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A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product.…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Adaptive networks have been recently introduced in the context of disease propagation on complex networks. They account for the mutual interaction between the network topology and the states of the nodes. Until now, existing models have…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
Various molecular interaction networks have been claimed to follow power-law decay for their global connectivity distribution. It has been proposed that there may be underlying generative models that explain this heavy-tailed behavior by…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…
We characterize the large-sample properties of network modularity in the presence of covariates, under a natural and flexible nonparametric null model. This provides for the first time an objective measure of whether or not a particular…
Distantly-Supervised Named Entity Recognition effectively alleviates the burden of time-consuming and expensive annotation in the supervised setting. But the context-free matching process and the limited coverage of knowledge bases…
Network Medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on…
In cheminformatics, network representations of the space of compounds have been suggested extensively. Among these, the threshold-network consists of nodes representing molecules. In this network representation, two molecules are connected…
Any network studied in the literature is inevitably just a sampled representative of its real-world analogue. Additionally, network sampling is lately often applied to large networks to allow for their faster and more efficient analysis.…
Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades,…
In genomics studies, the investigation of the gene relationship often brings important biological insights. Currently, the large heterogeneous datasets impose new challenges for statisticians because gene relationships are often local. They…
In network science, researchers often use mutual information to understand the difference between network partitions produced by community detection methods. Here we extend the use of mutual information to covers, that is, the cases where a…
In cancer research, profiling studies have been extensively conducted, searching for genes/SNPs associated with prognosis. Cancer is a heterogeneous disease. Examining similarity and difference in the genetic basis of multiple subtypes of…
Community annotation of biological entities with concepts from multiple bio-ontologies has created large and growing repositories of ontology-based annotation data with embedded implicit relationships among orthogonal ontologies.…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
We introduce the concept of communicability angle between a pair of nodes in a graph. We provide strong analytical and empirical evidence that the average communicability angle for a given network accounts for its spatial efficiency on the…