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

You might also read

Related Articles

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

Sort by

Same author

Restraint of melanoma progression by cells in the local skin environment.

eLife·2026

Same author

Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders.

bioRxiv : the preprint server for biology·2026

Same author

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis.

bioRxiv : the preprint server for biology·2026

Same author

Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.

bioRxiv : the preprint server for biology·2026

Same author

Author Correction: Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nature methods·2026

Same author

Spatial integration of protein and chromosomal states reveals early copy number changes and genotype-associated immune neighborhoods in serous ovarian cancer evolution.

Cancer discovery·2026

Same journal

Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research.

PLoS computational biology·2026

Same journal

Mobility data resolution needed to inform predictive models of spatial epidemic spread from mobile phone data.

PLoS computational biology·2026

Same journal

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.

PLoS computational biology·2026

Same journal

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.

PLoS computational biology·2026

Same journal

Optimized phenotype definitions boost GWAS power.

PLoS computational biology·2026

Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 2, 2026

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Published on: September 7, 2018

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory.

Shu Wang^1,2, Jia-Ren Lin¹, Eduardo D Sontag^1,3

¹Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.

Plos Computational Biology

|December 7, 2019

Summary

This summary is machine-generated.

We introduce Effective Stoichiometric Spaces (ESS) to reconstruct biochemical networks from single-cell data. This method uses toric geometry to map cell data to chemical reaction network structures.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Cortical Actin Flow in T Cells Quantified by Spatio-temporal Image Correlation Spectroscopy of Structured Illumination Microscopy Data

Cortical Actin Flow in T Cells Quantified by Spatio-temporal Image Correlation Spectroscopy of Structured Illumination Microscopy Data

Published on: December 17, 2015

Related Experiment Videos

Last Updated: Jan 2, 2026

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Published on: September 7, 2018

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Cortical Actin Flow in T Cells Quantified by Spatio-temporal Image Correlation Spectroscopy of Structured Illumination Microscopy Data

Cortical Actin Flow in T Cells Quantified by Spatio-temporal Image Correlation Spectroscopy of Structured Illumination Microscopy Data

Published on: December 17, 2015

Area of Science:

Biochemistry
Systems Biology
Computational Biology

Background:

Single-cell studies aim to understand biochemical reactions governing cell fate and state.
Reconstructing biochemical networks from complex single-cell data remains a challenge.

Purpose of the Study:

Introduce Effective Stoichiometric Spaces (ESS) for biochemical network reconstruction.
Leverage toric varieties to analyze single-cell data and infer chemical reaction network (CRN) structure.

Main Methods:

Developed the Effective Stoichiometric Spaces (ESS) concept.
Applied geometric theory of toric varieties to map data covariances to stoichiometric information.
Reframed aspects of CRN theory for enhanced data analysis.

Main Results:

ESS provides a data-driven approach to unravel CRN structure.
Each cell subpopulation is associated with an ESS interpretable via CRN theory.
Successfully processed cytometry and image-based single-cell datasets.

Conclusions:

ESS offers a novel framework for single-cell data analysis in systems biology.
The method facilitates the identification of differences in cell populations, such as responses to kinase inhibitors.
Applicable to data from methods like Fluorescence Activated Cell Sorting (FACS) and multiplex immunofluorescence.