Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

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...

Ribosome Profiling

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...

Regulated mRNA Transport

Regulated mRNA Transport

Real Time RT-PCR

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...

Alternative RNA Splicing

Alternative RNA Splicing

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Efficient and Tidy Manipulation of Annotated Matrix Data with plyxp.

bioRxiv : the preprint server for biology·2026

Same author

The IGVF catalog-from genetic variation to function.

Nucleic acids research·2025

Same author

Identifying Locally Recurrent Versus Second Primary Breast Cancer: Genomic Versus Clinical Criteria from Carolina Breast Cancer Study Phase III.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology·2025

Same author

Taming the reference genome jungle: the refget sequence collection standard.

bioRxiv : the preprint server for biology·2025

Same author

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.

bioRxiv : the preprint server for biology·2025

Same author

Tree-based differential testing using inferential uncertainty for RNA-seq.

Genome research·2025

Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026

Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026

Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026

Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026

Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026

Same journal

3D pathology-guided microdissection.

Nature methods·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 26, 2025

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Context-aware transcript quantification from long-read RNA-seq data with Bambu.

Ying Chen¹, Andre Sim¹, Yuk Kei Wan^1,2

¹Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.

|June 12, 2023

Summary

This summary is machine-generated.

Bambu, a new method using long-read RNA sequencing, offers precise transcript quantification by discovering novel transcripts specific to experimental contexts. This approach improves accuracy for both known and novel transcripts, overcoming limitations of static annotations.

More Related Videos

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Related Experiment Videos

Last Updated: Jul 26, 2025

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Area of Science:

Transcriptomics
Bioinformatics
Computational Biology

Background:

Current transcript quantification methods rely on static reference annotations, which are often incomplete or contain irrelevant inactive isoforms for specific biological contexts.
The dynamic nature of the transcriptome necessitates context-specific analysis for accurate gene expression profiling.

Purpose of the Study:

To introduce Bambu, a novel machine-learning-based method for transcript discovery and quantification using long-read RNA sequencing.
To enable context-specific transcript quantification by identifying novel transcripts and accurately quantifying known ones.
To improve the precision and sensitivity of transcript discovery compared to existing methods.

Main Methods:

Bambu utilizes long-read RNA sequencing data for transcript discovery.
It employs a machine-learning approach to identify novel transcripts.
Bambu introduces a novel discovery rate for precision-calibrated parameter estimation, replacing arbitrary per-sample thresholds.
The method retains full-length and unique read counts for accurate quantification, even with inactive isoforms.

Main Results:

Bambu achieves higher precision in transcript discovery without sacrificing sensitivity compared to existing methods.
Context-aware transcript annotations generated by Bambu improve quantification accuracy for both novel and known transcripts.
Application of Bambu to human embryonic stem cells demonstrates accurate quantification of isoforms from repetitive retrotransposons (HERVH-LTR7).

Conclusions:

Bambu provides a powerful and accurate method for context-specific transcript quantification using long-read RNA sequencing.
The developed approach enhances the understanding of transcriptomic complexity and gene expression dynamics in a context-dependent manner.
Bambu facilitates detailed analysis of isoform expression, particularly in complex genomic regions like retrotransposons.