Related papers: Analysis of a Population Model Structured by the C…

Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…

The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…

We study the problems of multi-person pose segmentation in natural images and instance segmentation in biological images with crowded cells. We formulate these distinct tasks as integer programs where variables correspond to poses/cells. To…

Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular…

Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…

We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of a cloned population of cells with their environment as though it were one large cell. The question is as to whether any…

Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…

Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various…

The general principles of Bayesian data analysis imply that models for survey responses should be constructed conditional on all variables that affect the probability of inclusion and nonresponse, which are also the variables used in survey…

We consider a population organised hierarchically with respect to size in such a way that the growth rate of each individual depends only on the presence of larger individuals. As a concrete example one might think of a forest, in which the…

Proliferating cell populations at steady state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by…

Human dynamics and sociophysics suggest statistical models that may explain and provide us with better insight into social phenomena. Here we tackle the problem of determining the distribution of the population density of a social space…

This paper concerns multiphase models of tumor growth in interaction with a surrounding tissue, taking into account also the interplay with diffusible nutrients feeding the cells. Models specialize in nonlinear systems of possibly…

We derive the full kinetic equations describing the evolution of the probability density distribution for a structured population such as cells distributed according to their ages and sizes. The kinetic equations for such a "sizer-timer"…

We study here the dynamics (and stability) of Probabilistic Population Protocols, via the differential equations approach. We provide a quite general model and we show that it includes the model of Angluin et. al. in the case of very large…

A probabilistic database with attribute-level uncertainty consists of relations where cells of some attributes may hold probability distributions rather than deterministic content. Such databases arise, implicitly or explicitly, in the…

In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…

We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…

We study a size-structured population model in which individual cells grow at a rate determined by a fluctuating internal variable (e.g., gene expression levels). Many previous models of phenotypically heterogeneous populations can be…