Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Kuan-Hao Chao"'
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-26 (2024)
Abstract 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 DNA using deep residual convolutional neural networks. Unl
Externí odkaz:
https://doaj.org/article/e21b028c70a6405ea75c6b5fdfa08414
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-12 (2023)
Abstract 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 basic sciences. We reveal that widely used splice-aware
Externí odkaz:
https://doaj.org/article/b8e5aab6833249a59acd5741ac2c1baa
Autor:
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
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-16 (2023)
Abstract 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 and algorithms, machine learning
Externí odkaz:
https://doaj.org/article/20e94c3931d244779a6859df07d6e08f
Publikováno v:
iScience, Vol 26, Iss 8, Pp 107402- (2023)
Summary: 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 pangenome, and it is the foundation for current graph-based pangenom
Externí odkaz:
https://doaj.org/article/2a6484f345c243dab7f5c716214b5895
Publikováno v:
G3: Genes, Genomes, Genetics, Vol 13, Iss 3 (2023)
AbstractWe 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 genome as a guide, yielding a gap-free genome, Han1,
Externí odkaz:
https://doaj.org/article/be1567c99ba84c8dbc35e5837abac91a
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 basic sciences. We have discovered that widely used splice-aware
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7f29618dc8a60cde16550b5bc3123bb8
https://doi.org/10.1101/2023.05.10.540179
https://doi.org/10.1101/2023.05.10.540179
Autor:
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
The original CHESS database of human genes was assembled from nearly 10,000 RNA sequencing experiments in 53 human body sites produced by the Genotype-Tissue Expression (GTEx) project, and then augmented with genes from other databases to yield a com
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::26cb2390259bcb782b79850651274db3
https://doi.org/10.1101/2022.12.21.521274
https://doi.org/10.1101/2022.12.21.521274
SummaryA 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 pangenome, and it is the foundation for current graph-based pangenome
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c8b6c5a7bc2e42b035c602936a03451b
https://doi.org/10.1101/2022.10.15.512390
https://doi.org/10.1101/2022.10.15.512390
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 genome as a guide, yielding a gap-free genome, Han1, containi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::545db0708a97c3b272523e091f1783da
https://doi.org/10.1101/2022.08.08.503226
https://doi.org/10.1101/2022.08.08.503226
Publikováno v:
Genome Biology and Evolution
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 R code by using sensible defaults for most actions. It also pr