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Related Experiment Video

Updated: Jun 13, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Towards reliable isoform quantification using RNA-SEQ data.

Brian E Howard¹, Steffen Heber

¹Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA. itsbehoward@hotmail.com

BMC Bioinformatics

|May 5, 2010

Summary

This summary is machine-generated.

This study introduces a new method for quantifying alternative splicing variants using RNA sequencing (RNA-Seq) data. The approach accurately estimates isoform ratios, revealing complex expression patterns independent of overall gene expression levels.

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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Published on: March 7, 2018

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Alternative splicing in eukaryotes generates multiple splice variants from a single gene.
Accurate quantification of splice variants is crucial for understanding gene expression complexity.
RNA sequencing (RNA-Seq) offers a powerful approach for isoform quantification.

Purpose of the Study:

To develop and validate a method for estimating the relative abundance of known splice variants from RNA-Seq data.
To address the challenge of isoform quantification in the transcriptome.
To investigate differential alternative splicing events.

Main Methods:

Utilizes a linear models framework to estimate isoform ratios.
Incorporates RNA-Seq read position non-uniformity into the model.
Applies the method to simulated and real RNA-Seq datasets.

Main Results:

The developed method demonstrates strong performance on both simulated and real data.
Identified alternatively spliced genes with switch-like and subtle expression variations in public RNA-Seq datasets.
Observed that differential alternative splicing events are often independent of overall gene-level differential expression.

Conclusions:

Changes in isoform expression often occur as a continuum, not binary on/off switches.
Alternative splicing variations can be independent of general gene expression changes.
Future functional analyses should consider both gene and isoform expression levels for a comprehensive understanding of the transcriptome.