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Themed collection Molecular BioSystems Network Biology

26 items
Editorial

Network Biology editorial 2013

The guest editors introduce the Network Biology themed issue.

Graphical abstract: Network Biology editorial 2013
From the themed collection: Molecular BioSystems Network Biology
Paper

iPoint: an integer programming based algorithm for inferring protein subnetworks

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

Graphical abstract: iPoint: an integer programming based algorithm for inferring protein subnetworks
From the themed collection: Molecular BioSystems Network Biology
Paper

Finding the targets of a drug by integration of gene expression data with a protein interaction network

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

Graphical abstract: Finding the targets of a drug by integration of gene expression data with a protein interaction network
From the themed collection: Molecular BioSystems Network Biology
Paper

Tethering preferences of domain families co-occurring in multi-domain proteins

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

Graphical abstract: Tethering preferences of domain families co-occurring in multi-domain proteins
From the themed collection: Molecular BioSystems Network Biology
Paper

A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks

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.

Graphical abstract: A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks
From the themed collection: Molecular BioSystems Network Biology
Paper

Structural comparison of biological networks based on dominant vertices

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

Graphical abstract: Structural comparison of biological networks based on dominant vertices
From the themed collection: Molecular BioSystems Network Biology
Paper

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies

Protein-protein interactions can also be represented into networks.

Graphical abstract: Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies
From the themed collection: Molecular BioSystems Network Biology
Review Article

Social networks to biological networks: systems biology of Mycobacterium tuberculosis

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

Graphical abstract: Social networks to biological networks: systems biology of Mycobacterium tuberculosis
From the themed collection: Molecular BioSystems Network Biology
Open Access Review Article

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

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

Graphical abstract: Building synthetic gene circuits from combinatorial libraries: screening and selection strategies
Paper

Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes

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

Graphical abstract: Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes
From the themed collection: Molecular BioSystems Network Biology
Open Access Paper

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster

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

Graphical abstract: Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster
From the themed collection: Molecular BioSystems Network Biology
Paper

Regulation of proteinprotein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes

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

Graphical abstract: Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes
From the themed collection: Molecular BioSystems Network Biology
Method

PheNetic: network-based interpretation of unstructured gene lists in E. coli

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

Graphical abstract: PheNetic: network-based interpretation of unstructured gene lists in E. coli
From the themed collection: Molecular BioSystems Network Biology
Review Article

Emerging trends in G-quadruplex biology – role in epigenetic and evolutionary events

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

Graphical abstract: Emerging trends in G-quadruplex biology – role in epigenetic and evolutionary events
Paper

A disease-drug-phenotype matrix inferred by walking on a functional domain network

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

Graphical abstract: A disease-drug-phenotype matrix inferred by walking on a functional domain network
From the themed collection: Molecular BioSystems Network Biology
Paper

DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle

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

Graphical abstract: DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle
From the themed collection: Molecular BioSystems Network Biology
Open Access Paper

Stress induces remodelling of yeast interaction and co-expression networks

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

Graphical abstract: Stress induces remodelling of yeast interaction and co-expression networks
From the themed collection: Molecular BioSystems Network Biology
Open Access Review Article

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

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

Graphical abstract: Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
From the themed collection: Molecular BioSystems Network Biology
Open Access Paper

Logical modelling of Drosophila signalling pathways

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

Graphical abstract: Logical modelling of Drosophila signalling pathways
From the themed collection: Molecular BioSystems Network Biology
Paper

Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae

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

Graphical abstract: Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae
From the themed collection: Molecular BioSystems Network Biology
Paper

Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network

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

Graphical abstract: Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network
From the themed collection: Molecular BioSystems Network Biology
Paper

Graphical modelling of molecular networks underlying sporadic inclusion body myositis

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.

Graphical abstract: Graphical modelling of molecular networks underlying sporadic inclusion body myositis
From the themed collection: Molecular BioSystems Network Biology
Paper

Predicting cancer drug mechanisms of action using molecular network signatures

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

Graphical abstract: Predicting cancer drug mechanisms of action using molecular network signatures
From the themed collection: Molecular BioSystems Network Biology
Paper

MGclus: network clustering employing shared neighbors

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

Graphical abstract: MGclus: network clustering employing shared neighbors
From the themed collection: Molecular BioSystems Network Biology
Paper

Network properties of decoys and CASP predicted models: a comparison with native protein structures

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

Graphical abstract: Network properties of decoys and CASP predicted models: a comparison with native protein structures
From the themed collection: Molecular BioSystems Network Biology
Paper

A design automation framework for computational bioenergetics in biological networks

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

Graphical abstract: A design automation framework for computational bioenergetics in biological networks
From the themed collection: Molecular BioSystems Network Biology
26 items

About this collection

Molecular BioSystems brings together cutting-edge research addressing the many and varied aspects of Network Biology in this themed web collection. This collection of articles includes reviews and papers from a themed issue on Network Biology, guest edited by Edward Marcotte, Charles Boone, M. Madan Babu and Anne-Claude Gavin.

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