Kuan-Hao Chao

Research output

Publications

Peer-reviewed papers and preprints in computational biology and machine learning. 15 publications — see Google Scholar for the complete, up-to-date list.

  1. P588: AI and drug discovery with 100 million cells of genome-wide Perturb-seq

    Kwontae You, Jiang Zhu, Dulguun Amgalan, …, Kuan-Hao Chao, …, Kyle Kai-How Farh

    Genetics in Medicine Open Conference

    DOI
    BibTeX 
    @article{you2026perturbseq,
  title   = {P588: AI and drug discovery with 100 million cells of genome-wide Perturb-seq},
  author  = {You, Kwontae and others},
  journal = {Genetics in Medicine Open},
  volume  = {4},
  pages   = {104079},
  year    = {2026},
  doi     = {10.1016/j.gimo.2026.104079}
}

  2. A complete diploid human genome benchmark for personalized genomics

    Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, …, Kuan-Hao Chao, …, Steven L. Salzberg, Adam M. Phillippy

    bioRxiv Preprint

    DOI Code
    BibTeX 
    @article{hansen2025diploid,
  title   = {A complete diploid human genome benchmark for personalized genomics},
  author  = {Hansen, Nancy F. and others},
  journal = {bioRxiv},
  year    = {2025},
  doi     = {10.1101/2025.09.21.677443}
}

  3. Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

    Kuan-Hao Chao*, Majed Mohamed Magzoub, Emily Stoops, Sean R. Hackett, Johannes Linder*, David R. Kelley*

    bioRxiv Preprint

    DOI Code Slides Talk
    BibTeX 
    @article{chao2025shorkie,
  title   = {Predicting dynamic expression patterns in budding yeast with a fungal DNA language model},
  author  = {Chao, Kuan-Hao and Magzoub, Majed Mohamed and Stoops, Emily and Hackett, Sean R. and Linder, Johannes and Kelley, David R.},
  journal = {bioRxiv},
  year    = {2025},
  doi     = {10.1101/2025.09.19.677475}
}

  5. OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species

    Kuan-Hao Chao*†, Alan Mao†, Anqi Liu, Steven L. Salzberg*, Mihaela Pertea*

    eLife Journal

    DOI Code Docs Poster
    BibTeX 
    @article{chao2025openspliceai,
  title   = {OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species},
  author  = {Chao, Kuan-Hao and Mao, Alan and Liu, Anqi and Salzberg, Steven L. and Pertea, Mihaela},
  journal = {eLife},
  year    = {2025},
  doi     = {10.7554/eLife.107454.3}
}

  6. SARS-CoV-2 induces neutrophil degranulation and differentiation into myeloid-derived suppressor cells associated with severe COVID-19

    Leon L. Hsieh, Elizabeth A. Thompson, Nirvani P. Jairam, …, Kuan-Hao Chao, …, Andrew H. Karaba, Andrea L. Cox

    Science Translational Medicine Journal

    DOI
    BibTeX 
    @article{hsieh2025sarscov2,
  title   = {SARS-CoV-2 induces neutrophil degranulation and differentiation into myeloid-derived suppressor cells associated with severe COVID-19},
  author  = {Hsieh, Leon L. and others},
  journal = {Science Translational Medicine},
  volume  = {17},
  number  = {799},
  pages   = {eadn7527},
  year    = {2025},
  doi     = {10.1126/scitranslmed.adn7527}
}

  7. Combining DNA and protein alignments to improve genome annotation with LiftOn

    Kuan-Hao Chao*, Jakob M. Heinz, Celine Hoh, Alan Mao, Mihaela Pertea, Steven L. Salzberg*

    Genome Research Journal

    DOI Code Docs Talk
    BibTeX 
    @article{chao2025lifton,
  title   = {Combining DNA and protein alignments to improve genome annotation with LiftOn},
  author  = {Chao, Kuan-Hao and Heinz, Jakob M. and Hoh, Celine and Mao, Alan and Pertea, Mihaela and Salzberg, Steven L.},
  journal = {Genome Research},
  year    = {2025},
  doi     = {10.1101/gr.279620.124}
}

