Themed collection Molecular BioSystems Network Biology

The guest editors introduce the Network Biology themed issue.

Contextualizing relevant information to construct a network that represents a given biological process presents a fundamental challenge in the network science of biology.

Mathematical modelling is increasingly becoming an indispensable tool for the study of cellular processes, allowing their analysis in a systematic and comprehensive manner.

This review introduces quadruplex motifs in roles supporting epigenetic events, in determining evolutionary selection and as determinants of quantitative trait loci.

An overview of how screening or selection of combinatorial libraries can be used to build synthetic gene circuits.

Investigating the bioenergetic activity of the mitochondrial and algal metabolisms using optimization methods.

This manuscript presents predictive logical models for the nine main signalling pathways recurrently used in Drosophila development.

The protein structure network [PSN] profile clearly distinguishes the native [black] from the non-native [red, pink] models.

A mathematical tool to compare topology and dynamics of six bacterial networks with equivalent homogeneous, scale-free and geometric random networks.

Here we present a novel statistical methodology that allows us to analyze gene expression data that have been collected from a number of different cases or conditions in a unified framework.

Using manually curated signalling models of the IIS/TOR pathways, transcriptional feedback is shown to modulate ageing in worms and flies.

Increased availability of quantitative -omics data from the same biological source allows integrative studies, yielding functional conclusions on cell physiology.

Many biological networks have been reconstructed, leading to the question of how to interpret their structural features.

Genomic data of several organisms have revealed that domain families in multi-domain proteins have diverse tethering preferences.

Protein-protein interactions can also be represented into networks.

Network approaches applied to microarray, RNA-seq and proteomics data reveal that stress induces modularization in co-expression and protein interaction networks.

Finding the targets of a drug: a matter of looking into the neighborhood.

The dcGOnet is a functional domain network that can be globally explored for linking together diseases, drugs and cross-species phenotypes.

When selection is strong and mutations are rare, evolution can be thought of as an uphill trajectory in a rugged fitness landscape.

The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information.

Pearson and partial correlation analysis was used to build networks to explore the central role of daf-2 in regulating fatty acid and amino acid metabolism in Caenorhabditis elegans.

MGclus is a new algorithm designed to detect network modules by accounting for shared network neighbors in large scale biological interaction networks.

A significant association was found between phosphorylation, disorder and binding for serine and threonine in human protein complexes.

iPoint attains very compact and accurate solutions that outperform previous network inference algorithms.

Molecular signatures are a powerful approach to characterize novel small molecules and derivatized small molecule libraries.

PheNetic, a method to use interaction networks for the interpretation of in-house generated omics data.