相关论文: In silico network topology-based prediction of gen…
The Critical Node Problem (CNP) is concerned with identifying the critical nodes in a complex network. These nodes play a significant role in maintaining the connectivity of the network, and removing them can negatively impact network…
Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of…
Topology inference is a powerful tool to better understand the behaviours of network systems (NSs). Different from most of prior works, this paper is dedicated to inferring the directed topology of NSs from noisy observations, where the…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
The process of identifying and characterizing B-cell epitopes, which are the portions of antigens recognized by antibodies, is important for our understanding of the immune system, and for many applications including vaccine development,…
Vital node identification is the problem of finding nodes of highest importance in complex networks. This problem has crucial applications in various contexts such as viral marketing or controlling the propagation of virus or rumours in…
The network inference problem consists of reconstructing the edge set of a network given traces representing the chronology of infection times as epidemics spread through the network. This problem is a paradigmatic representative of…
Interaction networks are of central importance in post-genomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks or protein interaction maps. The main…
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…
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic…
Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Network tomography, a classic research problem in the realm of network monitoring, refers to the methodology of inferring unmeasured network attributes using selected end-to-end path measurements. In the research community, network…
Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Identification of cancer driver genes is fundamental for the development of targeted therapeutic interventions. The integration of mutational profiles with protein-protein interaction (PPI) networks offers a promising avenue for their…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
Classification of biological neuron types and networks poses challenges to the full understanding of the brain's organisation and functioning. In this paper, we develop a novel objective classification model of biological neuronal types and…