Related papers: Seeding hESCs to achieve optimal colony clonality
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
Recent progress in genetic techniques has shed light on the complex co-evolution of malignant cell clones in leukemias. However, several aspects of clonal selection still remain unclear. In this paper, we present a multi-compartmental…
Seagrass meadows are among the most important coastal ecosystems, in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for…
Despite rapid advances in experimental cell biology, the in vivo behavior of hematopoietic stem cells (HSC) cannot be directly observed and measured. Previously we modeled feline hematopoiesis using a two-compartment hidden Markov process…
Originally motivated by the morphogenesis of bacterial microcolonies, the aim of this article is to explore models through different scales for a spatial population of interacting, growing and dividing particles. We start from a microscopic…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…
The self-organization of cells into complex tissues relies on a tight coordination of cell behavior. Identifying the cellular processes driving tissue growth is key to understanding the emergence of tissue forms and devising targeted…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
We investigate the dynamics of a colony of crawling, proliferating cells with a minimal, mechanical cell model. The cells consist of two disks, modelling the cell body and a pseudopod, connected by a finite extensible spring. The cells…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity which arises from stochastic intrinsic dynamics of cells. The internal state of the cell can be transmitted epigenetically in…
It is well known that excessive harvesting or hunting has driven species to extinction both on local and global scales. This leads to one of the fundamental problems of conservation ecology: how should we harvest a population so that…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…
We study the stochastic hydrodynamics of colonies of flagellated swimming cells, typified by multicellular choanoflagellates, which can form both rosette and chainlike shapes. The objective is to link cell-scale dynamics to colony-scale…
The machine-part cell formation problem consists of creating machine cells and their corresponding part families with the objective of minimizing the inter-cell and intra-cell movement while maximizing the machine utilization. This article…
We construct a cross-entropy clustering (CEC) theory which finds the optimal number of clusters by automatically removing groups which carry no information. Moreover, our theory gives simple and efficient criterion to verify cluster…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
We study the dynamics of a seeding experiment where a fibrous scaffold material is colonized by two types of cell populations. The specific application that we have in mind is related to the idea of meniscus tissue regeneration. In order to…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
Ensemble clustering is a fundamental problem in the machine learning field, combining multiple base clusterings into a better clustering result. However, most of the existing methods are unsuitable for large-scale ensemble clustering tasks…