Combining DNA and protein alignments to improve genome annotation with LiftOn
bioRxiv, May 2024
Kuan-Hao Chao*, Jakob M. Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, and Steven L. Salzberg*
PDF Cite Code Documentation Poster 
đź“” Publications
PDF Cite Code Documentation Poster Splam: a deep-learning-based splice site predictor that improves spliced alignments
bioRxiv, Aug 2023
Kuan-Hao Chao*, Alan Mao, Steven L Salzberg, Mihaela Pertea*
PDF Cite Code Documentation Poster WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
iScience, Jul 2023
Kuan-Hao Chao*†, Pei-Wei Chen†, Sanjit A. Seshia, Ben Langmead*
PDF Cite Code Documentation Poster A feature extraction free approach for protein interactome inference from co-elution data
Briefings in Bioinformatics, Jun 2023
Yu-Hsin Chen†, Kuan-Hao Chao†, Jin Yung Wong, Chien-Fu Liu, Jun-Yi Leu*, Huai-Kuang Tsai*
PDF Cite Code Documentation EASTR: Correcting systematic alignment errors in multi-exon genes
Nature communications, May 2023
Ida Shinder*, Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea*
PDF Cite Code Documentation The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
G3: Genes, Genomes, Genetics, Jan 2023
Kuan-Hao Chao*, A.V. Zimin, M. Pertea, S.L. Salzberg*
PDF Cite Code Documentation PosterCHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
Genome Biology, Dec 2022
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
PDF Cite Code DocumentationsangeranalyseR: simple and interactive processing of Sanger sequencing data in R
Genome Biology and Evolution(GBE), Feb 2021
Kuan-Hao Chao*, Kirston Barton, Sarah Palmer, and Robert Lanfear*
PDF Cite Code Documentation Poster RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Dec 2019
Kuan-Hao Chao, Y.W. Hsiao, Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, and E.Y. Chuang*
PDF Cite Code Documentation Slides