Multilayer network modeling of integrated biological systems: Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

  title={Multilayer network modeling of integrated biological systems: Comment on "Network science of biological systems at different scales: A review" by Gosak et al.},
  author={Manlio De Domenico},
  journal={Physics of Life Reviews},

A propagation-based seed-centric local community detection for multilayer environment: The case study of colon adenocarcinoma

A novel method based on the information cascade concept, called PLCDM, is developed and applied on a biological two-layer network of Colon Adenocarcinoma, reconstructed from transcriptomic and post-transcriptomic datasets, and assessed the output modules.

Visual Analysis of Multilayer Networks

Abstract The emergence of multilayer networks as a concept from the field of complex systems provides many new opportunities for the visualization of network complexity, and has also raised many ne...

CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19

CovMulNet19 can be suitably used for network medicine analysis, as a valuable tool for exploring drug repurposing while accounting for the intervening multidimensional factors, from molecular interactions to symptoms.

Construction, comparison and evolution of networks in life sciences and other disciplines

This work will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed, and envision how borrowing ideas from these disciplines could enrich the future of life science research.

Multilayer Flows in Molecular Networks Identify Biological Modules in the Human Proteome

This study proposes one measure, grounded on information theory, to find the optimal value of the relax rate characterizing Multiplex Infomap, and uses this measure to identify the most reliable meso-scale functional organization in the human protein-protein interaction multiplex network and compares the observed clusters against a collection of independently annotated gene sets from the Molecular Signatures Database.

Epigene Networks: Theory, Models, and Experiment

The article describes a concept of epigene networks that attempts to clarify the phenomenon of heredity and presents the results of long-term studies of the control gene and epigene networks in which



Methods for the integration of multi-omics data: mathematical aspects

A review of the most advanced strategies for integrating multi-omics datasets, focusing on mathematical and methodological aspects, to draw a more complete and accurate picture of the dynamics of molecular systems.

The interdependent network of gene regulation and metabolism is robust where it needs to be

A statistical framework for interdependent networks is applied to the interdependent network of gene regulation and metabolism for the model organism Escherichia coli, and it is found to be sensitive to gene and protein perturbations but robust against metabolic changes.

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

This work presents a novel approach to combining multiple functional association networks where network weights are simultaneously optimized on sets of related function categories, and shows that it produces composite networks with improved function prediction accuracy.

Unbiased community detection for correlation matrices

Multilayer modeling and analysis of human brain networks.

This work will review the main achievements obtained from interdisciplinary research based on magnetic resonance imaging and establish de facto, the birth of multilayer network analysis and modeling of the human brain.

Structure-function clustering in multiplex brain networks

This letter explores important structure-function relations in the Macaque cortical network by modelling it as a duplex network that comprises an anatomical layer, describing the known network topology of the Macaques, and a functional layer derived from simulated neural activity.

Selective impairment of hippocampus and posterior hub areas in Alzheimer’s disease: an MEG-based multiplex network study

This multiplex network study provides an effective framework to integrate the frequency-specific networks with different frequency patterns and reveal neuropathological mechanism of hub disruption in Alzheimer's disease.

Improving Validation Practices in “Omics” Research

“Omics” research poses acute challenges regarding how to enhance validation practices and eventually the utility of this rich information. Several strategies may be useful, including routine

The integrated disease network.

The approach not only identified well-established connections between Crohn's disease and other diseases, but also revealed new, interesting connections consistent with emerging literature, making this a powerful approach for exploring connections between diseases.

Brain network dynamics are hierarchically organized in time

The important question of the temporal organization of large-scale brain networks is addressed, finding that the spontaneous transitions between networks of interacting brain areas are predictable and highly organized into a hierarchy of two distinct metastates.