Kuan-Hao Chao
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Explore the profile of Kuan-Hao Chao including associated specialties, affiliations and a list of published articles.
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11
Citations
54
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Recent Articles
1.
Chao K, Heinz J, Hoh C, Mao A, Shumate A, Pertea M, et al.
Genome Res
. 2024 Dec;
35(2):311-325.
PMID: 39730188
As the number and variety of assembled genomes continue to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge,...
2.
Chao K, Mao A, Salzberg S, Pertea M
Genome Biol
. 2024 Sep;
25(1):243.
PMID: 39285451
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. We describe Splam, a novel method for predicting splice junctions in...
3.
Chao K, Heinz J, Hoh C, Mao A, Shumate A, Pertea M, et al.
bioRxiv
. 2024 May;
PMID: 38798552
As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge,...
4.
Shinder I, Hu R, Ji H, Chao K, Pertea M
Nat Commun
. 2023 Nov;
14(1):7223.
PMID: 37940654
Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the...
5.
Varabyou A, Sommer M, Erdogdu B, Shinder I, Minkin I, Chao K, et al.
Genome Biol
. 2023 Oct;
24(1):249.
PMID: 37904256
CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data...
6.
Chao K, Chen P, Seshia S, Langmead B
iScience
. 2023 Aug;
26(8):107402.
PMID: 37575187
A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped...
7.
Chao K, Mao A, Salzberg S, Pertea M
bioRxiv
. 2023 Aug;
PMID: 37546880
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. Here we describe Splam, a novel method for predicting splice junctions...
8.
Chen Y, Chao K, Wong J, Liu C, Leu J, Tsai H
Brief Bioinform
. 2023 Jun;
24(4).
PMID: 37328692
Protein complexes are key functional units in cellular processes. High-throughput techniques, such as co-fractionation coupled with mass spectrometry (CF-MS), have advanced protein complex studies by enabling global interactome inference. However,...
9.
Chao K, Zimin A, Pertea M, Salzberg S
G3 (Bethesda)
. 2023 Jan;
13(3).
PMID: 36630290
We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed T2T-CHM13...
10.
Chao K, Barton K, Palmer S, Lanfear R
Genome Biol Evol
. 2021 Feb;
13(3).
PMID: 33591316
sangeranalyseR is feature-rich, free, and open-source R package for processing Sanger sequencing data. It allows users to go from loading reads to saving aligned contigs in a few lines of...