相关论文: Complex Systems Analysis of Cell Cycling Models in…

Chemotherapy is one of the most important therapeutic options used to treat human cancers, either alone or in combination with radiation therapy and surgery. Recent studies have indicated that intra-tumoural heterogeneity has a significant…

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…

Cancer research has traditionally focused on identifying driver genes, those with mutations that initiate tumorigenesis. The Cancer Driver Gene (CDG) paradigm, further supported by the observation of oncogene addiction in tumors, has…

DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…

The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…

Despite significant medical advancements, cancer remains the second leading cause of death, with over 600,000 deaths per year in the US. One emerging field, pathway analysis, is promising but still relies on manually derived wet lab data,…

Quantum systems interacting with an unknown environment are notoriously difficult to model, especially in presence of non-Markovian and non-perturbative effects. Here we introduce a neural network based approach, which has the mathematical…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…

The development of mathematical models of cancer informed by time-resolved measurements has enabled personalised predictions of tumour growth and treatment response. However, frequent cancer monitoring is rare, and many tumours are treated…

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…

Adaptive therapy is a promising paradigm for treating cancers, that exploits competitive interactions between drug-sensitive and drug-resistant cells, thereby avoiding or delaying treatment failure due to evolution of drug resistance within…

Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…

We give a very short introduction to discrete and continuum models for the evolutionary and spatial dynamics of cancer through two case studies: a model for the evolutionary dynamics of cancer cells under cytotoxic therapy and a model for…

We consider the decision making by mammalian cells, looking them as dynamic systems with rhythms. We calculate the effective dimension of the cell division model of the healthy mammalian cells consistent with the data: it is described via a…

Graph-based representation approaches have been proven to be successful in the analysis of biomedical data, due to their capability of capturing intricate dependencies between biological entities, such as the spatial organization of…

Biological networks have been recently found to exhibit many topological properties of the so-called complex networks. It has been reported that they are, in general, both highly skewed and directed. In this paper, we report on the dynamics…

The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial…

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell…