@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}
}
@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}
}
@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}
}
@phdthesis{chao2025decoding,
title = {Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning},
author = {Chao, Kuan-Hao},
school = {Johns Hopkins University},
year = {2025}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
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*
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
