Kuan-Hao Chao


Computer Science PhD Candidate
in Computational Genomics
@ Johns Hopkins University

Advisor: Steven Salzberg & Mihaela Pertea

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🧑🏻‍💻   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 “graphs” with genomics and transcriptomics:

  • In genome assembly, De Bruijn graphs are widely used. For an example of its application, check out my Han1 assembly, the first gapless Southern Chinese Han genome.
  • For pangenome indexing, I’ve contributed to making the Wheeler graph recognition problem computationally feasible through innovative heuristic methods combined with an SMT solver (Learn more).
  • In genome annotation, I have utilized graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Learn more).
  • My transcriptome assembly work focuses on modeling RNA-Seq data using directed acyclic splice graphs, with ongoing research into graph neural networks to decode the complexities of RNA splicing. (Learn more).

💻 As a staunch advocate for open-source software, 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

  • JHU Joint Biostats-Genomics Lab Meeting Talk, Baltimore, MD, 2024, Video, Slides
  • ISMB General Computational COSI Talk, International Conference on Intelligent Systems for Molecular Biology, Montreal, Canada, 2024, Expected: July
  • RECOMB-seq Talk, Research in Computational Molecular Biology on Biological Sequence Analysis, Boston, USA, 2024, Slides
  • RECOMB-seq Proceeding Talk, Research in Computational Molecular Biology on Biological Sequence Analysis, Istanbul, Türkiye, 2023, Video, Slides
  • ISMB/ECCB Poster, Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2023, Lyon, France, 2023, Link

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  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
    • Chromatographia: 2023
    • G3: Genes, Genomes, Genetics: 2024
    • BMC Bioinformatics: 2024
    • International Society for Computational Biology (ISCB): 2024
  • Sub-reviewer
    • Genome Research: 2024
    • Nature Machine Intelligence: 2023
    • G3: Genes, Genomes, Genetics: 2022