相关论文: Modelling Breakage-Fusion-Bridge Cycles as a Stoch…
Machine learning-based unfolding has enabled unbinned and high-dimensional differential cross section measurements. Two main approaches have emerged in this research area: one based on discriminative models and one based on generative…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…
We investigate a multiphase Cahn-Hilliard model for tumor growth with general source terms. The multiphase approach allows us to consider multiple cell types and multiple chemical species (oxygen and/or nutrients) that are consumed by the…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
We perform a phase-space analysis of strong-field enhanced ionisation in molecules, with emphasis on quantum-interference effects. Using Wigner quasi-probability distributions and the quantum Liouville equation, we show that the momentum…
We consider a phenotype-structured reaction-diffusion model of avascular glioma growth. The model describes the interaction dynamics between tumour cells and oxygen, and takes into account anisotropic cell movement and oxygen diffusion…
Initiation and development of a malignant tumor is a complex phenomenon that has critical stages determining its long time behavior. This phenomenon is mathematically described by means of various models: from simple heuristic models to…
In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and…
Cancer has been characterized as a constellation of hundreds of diseases differing in underlying mutations and depending on cellular environments. Carcinogenesis as a stochastic physical process has been studied for over sixty years, but…
Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent…
An explicit solution for a general two-type birth-death branching process with one way mutation is presented. This continuous time process mimics the evolution of resistance to treatment, or the onset of an extra driver mutation during…
Multitype branching processes are ideal for studying the population dynamics of stem cell populations undergoing mutation accumulation over the years following transplant. In such stochastic models, several quantities are of clinical…
Cancer is increasingly perceived as a systems-level, network phenomenon. The major trend of malignant transformation can be described as a two-phase process, where an initial increase of network plasticity is followed by a decrease of…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
In this study, we provide a dynamical systems perspective to the modelling of pathological states induced by tumors or infection. A unified disease model is established using the innate immune system as the reference point. We propose a…
Mutations in the epidermal growth factor receptor (EGFR) are common in non-small cell lung cancer (NSCLC), particularly in never-smoker patients. However, these mutations are not always carcinogenic, and have recently been reported in…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate…