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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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Related Experiment Video

Updated: May 29, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
11:04

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly.

Wei Li1, Jianxing Feng, Tao Jiang

  • 1Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92507, USA. liw@cs.ucr.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|September 29, 2011
PubMed
Summary
This summary is machine-generated.

IsoLasso is a new tool for transcriptome assembly using RNA-Seq data. It accurately reconstructs messenger RNA (mRNA) transcripts by balancing prediction accuracy, interpretation minimization, and completeness for improved biological research.

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Last Updated: May 29, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

Area of Science:

  • Computational Biology
  • Genomics
  • Bioinformatics

Background:

  • Second-generation sequencing (RNA-Seq) generates massive datasets, presenting computational challenges.
  • Transcriptome assembly aims to reconstruct full-length mRNA transcripts from millions of short RNA-Seq reads.

Purpose of the Study:

  • To develop a novel RNA-Seq based transcriptome assembly tool.
  • To address key objectives: maximizing prediction accuracy, minimizing interpretation, and maximizing completeness of assembled transcripts.

Main Methods:

  • Introduced IsoLasso, a tool based on the LASSO (Least Absolute Shrinkage and Selection Operator) algorithm.
  • Incorporated additional constraints into the LASSO quadratic programming for enhanced completeness.
  • Evaluated performance using simulated and real RNA-Seq datasets.

Main Results:

  • IsoLasso effectively balances prediction accuracy and interpretation minimization.
  • The tool achieves a high degree of completeness in assembled transcripts.
  • Experiments demonstrate IsoLasso's superior sensitivity and precision compared to existing state-of-the-art tools.

Conclusions:

  • IsoLasso offers a significant advancement in RNA-Seq based transcriptome assembly.
  • The tool provides a robust solution for reconstructing mRNA transcripts with high accuracy and completeness.
  • IsoLasso enhances the analysis of complex transcriptomes from next-generation sequencing data.