Related papers: SANTA: quantifying the functional content of molec…

The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the…

While the rapid adaptation of mobile devices changes our daily life more conveniently, the threat derived from malware is also increased. There are lots of research to detect malware to protect mobile devices, but most of them adopt only…

Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…

Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…

Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…

Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular…

Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…

An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with…

Biological network alignment (NA) aims to find a node mapping between species' molecular networks that uncovers similar network regions, thus allowing for transfer of functional knowledge between the aligned nodes. However, current NA…

Networks pervade many disciplines of science for analyzing complex systems with interacting components. In particular, this concept is commonly used to model interactions between genes and identify closely associated genes forming…

Genetic interactions confer robustness on cells in response to genetic perturbations. This often occurs through molecular buffering mechanisms that can be predicted using, among other features, the degree of coexpression between genes,…

Differences between biological networks corresponding to disease conditions can help delineate the underlying disease mechanisms. Existing methods for differential network analysis do not account for dependence of networks on covariates. As…

Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…

One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…

Network estimation and variable selection have been extensively studied in the statistical literature, but only recently have those two challenges been addressed simultaneously. In this paper, we seek to develop a novel method to…

Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…

Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark…

Disease awareness in infection dynamics can be modeled with adaptive contact networks whose rewiring rules reflect the attempt by susceptibles to avoid infectious contacts. Simulations of this type of models show an active phase with…

In this thesis we present the novel semi-supervised network-based algorithm P-Net, which is able to rank and classify patients with respect to a specific phenotype or clinical outcome under study. The peculiar and innovative characteristic…

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed…