Mean fixation time estimates in constant size populations.
Model based analysis of signaling pathways
The paper is concerned with application of mathematical modeling to the analysis of signaling pathways. Two issues, deterministic modeling of gene transcription and model-driven discovery of regulatory elements, are dealt with. First, the biological background is given and the importance of the stochastic nature of biological processes is addressed. The assumptions underlying deterministic modeling are presented. Special emphasis is put on describing gene transcription. A framework for including...
Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model
We present a brief review of molecular biological basis and mathematical modelling of circadian rhythms in Drosophila. We discuss pertinent aspects of a new model that incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are probabilistically...
Modelling Evolution of Regulatory Networks in Artificial Bacteria
Studying the evolutive and adaptative machanisms of prokayotes is a complicated task. As these machanisms cannot be easily studied "in vivo", it is necessary to consider other methods. We have therefore developed the RAevol model, a model designed to study the evolution of bacteria and their adaptationto the environment. Our model simulates the evolution of a population of artificial bacteria in a changing environment, providing us with an insight into the strategies that digital organisms develop...
On a functional equation with derivative and symmetrization
We study existence, uniqueness and form of solutions to the equation where α, β, γ and f are given, and stands for the even part of a searched-for differentiable function g. This equation emerged naturally as a result of the analysis of the distribution of a certain random process modelling a population genetics phenomenon.
On discrete-time multiallelic evolutionary dynamics driven by selection.
On the approximability of comparing genomes with duplicates.
On the complexity of the Double Digest Problem
On the Short Term Behaviour of Genetic Algorithms
Perturbations of Positive Semigroups and Applications to Population Genetics.
Population genetics models for the statistics of DNA samples under different demographic scenarios - Maximum likelihood versus approximate methods
The paper reviews the basic mathematical methodology of modeling neutral genetic evolution, including the statistics of the Fisher-Wright process, models of mutation and the coalescence method under various demographic scenarios. The basic approach is the use of maximum likelihood techniques. However, due to computational problems, intuitive or approximate methods are also of great importance.
Progressive diseases: Interpretation of genetic data.
Properties of a singular value decomposition based dynamical model of gene expression data
Recently, data on multiple gene expression at sequential time points were analyzed using the Singular Value Decomposition (SVD) as a means to capture dominant trends, called characteristic modes, followed by the fitting of a linear discrete-time dynamical system in which the expression values at a given time point are linear combinations of the values at a previous time point. We attempt to address several aspects of the method. To obtain the model, we formulate a nonlinear optimization problem...
Quality improvement of rule-based gene group descriptions using information about GO terms importance occurring in premises of determined rules
In this paper we present a method for evaluating the importance of GO terms which compose multi-attribute rules. The rules are generated for the purpose of biological interpretation of gene groups. Each multi-attribute rule is a combination of GO terms and, based on relationships among them, one can obtain a functional description of gene groups. We present a method which allows evaluating the influence of a given GO term on the quality of a rule and the quality of a whole set of rules. For each...
Recent developments in computational gene recognition.
Réflexions sur les méthodes de parenté
Repeat distributions from unequal crossovers
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with single crossovers is analysed that result in equilibrium distributions of this type. Due to the nonlinear and infinite-dimensional nature of these models, their analysis requires some nontrivial tools from measure theory and functional analysis, which makes them interesting...
Reversible distributions of multi-allelic Gillespie–Sato diffusion models
Sampling properties of estimators of nucleotide diversity at discovered SNP sites
SNP sites are generally discovered by sequencing regions of the human genome in a limited number of individuals. This may leave SNP sites present in the region, but containing rare mutant nucleotides, undetected. Consequently, estimates of nucleotide diversity obtained from assays of detected SNP sites are biased. In this research we present a statistical model of the SNP discovery process, which is used to evaluate the extent of this bias. This model involves the symmetric Beta distribution of...
SV40 assembly in vivo and in vitro.