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Kuan-Hao Chao

Research output

Publications

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

  1. SpliceCOV: Supervised Filtering of RNA-Seq-Derived Transcript Features Improves Transcriptome Assembly

    Full author list

    Celine Hoh, Ida Shinder, Kuan-Hao Chao, Ales Varabyou, Mihaela Pertea

    GenesJournal

    DOIPDFCode
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    BibTeX source

    @article{hoh2026splicecov,
  title   = {{SpliceCOV}: Supervised Filtering of {RNA-Seq}-Derived Transcript Features Improves Transcriptome Assembly},
  author  = {Hoh, Celine and Shinder, Ida and Chao, Kuan-Hao and Varabyou, Ales and Pertea, Mihaela},
  journal = {Genes},
  volume  = {17},
  number  = {10},
  pages   = {1307},
  year    = {2026},
  doi     = {10.3390/genes17101307},
  url     = {https://www.mdpi.com/2073-4425/17/10/1307}
}

  2. A unified framework for quantitative splicing and transcript prediction

    Full author list

    Kishore Jaganathan*†, Jianbin Chen†, Xin Liu†, Yan Zhang†, Yujin Kim, Abhimanyu Banerjee, Petko P. Fiziev, Naomi Wilcox, Ibrahim I. Taskiran, Yichao Cai, Emilie M. Wigdor, Guo-Liang Chew, Grace Png, Jeremy F. McRae, Aniketh Janardhan Reddy, Kuan-Hao Chao, Rami Mehio, Stephan J. Sanders, Kyle Kai-How Farh*

    bioRxivPreprint

    DOIPDFCodeDocsModelsNewsData
    Cite

    BibTeX source

    @article{jaganathan2026spliceai2,
  title   = {A unified framework for quantitative splicing and transcript prediction},
  author  = {Jaganathan, Kishore and Chen, Jianbin and Liu, Xin and Zhang, Yan and Kim, Yujin and Banerjee, Abhimanyu and Fiziev, Petko P. and Wilcox, Naomi and Taskiran, Ibrahim I. and Cai, Yichao and Wigdor, Emilie M. and Chew, Guo-Liang and Png, Grace and McRae, Jeremy F. and Reddy, Aniketh Janardhan and Chao, Kuan-Hao and Mehio, Rami and Sanders, Stephan J. and Farh, Kyle Kai-How},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.10.08.757673},
  url     = {https://www.biorxiv.org/content/10.64898/2026.10.08.757673v1}
}

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

    Full author list

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

    eLifePreprint

    DOIbioRxivCodeDocsLabSlidesTalkDataBlog
    Cite

    BibTeX source

    @article{chao2026shorkie,
  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 = {eLife},
  year    = {2026},
  doi     = {10.7554/eLife.112217.1},
  note    = {Reviewed preprint. First posted on bioRxiv: 10.1101/2025.09.19.677475}
}

  4. A complete diploid human genome benchmark for personalized genomics

    Full author list

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

    CellJournal

    DOICodeBlog
    Cite

    BibTeX source

    @article{hansen2026diploid,
  title   = {A complete diploid human genome benchmark for personalized genomics},
  author  = {Hansen, Nancy F. and others},
  journal = {Cell},
  volume  = {189},
  number  = {16},
  pages   = {4857--4875.e31},
  year    = {2026},
  doi     = {10.1016/j.cell.2026.06.016}
}

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

    Full author list

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

    Genetics in Medicine OpenConference

    DOI
    Cite

    BibTeX source

    @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}
}

  7. OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species

    Full author list

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

    eLifeJournal

    DOICodeDocsSlidesPosterBlog
    Cite

    BibTeX source

    @article{chao2025openspliceai,
  title   = {OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman 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}
}

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

    Full author list

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

    Science Translational MedicineJournal

    DOI
    Cite

    BibTeX source

    @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}
}

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

    Full author list

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

    Genome ResearchJournal

    DOICodeDocsSlidesPosterTalkBlog
    Cite

    BibTeX source

    @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}
}

  10. Splam: a deep-learning-based splice site predictor that improves spliced alignments

    Full author list

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

    Genome BiologyJournal

    DOICodeDocsSlidesPosterTalkNewsBlog
    Cite

    BibTeX source

    @article{chao2024splam,
  title   = {Splam: a deep-learning-based splice site predictor that improves spliced alignments},
  author  = {Chao, Kuan-Hao and Mao, Alan and Salzberg, Steven L. and Pertea, Mihaela},
  journal = {Genome Biology},
  year    = {2024},
  doi     = {10.1186/s13059-024-03379-4}
}

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

    Full author list

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

    Nature CommunicationsJournal

    DOI
    Cite

    BibTeX source

    @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}
}

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

    Full author list

    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 BiologyJournal

    DOI
    Cite

    BibTeX source

    @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}
}

  13. WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs

    Full author list

    Kuan-Hao Chao*†, Pei-Wei Chen†, Sanjit A. Seshia, Ben Langmead*

    iScienceJournal

    DOICodeSlidesPosterTalkNewsBlog
    Cite

    BibTeX source

    @article{chao2023wgt,
  title   = {WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs},
  author  = {Chao, Kuan-Hao and Chen, Pei-Wei and Seshia, Sanjit A. and Langmead, Ben},
  journal = {iScience},
  year    = {2023},
  doi     = {10.1016/j.isci.2023.107402}
}

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

    Full author list

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

    Briefings in BioinformaticsJournal

    DOI
    Cite

    BibTeX source

    @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}
}

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

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

    G3: Genes, Genomes, GeneticsJournal

    DOICodePosterDataBlog
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    BibTeX source

    @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}
}

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

    Full author list

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

    Genome Biology and EvolutionJournal

    DOICodeDocsPosterBlog
    Cite

    BibTeX source

    @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}
}

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

    Full author list

    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 BioinformaticsJournal

    DOICode
    Cite

    BibTeX source

    @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}
}

View all on Google Scholar →