相关论文: Modelling Breakage-Fusion-Bridge Cycles as a Stoch…
Through mechanical forces, biological cells remodel the surrounding collagen network, generating striking deformation patterns. Tethers-tracts of high densification and fiber alignment-form between cells, thinner bands emanate from cell…
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…
We investigate the fragmentation process of solid materials with crystalline and amorphous phases using the discrete element method. Damage initiates inside spherical samples above the contact zone in a region where the circumferential…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
We investigate, both experimentally and theoretically, the bifurcation to alternans in heart tissue. Previously, this phenomenon has been modeled either as a smooth or as border-collision period-doubling bifurcation. Using a new…
Cancer is a complex disease driven by dynamic regulatory shifts that cannot be fully captured by individual molecular profiling. We employ a data-driven approach to construct a coarse-grained dynamic network model based on hallmark…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth…
Local cancer cell invasion is a complex process involving many cellular and tissue interactions and is an important prerequisite for metastatic spread, the main cause of cancer related deaths. Occurring over many different temporal and…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
We aim to understand the evolution of the genetic composition of cancer cell populations. To achieve this, we consider an individual-based model representing a cell population where cells divide, die and mutate along the edges of a finite…
Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation…
Cells are dynamic systems characterized by temporal variations in biophysical properties such as stiffness and contractility. Recent studies show that the recruitment and release of actin filaments into and out of the cell cortex - a…
We consider the process of uncovering the vertices of a random labeled tree according to their labels. First, a labeled tree with $n$ vertices is generated uniformly at random. Thereafter, the vertices are uncovered one by one, in order of…
Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…
We study experimentally the fracture mechanisms of a model cohesive granular medium consisting of glass beads held together by solidified polymer bridges. The elastic response of this material can be controlled by changing the cross-linking…
Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…
Cancer progression is an evolutionary process that is driven by mutation and selection in a population of tumor cells. We discuss mathematical models of cancer progression, starting from traditional multistage theory. Each stage is…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…