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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...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

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Related Experiment Video

Updated: Jul 9, 2026

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture
11:00

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

A dependency-aware deep generative model for inferring RNA velocity from spatial transcriptomics.

Sishuo Chen1, Liyi Yu1, Peng Jiang1

  • 1School of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, Hubei 430072, China.

Bioinformatics (Oxford, England)
|July 7, 2026
PubMed
Summary
This summary is machine-generated.

We developed spaVelo, a new method for RNA velocity analysis in spatial transcriptomics. It models cell dynamics within tissues, improving predictions of cell state transitions and developmental trajectories.

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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Last Updated: Jul 9, 2026

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture
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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Published on: August 6, 2014

Area of Science:

  • Spatial transcriptomics
  • Computational biology
  • Single-cell analysis

Background:

  • Spatial transcriptomics allows gene expression profiling within tissue context.
  • RNA velocity infers cell dynamics but often ignores spatial information.

Purpose of the Study:

  • To develop a novel RNA velocity method for spatial transcriptomics data.
  • To integrate spatial information into transcriptional dynamics modeling.

Main Methods:

  • Developed spaVelo, a dependency-aware deep generative model.
  • Utilized a spatial-aware variational autoencoder and modulated transcriptional scaling factor.
  • Integrated spatial context into RNA velocity inference.

Main Results:

  • spaVelo reconstructs biologically coherent velocity fields and developmental trajectories.
  • The method effectively models spot-specific and heterogeneous cellular dynamics.
  • spaVelo outperforms existing methods, especially in complex tissues.

Conclusions:

  • spaVelo advances RNA velocity analysis for spatial transcriptomics.
  • The model captures spatially organized cellular state transitions.
  • spaVelo provides a powerful tool for studying tissue development and dynamics.