Related papers: Cell lineage statistics with incomplete population…
In many biological processes heterogeneity within cell populations is an important issue. In this work we consider populations where the behavior of every single cell can be described by a system of ordinary differential equations.…
We consider a binary branching process structured by a stochastic trait that evolves according to a diffusion process that triggers the branching events, in the spirit of Kimmel's model of cell division with parasite infection. Based on the…
Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…
Mathematical models of biological populations commonly use discrete structure classes to capture trait variation among individuals (e.g. age, size, phenotype, intracellular state). Upscaling these discrete models into continuum descriptions…
We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population. The resolution of our kinetic theory also allows one to…
It is well known that the different cell-division models, such as Timer, Sizer, and Adder, can be distinguished based on the correlations between different single-cell-level quantities such as birth-size, division-time, division-size, and…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
We consider a size-structured population describing the cell divisions. The cell population is described by an empirical measure and we observe the divisions in the continuous time interval [0, T ]. We address here the problem of estimating…
In this paper, we propose the use of causal inference techniques for survival function estimation and prediction for subgroups of the data, upto individual units. Tree ensemble methods, specifically random forests were modified for this…
Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future…
In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…
What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups…
We calculate the density and expectation for the number of lineages in a reconstructed tree with $n$ extant species. This is done with conditioning on the age of the tree as well as with assuming a uniform prior for the age of the tree.
We consider populations structured by a phenotypic trait and a space variable, in a non-homogeneous environment. In the case of sex- ual populations, we are able to derive models close to existing mod- els in theoretical biology, from a…
Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates.…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
In some randomized clinical trials, patients may die before the measurements of their outcomes. Even though randomization generates comparable treatment and control groups, the remaining survivors often differ significantly in background…
Since the seminal work of Powell, the relationships between the population growth rate, the probability distributions of generation time, and the distribution of cell age have been known for the bacterial population in a steady state of…