About me
I am a Senior Deep Learning Scientist at the Illumina AI Lab. I earned my Ph.D. in Computer Science from the Center for Computational Biology, Johns Hopkins University (August 2025), advised by Dr. Steven Salzberg and Dr. Mihaela Pertea. My research focuses on AI for genomics—including sequence-to-function modeling, genome annotation, and DNA language models. I hold a B.S. in Electrical Engineering from National Taiwan University and completed a final-year exchange at the College of Engineering & Computer Science, Australian National University.
🧬 My research interest intersects deep learning with genomics and transcriptomics:
- In RNA-Seq gene expression prediction, I developed Shorkie, a masked‑DNA language model pretrained on 165 fungal genomes and fine‑tuned on high‑resolution yeast TF induction time‑course RNA‑seq data. (See what my model has learned; Learn more; Talk).
- In splice site prediction, I built a dilated residual convolutional neural network to decode the complexities of RNA splicing, alternative splicing, and the impact of genetic variants on cryptic splicing (Paper I; Paper II; News; Talk).
- In genome annotation, I used graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Paper; Talk).
- In genome assembly, I assembled and annotated the first gapless Southern Chinese Han genome, Han1, using PacBio HiFi and Oxford Nanopore long reads, with T2T-CHM13 as a guide (Paper; Genome).
- For pangenome indexing, I applied new renaming heuristics and an SMT solver to make the Wheeler graph recognition problem computationally feasible (Paper; News; Talk).
💻 I am an advocate for open-source software, embracing the philosophy of “build what you need, use what you build”. I invite you to explore my NEWS page for the latest updates on my projects.
💬 Feel free to reach out to me for collaborations, discussions, or just to say hi! Coffee chat! ☕️
Selected Publication
- Kuan-Hao Chao*†, Alan Mao†, Anqi Liu, Steven L Salzberg*, Mihaela Pertea* (2025) OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species, eLife
- Kuan-Hao Chao*, Jakob M. Heinz, Celine Hoh, Alan Mao, Mihaela Pertea, Steven L. Salzberg* (2025) Combining DNA and protein alignments to improve genome annotation with LiftOn, Genome Research
- Kuan-Hao Chao*, Alan Mao, Steven L. Salzberg, Mihaela Pertea* (2024). Splam: a deep-learning-based splice site predictor that improves spliced alignments, Genome Biology
- Kuan-Hao Chao*, K. Barton, S. Palmer, and R. Lanfear* (2021). sangeranalyseR: simple and interactive processing of Sanger sequencing data in R, Genome Biology and Evolution
- Kuan-Hao Chao*, A.V. Zimin, M. Pertea, S.L. Salzberg* (2023). The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual, G3: Genes, Genomes, Genetics
- Kuan-Hao Chao*†, Pei-Wei Chen†, Sanjit A. Seshia, Ben Langmead* (2023). WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs, iScience
Selected Presentation
- Doctoral Dissertation Defense Seminar: "Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning", Baltimore, MD, August 2025, Slides, Website
- Robbins Prize Awardee Talk, JHU Symposium on High-Performance Computing (HPC 2025), Baltimore, MD, April 2025, Photo, Slides
- JHU Joint Biostats-Genomics Lab Meeting Talk, Baltimore, MD, Jan 2025, Video, Slides
- Calico internship 1-hour Talk, Calico, South San Francisco, CA, August 2024, Photo, Slides
- Invited Google Deep Dive 1-hour Talk, Google Health, Virtual & Mountain View, CA, August 2024, Video [Google internal only], Slides
- ISMB General Computational COSI Talk, International Conference on Intelligent Systems for Molecular Biology, Montréal, Canada, July 2024, Video, Slides
- JHU Joint Biostats-Genomics Lab Meeting Talk, Baltimore, MD, May 2024, Video, Slides
- RECOMB-seq Talk, Research in Computational Molecular Biology on Biological Sequence Analysis, Cambridge, USA, April 2024, Slides
- RECOMB-seq Proceeding Talk, Research in Computational Molecular Biology on Biological Sequence Analysis, Istanbul, Türkiye, April 2023, Video, Slides
- ISMB/ECCB Poster, Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2023, Lyon, France, July 2023, Link
Education
- Ph.D. Candidate in Computer Science, Johns Hopkins University, Sep/2021 - Present
- M.S.E. in Computer Science, Johns Hopkins University, Sep/2021 - May/2023
- B.S. in Electrical Engineering, National Taiwan University, Sep/2016 - Jan/2021
Experience
- Sr. Deep Learning Scientist & Engineer, Artificial Intelligence Lab,
, Aug/2025 - Present - Genomics Machine Learning Research Intern, Kelley Lab,
, May/2024 - Aug/2024 - Research Assistant, Institute of Information Science, Academia Sinica, Jul/2020 - Jan/2021
- Research Student, Research School of Biology, The Australian National University, Jul/2019 - Jun/2020
- Research Student, Centers of Genomic and Precision Medicine, National Taiwan University, Aug/2018 - Jul/2019
Honor & Fellowship
- Research highlight by JHU HUB, Whiting School of Engineering and CS Department [Article], 2024
- Mark O. Robbins Prize awarded by Advanced Research Computing at Hopkins (ARCH) [Article], 2024
- Taiwan Government Scholarship to Study Abroad (GSSA) awarded by Taiwan Ministry of Education, 2024
- Research highlight by JHU Whiting School of Engineering and CS Department [Article], 2024
- Best Poster Award, Bioconductor Conference (Bioc2021), 2021
- College Student Research Fellowship awarded by Taiwan Ministry of Science and Technology, 2019
- Elite Prize (1st prize), 2017 HackNTU (500+ participants Hackathon) [Photo], 2019
Selected open-source software
- OpenSpliceAI, splice site prediction framework
Code Documentation Poster Paper Cite - Splam, splice site predictor
Code Documentation Poster Paper Cite - LiftOn, annotation lift-over tool Code Documentation Paper
- sangeranalyseR, R package for analyzing Sanger sequence Code Documentation Poster Paper Cite
- Wheele Graph Toolkit Code Poster Paper Cite
Side Projects
- Biobaby, Unity WebGL game, ▶️ Play it now!
- Flappy penguin, Unity WebGL game, ▶️ Play it now!
- Tank fire, Unity WebGL game, ▶️ Play it now!
Teaching
- Johns Hopkins University
- EN.580.458 / 658 Computing the Transcriptome, Teaching assistant, Spring 2023
- National Taiwan University
- CSX 4001 Data Science Programming, Teaching assistant, Spring 2019
- EE 1006 Cornerstone EECS Design and Implementation, Teaching assistant, Fall 2018
Service
- Co-founder and Organizer
- Johns Hopkins Deep Learning + Genomics Study Group, 2024 - Present Slides, Repository
- Reviewer
- Human Genetics and Genomics Advances: 2025
- BMC Genomics: 2025
- Scientific Reports: 2025
- Genome Research: 2024
- G3: Genes, Genomes, Genetics: 2024
- BMC Bioinformatics: 2024
- International Society for Computational Biology (ISCB): 2024
- Chromatographia: 2023
- Sub-reviewer
- Genome Research: 2024
- Nature Machine Intelligence: 2023
- G3: Genes, Genomes, Genetics: 2022