Related papers: Inferring Epigenetic Dynamics from Kin Correlation…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…
Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
Populations are heterogeneous, deviating in numerous ways. Phenotypic diversity refers to the range of traits or characteristics across a population, where for cells this could be the levels of signalling, movement and growth activity, etc.…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
In many indigenous societies, people are categorised into several cultural groups, or clans, within which they believe to share ancestors. Clan attributions provide certain rules for marriage and descent. Such rules between clans constitute…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…