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...

Assessment of Diffusion and Perfusion

Assessment of Diffusion and Perfusion

Understanding and evaluating diffusion and perfusion is critical in assessing a patient's respiratory and circulatory health. These processes play key roles in maintaining the body's internal environment, ensuring that tissues receive adequate oxygen while waste products are efficiently removed.
The Role of Diffusion in Respiration
Diffusion is the process by which molecules move from an area of higher concentration to an area of lower concentration. In the respiratory system, this...

You might also read

Related Articles

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

Sort by

Same author

Optimal gene panel selection for targeted spatial transcriptomics experiments.

Nucleic acids research·2026

Same author

Pseudo-time reconstruction for analyzing transmission direction in COVID-19 contact-tracing data.

Epidemics·2026

Same author

Prognostic value of plasma cortisol concentration in dogs with congestive heart failure.

Journal of veterinary internal medicine·2026

Same author

Analyzing Complex Educational Data: A Data Analytic Framework for Integrating Structured and Unstructured Eye-Tracking Data.

Psychometrika·2026

Same author

Large language models for bioinformatics.

Quantitative biology (Beijing, China)·2026

Same author

Multicenter Retrospective Evaluation of the Use of Lyophilized Platelets in Dogs.

Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)·2026

Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026

Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026

Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026

Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026

Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026

Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 10, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process.

Jiazhang Cai¹, Yongkai Chen², Luyang Fang¹

¹Department of Statistics, University of Georgia, 310 Herty Drive, Athens, 30602, GA, United States.

Biorxiv : the Preprint Server for Biology

|November 24, 2025

Summary

This summary is machine-generated.

We developed SpaDiff, a new method to fix spot-swapping in spatial transcriptomics. This diffusion-based approach improves gene expression data accuracy and spatial analysis for better biological insights.

Keywords:

Data Denoising Diffusion Model Score Function Sequence-based Spatial Transcriptomics

More Related Videos

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

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

Related Experiment Videos

Last Updated: Jan 10, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

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

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Spatial transcriptomics offers gene expression analysis with spatial resolution.
Spot-swapping, or RNA molecule drift, introduces noise and reduces spatial specificity in this data.
Accurate spatial information is crucial for understanding tissue architecture and cellular interactions.

Purpose of the Study:

To introduce SpaDiff, a novel denoising method for spatial transcriptomics data.
To address the challenge of spot-swapping and its impact on data integrity.
To improve the accuracy of downstream spatial analysis.

Main Methods:

SpaDiff models spot-swapping as a diffusion process.
The method simulates RNA molecule displacement and reverses it to restore original positions.
Molecular counts are preserved throughout the denoising process.

Main Results:

SpaDiff effectively enhances the spatial specificity of gene expression.
The method improves overall data integrity by reducing noise from spot-swapping.
Evaluations on simulated and real data confirm SpaDiff's efficacy.

Conclusions:

SpaDiff is a powerful tool for correcting spot-swapping in spatial transcriptomics.
The enhanced data quality supports more accurate downstream analyses, including clustering and spatial domain identification.
This method advances the reliable application of spatial transcriptomics in biological research.