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

Search research articles

Related Experiment Video

Updated: Dec 2, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Depicting combinatorial complexity with the molecular interaction map notation.

Kurt W Kohn¹, Mirit I Aladjem, Sohyoung Kim

¹Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. kohnk@dc37a.nci.nih.gov

Molecular Systems Biology

|October 4, 2006

Summary

This summary is machine-generated.

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

Polycomb-mediated 3D-genome organization controls replication timing.

Science advances·2026

Same author

Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation.

bioRxiv : the preprint server for biology·2026

Same author

CROCHET: a versatile pipeline for automated analysis and visual atlas creation from single-cell spatialomic data.

bioRxiv : the preprint server for biology·2026

Same author

Replication origin flexibility: a tool to mitigate the hazards of excess replication.

Trends in genetics : TIG·2026

Same author

Microhomology-mediated end joining acts directly on replication forks to repair single-ended double-strand breaks.

Molecular cell·2026

Same author

Impact of Tau overexpression on DNA replication dynamics in centromeres of human neural progenitor cells.

iScience·2026

Same journal

Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models.

Molecular systems biology·2026

Same journal

Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains.

Molecular systems biology·2026

Same journal

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients.

Molecular systems biology·2026

Same journal

Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro.

Molecular systems biology·2026

Same journal

ParTIpy: a scalable framework for archetypal analysis and Pareto task inference.

Molecular systems biology·2026

Same journal

Quantitative interactome mapping of skeletal muscle insulin resistance.

Molecular systems biology·2026

See all related articles

Scientists developed a new standard notation, the Molecular Interaction Map (MIM) notation, to clearly diagram complex biological networks like protein modifications and signaling pathways. This system aids understanding and communication in cell and systems biology.

Area of Science:

Systems Biology
Molecular Biology
Bioinformatics

Background:

Bioregulatory networks are complex, involving intricate protein modifications and multiprotein complexes.
Existing diagrammatic methods struggle to represent this complexity unambiguously.
A standardized graphical language is needed for clear communication and analysis in systems biology.

Purpose of the Study:

To introduce and demonstrate the utility of the Molecular Interaction Map (MIM) notation.
To provide a standard notation for diagrams of bioregulatory networks, analogous to electronic circuit diagrams.
To address the challenges of representing complex biological interactions, including protein modifications and combinatorial complexity.

Main Methods:

Design and proposal of the Molecular Interaction Map (MIM) notation.

More Related Videos

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

Related Experiment Videos

Last Updated: Dec 2, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

Application of MIM notation to three types of biological diagrams: explicit pathway models, heuristic maps, and combinatorially complex models.

Comparative analysis of MIM diagrams with existing representations of the epidermal growth factor receptor (EGFR) signaling network.

Main Results:

The MIM notation effectively represents complex biological networks, including signaling pathways like that of the epidermal growth factor receptor (EGFR) family.
MIM diagrams facilitate the representation of specific pathway models for computer simulation.
The notation aids in organizing information for heuristic maps and visualizing combinatorially complex models.

Conclusions:

The Molecular Interaction Map (MIM) notation offers a clear, unambiguous graphical language for representing complex bioregulatory networks.
MIM notation enhances the understanding and communication of molecular interactions and pathways in cell and systems biology.
Adoption of MIM notation can improve the standardization and clarity of biological network diagrams.