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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...

Decay and asymptotic behavior of solutions of the Keller-Segel system of degenerate and nondegenerate type

Takayoshi Ogawa (2006)

Banach Center Publications

We classify the global behavior of weak solutions of the Keller-Segel system of degenerate and nondegenerate type. For the stronger degeneracy, the weak solution exists globally in time and has a uniform time decay under some extra conditions. If the degeneracy is weaker, the solution exhibits a finite time blow up if the data is nonnegative. The situation is very similar to the semilinear case. Some additional discussion is also presented.

Delay Model of Hematopoietic Stem Cell Dynamics: Asymptotic Stability and Stability Switch

F. Crauste (2009)

Mathematical Modelling of Natural Phenomena

A nonlinear system of two delay differential equations is proposed to model hematopoietic stem cell dynamics. Each equation describes the evolution of a sub-population, either proliferating or nonproliferating. The nonlinearity accounting for introduction of nonproliferating cells in the proliferating phase is assumed to depend upon the total number of cells. Existence and stability of steady states are investigated. A Lyapunov functional is built to obtain the global asymptotic stability of the...

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...

Different models of chemotherapy taking into account drug resistance stemming from gene amplification

Jarosław Śmieja, Andrzej Świerniak (2003)

International Journal of Applied Mathematics and Computer Science

This paper presents an analysis of some class of bilinear systems that can be applied to biomedical modelling. It combines models that have been studied separately so far, taking into account both the phenomenon of gene amplification and multidrug chemotherapy in their different aspects. The mathematical description is given by an infinite dimensional state equation with a system matrix whose form allows decomposing the model into two interacting subsystems. While the first one, of a finite dimension,...

Diffusion models of multicomponent mixtures in the lung*

L. Boudin, D. Götz, B. Grec (2010)

ESAIM: Proceedings

In this work, we are interested in two different diffusion models for multicomponent mixtures. We numerically recover experimental results underlining the inadequacy of the usual Fick diffusion model, and the importance of using the Maxwell-Stefan model in various situations. This model nonlinearly couples the mole fractions and the fluxes of each component of the mixture. We then consider a subregion of the lower part of the lung, in which we compare...

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 time markovian agents interacting through a potential

Amarjit Budhiraja, Pierre Del Moral, Sylvain Rubenthaler (2013)

ESAIM: Probability and Statistics

A discrete time stochastic model for a multiagent system given in terms of a large collection of interacting Markov chains is studied. The evolution of the interacting particles is described through a time inhomogeneous transition probability kernel that depends on the ‘gradient’ of the potential field. The particles, in turn, dynamically modify the potential field through their cumulative input. Interacting Markov processes of the above form have been suggested as models for active biological transport...

Drugs in the Classroom: Using Pharmacokinetics to Introduce Biomathematical Modeling

G. A. Koch-Noble (2011)

Mathematical Modelling of Natural Phenomena

Pharmacokinetics is an excellent way to introduce biomathematical modeling at the sophomore level. Students have the opportunity to develop a mathematical model of a biological phenomenon to which they all can relate. Exploring pharmacokinetics takes students through the necessary stages of mathematical modeling: determining the goals of the model, deciphering between the biological aspects to include in the model, defining the assumptions of the model, and finally, building, analyzing, using, and...

Dynamics and patterns of an activator-inhibitor model with cubic polynomial source

Yanqiu Li, Juncheng Jiang (2019)

Applications of Mathematics

The dynamics of an activator-inhibitor model with general cubic polynomial source is investigated. Without diffusion, we consider the existence, stability and bifurcations of equilibria by both eigenvalue analysis and numerical methods. For the reaction-diffusion system, a Lyapunov functional is proposed to declare the global stability of constant steady states, moreover, the condition related to the activator source leading to Turing instability is obtained in the paper. In addition, taking the...

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