Kuan-Hao Chao


Computer Science PhD Candidate
in Computational Genomics
@ Johns Hopkins University

Advisor: Steven Salzberg & Mihaela Pertea

More Info

🧑🏻‍💻   About me

🎓 I’m a third-year Ph.D. Candidate in Computer Science at the Center for Computational Biology, Johns Hopkins University, working with Steven Salzberg and Mihaela Pertea. My academic journey started in Electrical Engineering at National Taiwan University (NTU), shifting towards computer science in my final year at the College of Engineering & Computer Science at Australian National University (ANU).

🧬 My research interest intersects deep learning with genomics and transcriptomics:

  • In transcriptional regulatory networks,my work uses sequence models to decode DNA patterns, aiming to uncover insights into how cis-regulatory DNA sequences and trans-regulators interact. I am developing a yeast large language model (LLM) to better understand the mechanisms of yeast gene expression regulation.
  • In splice site predictiong, I built a deep dilated residual convolutional neural network to decode the complexities of RNA splicing, alternative splicing, and the impact of genetic variants on cryptic splicing (Learn more).
  • 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 (Learn more).
  • For pangenome indexing, I applied new renaming heuristics and an SMT solver to make the Wheeler graph recognition problem computationally feasible (Learn more).
  • In genome annotation, I used graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Learn more).

💻 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

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  Selected Presentation

  • ISMB General Computational COSI Talk, International Conference on Intelligent Systems for Molecular Biology, Montréal, Canada, July 2024, Slides, Video coming soon
  • 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

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  Honor & Fellowship

  Selected open-source software

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  Side Projects

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  • 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

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  • Reviewer
    • 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