Research output
Publications
Peer-reviewed papers and preprints in computational biology and machine learning. See Google Scholar for the complete, up-to-date list.
P588: AI and drug discovery with 100 million cells of genome-wide Perturb-seq
DOIBibTeX
@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} }Predicting dynamic expression patterns in budding yeast with a fungal DNA language model
DOICodeDocsSlidesTalkDataBlogBibTeX
@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} }OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species
DOICodeDocsSlidesPosterBlogBibTeX
@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} }SARS-CoV-2 induces neutrophil degranulation and differentiation into myeloid-derived suppressor cells associated with severe COVID-19
DOIBibTeX
@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} }Combining DNA and protein alignments to improve genome annotation with LiftOn
DOICodeDocsSlidesPosterTalkBlogBibTeX
@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} }Splam: a deep-learning-based splice site predictor that improves spliced alignments
DOICodeDocsSlidesPosterTalkNewsBlogBibTeX
@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} }EASTR: Correcting systematic alignment errors in multi-exon genes
DOIBibTeX
@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} }CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
DOIBibTeX
@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} }WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
DOICodeSlidesPosterTalkNewsBlogBibTeX
@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} }A feature extraction free approach for protein interactome inference from co-elution data
DOIBibTeX
@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} }The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
DOICodePosterDataBlogBibTeX
@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} }sangeranalyseR: simple and interactive processing of Sanger sequencing data in R
DOICodeDocsPosterBlogBibTeX
@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} }RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
DOICodeBibTeX
@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} }
No publications match your search.