Jove
Visualize
Contact Us

Related Concept Videos

Non-equilibrium in the Cell01:16

Non-equilibrium in the Cell

4.9K
An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system...
4.9K

You might also read

Related Articles

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

Sort by
Same author

High-purity stem cell-derived β-cells recapitulate key transcriptional and functional features of human islets.

bioRxiv : the preprint server for biology·2026
Same author

Clonal biases dictate availability of colonic cancer driver mutations for transformation.

Nature communications·2026
Same author

Dlk1 is a novel adrenocortical stem/progenitor cell marker that predicts malignancy in adrenocortical carcinoma.

Cancer communications (London, England)·2025
Same author

Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.

EMBO reports·2025
Same author

ccfDNA analysis for the classification of adrenocortical adenomas.

Journal of endocrinological investigation·2025
Same author

Cellular landscape of adrenocortical carcinoma at single-nuclei resolution.

Molecular and cellular endocrinology·2024
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Oct 13, 2025

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.0K

Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm.

David S Tourigny1, Arthur P Goldberg2, Jonathan R Karr2

  • 1Irving Institute for Cancer Dynamics, Columbia University, New York, New York; School of Mathematics, University of Birmingham, Birmingham, United Kingdom.

Biophysical Journal
|November 10, 2021
PubMed
Summary

We developed a computational framework, stochastic simulation algorithm with flux-balance analysis embedded (SSA-FBA), to simulate single-cell metabolism. This method helps understand metabolic heterogeneity and its impact on diseases like cancer.

More Related Videos

Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes
06:26

Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes

Published on: March 28, 2025

472
A Method for Measuring Metabolism in Sorted Subpopulations of Complex Cell Communities Using Stable Isotope Tracing
07:41

A Method for Measuring Metabolism in Sorted Subpopulations of Complex Cell Communities Using Stable Isotope Tracing

Published on: February 4, 2017

8.6K

Related Experiment Videos

Last Updated: Oct 13, 2025

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.0K
Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes
06:26

Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes

Published on: March 28, 2025

472
A Method for Measuring Metabolism in Sorted Subpopulations of Complex Cell Communities Using Stable Isotope Tracing
07:41

A Method for Measuring Metabolism in Sorted Subpopulations of Complex Cell Communities Using Stable Isotope Tracing

Published on: February 4, 2017

8.6K

Area of Science:

  • Systems biology
  • Metabolic modeling
  • Single-cell analysis

Background:

  • Gene expression stochasticity drives metabolic heterogeneity in cell populations.
  • This heterogeneity impacts microbial drug tolerance and cancer treatment.
  • Experimental characterization of single-cell metabolism remains challenging.

Purpose of the Study:

  • To bridge the gap between single-cell biology and genome-scale metabolic characterization.
  • To develop a computational framework for simulating single-cell metabolism.
  • To enable a systems understanding of metabolic dynamics at the single-cell level.

Main Methods:

  • Developed stochastic simulation algorithm with flux-balance analysis embedded (SSA-FBA).
  • Integrated genome-scale metabolic models with gene expression and reaction rate data.
  • Extended constraint-based modeling to the single-cell regime.
  • Created an efficient SSA-FBA implementation leveraging model topology.

Main Results:

  • SSA-FBA enables simulation of stochastic single-cell metabolic dynamics.
  • The framework reduces computational cost through efficient implementation.
  • Demonstrated SSA-FBA's utility in a case study with Mycoplasma pneumoniae.

Conclusions:

  • SSA-FBA provides a novel computational approach for studying single-cell metabolism.
  • The method facilitates understanding the role of stochasticity in metabolic heterogeneity.
  • This framework advances systems biology and has implications for disease research.