A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.







LiftOn, my new genome lift-over tool, is selected as a talk at RECOMB-Seq 2024. Friends, see you in Boston, MA – preprint coming soon!

LiftOn is selected for a 20-min talk at the ISMB 2024,General Computational COSI track. Preprint is available. See you in Montreal, Canada!






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*

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sangeranalyseR: 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*

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CHESS 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

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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*

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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*

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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*

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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*

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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*

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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