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Data mining methods for gene selection on the basis of gene expression arrays

Michał Muszyński, Stanisław Osowski (2014)

International Journal of Applied Mathematics and Computer Science

The paper presents data mining methods applied to gene selection for recognition of a particular type of prostate cancer on the basis of gene expression arrays. Several chosen methods of gene selection, including the Fisher method, correlation of gene with a class, application of the support vector machine and statistical hypotheses, are compared on the basis of clustering measures. The results of applying these individual selection methods are combined together to identify the most often selected...

Delays induced in population dynamics

Eva Sánchez (2003)

Banach Center Publications

This paper provides an introduction to delay differential equations together with a short survey on state-dependent delay differential equations arising in population dynamics. Our main goal is to examine how the delays emerge from inner mechanisms in the model, how they induce oscillations and stability switches in the system and how the qualitative behaviour of a biological model depends on the form of the delay.

Deterministic and stochastic simulations of simple genetic circuits

Ofer Biham, Nathalie Q. Balaban, Adiel Loinger, Azi Lipshtat, Hagai B. Perets (2008)

Banach Center Publications

We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated using rate equations, that account for the concentrations of the mRNAs and proteins produced by these genes. Rate equations are suitable when the concentrations of the relevant molecules in a cell are large and fluctuations are negligible. However, when some...

Deterministic Chaos vs. Stochastic Fluctuation in an Eco-epidemic Model

P.S. Mandal, M. Banerjee (2012)

Mathematical Modelling of Natural Phenomena

An eco-epidemiological model of susceptible Tilapia fish, infected Tilapia fish and Pelicans is investigated by several author based upon the work initiated by Chattopadhyay and Bairagi (Ecol. Model., 136, 103–112, 2001). In this paper, we investigate the dynamics of the same model by considering different parameters involved with the model as bifurcation parameters in details. Considering the intrinsic growth rate of susceptible Tilapia fish as bifurcation parameter, we demonstrate the period doubling...

Differential growth models for microbial populations

Jaroslav Milota (1982)

Aplikace matematiky

Two models of microbial growth are derived as a resuslt of a discussion of the models of Monod and Hinshelwood types. The approach takes account of the lyse of dead cells in inhibitory products as well as in those which stimulate the growth. The asymptotic behaviour of the models is proved and the models applied to a chemostat.

Differential stability of solutions to air quality control problems in urban area

Piotr Holnicki, Jan Sokołowski, Antoni Żochowski (1987)

Aplikace matematiky

The convex optimal control problem for a system described by the parabolic equation is considered. The form of the right derivative of an optimal solution with respect to the parameter is derived. The applications to an air quality control problem are discussed. Numerical result are provided.

Diffusion limit for the phenomenon of random genetic drift

Anna Marciniak (2000)

Applicationes Mathematicae

The paper deals with mathematical modelling of population genetics processes. The formulated model describes the random genetic drift. The fluctuations of gene frequency in consecutive generations are described in terms of a random walk. The position of a moving particle is interpreted as the state of the population expressed as the frequency of appearance of a specific gene. This leads to a continuous model on the microscopic level in the form of two first order differential equations (known as...

Digital search trees and chaos game representation*

Peggy Cénac, Brigitte Chauvin, Stéphane Ginouillac, Nicolas Pouyanne (2009)

ESAIM: Probability and Statistics

In this paper, we consider a possible representation of a DNA sequence in a quaternary tree, in which one can visualize repetitions of subwords (seen as suffixes of subsequences). The CGR-tree turns a sequence of letters into a Digital Search Tree (DST), obtained from the suffixes of the reversed sequence. Several results are known concerning the height, the insertion depth for DST built from independent successive random sequences having the same distribution. Here the successive inserted words...

Discrete Groups and Internal Symmetries of Icosahedral Viral Capsids

Richard Kerner (2014)

Molecular Based Mathematical Biology

A classification of all possible icosahedral viral capsids is proposed. It takes into account the diversity of hexamers’ compositions, leading to definite capsid size.We showhowthe self-organization of observed capsids during their production results from definite symmetries of constituting hexamers. The division of all icosahedral capsids into four symmetry classes is given. New subclasses implementing the action of symmetry groups Z2, Z3 and S3 are found and described. They concern special cases...

Discrete stochastic processes, replicator and Fokker-Planck equations of coevolutionary dynamics in finite and infinite populations

Jens Christian Claussen (2008)

Banach Center Publications

Finite-size fluctuations in coevolutionary dynamics arise in models of biological as well as of social and economic systems. This brief tutorial review surveys a systematic approach starting from a stochastic process discrete both in time and state. The limit N → ∞ of an infinite population can be considered explicitly, generally leading to a replicator-type equation in zero order, and to a Fokker-Planck-type equation in first order in 1/√N. Consequences and relations to some previous approaches...

Do Demographic and Disease Structures Affect the Recurrence of Epidemics ?

A. Castellazzo, A. Mauro, C. Volpe, E. Venturino (2012)

Mathematical Modelling of Natural Phenomena

In this paper we present an epidemic model affecting an age-structured population. We show by numerical simulations that this demographic structure can induce persistent oscillations in the epidemic. The model is then extended to encompass a stage-structured disease within an age-dependent population. In this case as well, persistent oscillations are observed in the infected as well as in the whole population.

Drift, draft and structure: some mathematical models of evolution

Alison M. Etheridge (2008)

Banach Center Publications

Understanding the evolution of individuals which live in a structured and fluctuating environment is of central importance in mathematical population genetics. Here we outline some of the mathematical challenges arising from modelling structured populations, primarily focussing on the interplay between forwards in time models for the evolution of the population and backwards in time models for the genealogical trees relating individuals in a sample from that population. In addition to classical...

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