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Updated: Jun 21, 2026

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

Molecular networks and system-level properties.

Lilia Alberghina¹, Thomas Höfer, Marco Vanoni

¹Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy. lilia.alberghina@unimib.it

Journal of Biotechnology

|July 21, 2009

Summary

Molecular systems biology reveals how network interactions generate biological functions. Modulating interaction strength offers a tunable way to regulate processes and enhance robustness, crucial for drug discovery.

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A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

Published on: October 6, 2019

Area of Science:

Molecular systems biology
Systems biology
Biochemistry

Background:

Biological functions emerge from complex molecular networks (genes, proteins, metabolites).
Network robustness against perturbations relies on permissible ranges of biochemical parameters.
Understanding these networks is key to deciphering cellular processes.

Purpose of the Study:

To investigate the relationship between network structure, emergent properties, and robustness.
To demonstrate how interaction strength modulation affects biological functions.
To explore the role of multi-site phosphorylation in cell cycle timing.

Main Methods:

Utilized the yeast G(1)-to-S transition network as a model system.
Employed molecular analysis, modeling, and simulation.
Analyzed changes in emergent properties by altering interaction strengths and phosphorylation states.

Main Results:

Sophisticated relationships exist between network structure, emergent properties, and robustness.
Altering interaction strength, not just expression levels, generates different emergent properties.
Multi-site protein phosphorylation modules contribute to robust cell cycle timing, exemplified by DNA replication onset.

Conclusions:

Modulating interaction strength is an efficient, tunable mechanism for regulating biological functions.
Principles derived from network analysis offer insights for drug discovery.
Systems biology approaches provide a framework for understanding cellular robustness and regulation.