-
Article
Open AccessSystem-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution
Muscular dystrophies (MDs) are inherited genetic diseases causing weakness and degeneration of muscles. The distribution of muscle weakness differs between MDs, involving distal muscles or proximal muscles. Wh...
-
Article
Open AccessRandom walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond
Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks...
-
Article
Open Accessorsum: a Python package for filtering and comparing enrichment analyses using a simple principle
Enrichment analyses are widely applied to investigate lists of genes of interest. However, such analyses often result in long lists of annotation terms with high redundancy, making the interpretation and repor...
-
Article
Open AccessUniversal multilayer network exploration by random walk with restart
The amount and variety of data have been increasing drastically for several years. These data are often represented as networks and explored with approaches arising from network theory. Recent years have witne...
-
Article
Open AccessMultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach
Network embedding approaches are gaining momentum to analyse a large variety of networks. Indeed, these approaches have demonstrated their effectiveness in tasks such as community detection, node classificatio...
-
Article
Open AccessBenchmarking joint multi-omics dimensionality reduction approaches for the study of cancer
High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality ...
-
Article
Open AccessInterpreting molecular similarity between patients as a determinant of disease comorbidity relationships
Comorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential molecular factors leading to the emergence of a spec...
-
Article
Open AccessTranscriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also be...
-
Article
Open AccessA molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer
Epidemiological studies indicate that patients suffering from Alzheimer’s disease have a lower risk of develo** lung cancer, and suggest a higher risk of develo** glioblastoma. Here we explore the molecula...
-
Article
Open AccessThe gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms
The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via cholecystokinin receptors CCK1R and CCK2R respectively. Gastrin, a central regulator of gastric acid secre...
-
Protocol
Network Analysis and Protein Function Prediction with the PRODISTIN Web Site
Interactions between macromolecules are deciphered to gain information about biological processes and protein function. This information is hidden in large interaction networks, yet very complicated to dissect...
-
Article
Open AccessExtending pathways and processes using molecular interaction networks to analyse cancer genome data
Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. Howev...
-
Article
Translational disease interpretation with molecular networks
Molecular networks are being used to reconcile genotypes and phenotypes by integrating medical information. In this context, networks will be instrumental for the interpretation of disease at the personalized ...
-
Article
Open AccessDefining a Modular Signalling Network from the Fly Interactome
Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involv...
-
Article
Two local dissimilarity measures for weighted graphs with application to protein interaction networks
We extend the Czekanowski-Dice dissimilarity measure, classically used to cluster the vertices of unweighted graphs, to weighted ones. The first proposed formula corresponds to edges weighted by a probability ...
-
Article
Open AccessA scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network
Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of actual sequences. This only re...
-
Chapter
The Use of Protein—protein Interaction Networks for Genome Wide Protein Function Comparisons and Predictions
The concept of protein function is widely used by biologists. However, the means of the concept and its understanding can vary largely depending on the functional level under consideration (molecular, cellular...
