Honor at Taipei Municipal Jianguo High School
English, taiwanese mandarin
Github Skills (22)
r-package10
package-management10
seq10
conda10
sequencing10
rna-seq10
bioinformatics10
bioconda10
genome-annotation9
bioconductor7
prediction6
prediction-model6
agent-based-modeling5
simulation4
simulation-framework4
Programming languages (7)
Github contributions (5)
Kuanhao-Chao/Kuanhao-Chao
Jul 2020 - Mar 2025
Contributions:31 pushes, 1 branch in 4 years 9 months
roblanf/sangeranalyseR
Sep 2019 - Oct 2022
functions to analyse sanger sequencing reads in R
Contributions:612 commits, 2 PRs, 604 pushes in 3 years
bioinformaticssangersanger-sequencingsequencing
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