hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …
functional units based on tightly regulated interactions between distinct molecules, cells …
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
Motivation The advent of long-read sequencing technologies has increased demand for the
visualization and interpretation of transcripts. However, tools that perform such visualizations …
visualization and interpretation of transcripts. However, tools that perform such visualizations …
Accurate isoform discovery with IsoQuant using long reads
Annotating newly sequenced genomes and determining alternative isoforms from long-read
RNA data are complex and incompletely solved problems. Here we present IsoQuant—a …
RNA data are complex and incompletely solved problems. Here we present IsoQuant—a …
Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease
Aberrant splicing underlies many human diseases, including cancer, cardiovascular
diseases and neurological disorders. Genome-wide map** of splicing quantitative trait …
diseases and neurological disorders. Genome-wide map** of splicing quantitative trait …
Enhancing novel isoform discovery: leveraging nanopore long-read sequencing and machine learning approaches
K Santucci, Y Cheng, SM Xu… - Briefings in Functional …, 2024 - academic.oup.com
Long-read sequencing technologies can capture entire RNA transcripts in a single
sequencing read, reducing the ambiguity in constructing and quantifying transcript models in …
sequencing read, reducing the ambiguity in constructing and quantifying transcript models in …
Map** and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
The rise in throughput and quality of long-read sequencing should allow unambiguous
identification of full-length transcript isoforms. However, its application to single-cell RNA …
identification of full-length transcript isoforms. However, its application to single-cell RNA …
High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly-regulated interactions between distinct molecules, cells …
functional units based on tightly-regulated interactions between distinct molecules, cells …
Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure
Expansion of the glutamine tract (poly-Q) in the protein huntingtin (HTT) causes the
neurodegenerative disorder Huntington's disease (HD). Emerging evidence suggests that …
neurodegenerative disorder Huntington's disease (HD). Emerging evidence suggests that …
IsoTools: a flexible workflow for long-read transcriptome sequencing analysis
Motivation Long-read transcriptome sequencing (LRTS) has the potential to enhance our
understanding of alternative splicing and the complexity of this process requires the use of …
understanding of alternative splicing and the complexity of this process requires the use of …
[HTML][HTML] The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity
F Reese, B Williams, G Balderrama-Gutierrez… - bioRxiv, 2023 - ncbi.nlm.nih.gov
The majority of mammalian genes encode multiple transcript isoforms that result from
differential promoter use, changes in exonic splicing, and alternative 3'end choice. Detecting …
differential promoter use, changes in exonic splicing, and alternative 3'end choice. Detecting …