  9. EASTR: Correcting systematic alignment errors in multi-exon genes

    Ida Shinder*, Richard Hu, Hyun Joo Ji, Kuan-Hao Chao*, Mihaela Pertea*

    Nature Communications Journal

    DOI
    BibTeX 
    @article{shinder2023eastr,
  title   = {EASTR: Correcting systematic alignment errors in multi-exon genes},
  author  = {Shinder, Ida and Hu, Richard and Ji, Hyun Joo and Chao, Kuan-Hao and Pertea, Mihaela},
  journal = {Nature Communications},
  year    = {2023},
  doi     = {10.1038/s41467-023-43017-4}
}

  10. CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

    Ales Varabyou*, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg*, Mihaela Pertea*

    Genome Biology Journal

    DOI
    BibTeX 
    @article{varabyou2023chess3,
  title   = {CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure},
  author  = {Varabyou, Ales and Sommer, Markus J. and Erdogdu, Beril and Shinder, Ida and Minkin, Ilia and Chao, Kuan-Hao and Park, Sukhwan and Heinz, Jakob and Pockrandt, Christopher and Shumate, Alaina and Rincon, Natalia and Puiu, Daniela and Steinegger, Martin and Salzberg, Steven L. and Pertea, Mihaela},
  journal = {Genome Biology},
  year    = {2023},
  doi     = {10.1186/s13059-023-03088-4}
}

  12. A feature extraction free approach for protein interactome inference from co-elution data

    Yu-Hsin Chen†, Kuan-Hao Chao†, Jin Yung Wong, Chien-Fu Liu, Jun-Yi Leu*, Huai-Kuang Tsai*

    Briefings in Bioinformatics Journal

    DOI
    BibTeX 
    @article{chen2023spiffed,
  title   = {A feature extraction free approach for protein interactome inference from co-elution data},
  author  = {Chen, Yu-Hsin and Chao, Kuan-Hao and Wong, Jin Yung and Liu, Chien-Fu and Leu, Jun-Yi and Tsai, Huai-Kuang},
  journal = {Briefings in Bioinformatics},
  year    = {2023},
  doi     = {10.1093/bib/bbad229}
}

  13. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

    Kuan-Hao Chao*, Aleksey V. Zimin, Mihaela Pertea, Steven L. Salzberg*

    G3: Genes, Genomes, Genetics Journal

    DOI News
    BibTeX 
    @article{chao2023han1,
  title   = {The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual},
  author  = {Chao, Kuan-Hao and Zimin, Aleksey V. and Pertea, Mihaela and Salzberg, Steven L.},
  journal = {G3: Genes, Genomes, Genetics},
  year    = {2023},
  doi     = {10.1093/g3journal/jkac321}
}

  14. sangeranalyseR: simple and interactive processing of Sanger sequencing data in R

    Kuan-Hao Chao*, Kirsten Barton, Sarah Palmer, Robert Lanfear*

    Genome Biology and Evolution Journal

    DOI Code Docs Poster
    BibTeX 
    @article{chao2021sangeranalyser,
  title   = {sangeranalyseR: simple and interactive processing of Sanger sequencing data in R},
  author  = {Chao, Kuan-Hao and Barton, Kirsten and Palmer, Sarah and Lanfear, Robert},
  journal = {Genome Biology and Evolution},
  year    = {2021},
  doi     = {10.1093/gbe/evab028}
}

  15. RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

    Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang*

    IEEE/ACM Transactions on Computational Biology and Bioinformatics Journal

    DOI Code
    BibTeX 
    @article{chao2019rnaseqr,
  title   = {RNASeqR: an R package for automated two-group RNA-Seq analysis workflow},
  author  = {Chao, Kuan-Hao and Hsiao, Yi-Wen and Lee, Yi-Fang and Lee, Chien-Yueh and Lai, Liang-Chuan and Tsai, Mong-Hsun and Lu, Tzu-Pin and Chuang, Eric Y.},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year    = {2019},
  doi     = {10.1109/TCBB.2019.2956708}
}

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