Analysis and characterization of asynchronous state transition graphs using extremal states.

Abstract:

:Logical modeling of biological regulatory networks gives rise to a representation of the system's dynamics as a so-called state transition graph. Analysis of such a graph in its entirety allows for a comprehensive understanding of the functionalities and behavior of the modeled system. However, the size of the vertex set of the graph is exponential in the number of the network components making analysis costly, motivating development of reduction methods. In this paper, we present results allowing for a complete description of an asynchronous state transition graph of a Thomas network solely based on the analysis of the subgraph induced by certain extremal states. Utilizing this notion, we compare the behavior of a simple multivalued network and a corresponding Boolean network and analyze the conservation of dynamical properties between them. Understanding the relation between such coarser and finer models is a necessary step toward meaningful network reduction as well as model refinement methods.

journal_name

Bull Math Biol

authors

Lorenz T,Siebert H,Bockmayr A

doi

10.1007/s11538-012-9782-5

subject

Has Abstract

pub_date

2013-06-01 00:00:00

pages

920-38

issue

6

eissn

0092-8240

issn

1522-9602

journal_volume

75

pub_type

杂志文章
  • Fixation of strategies for an evolutionary game in finite populations.

    abstract::A stochastic evolutionary dynamics of two strategies given by 2x 2 matrix games is studied in finite populations. We focus on stochastic properties of fixation: how a strategy represented by a single individual wins over the entire population. The process is discussed in the framework of a random walk with site depend...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-006-9061-4

    authors: Antal T,Scheuring I

    更新日期:2006-11-01 00:00:00

  • Culture analysis and external interaction models of mycelial growth.

    abstract::To investigate morphogenesis and in particular circularization mechanisms in young mycelia, we observe cultures of the zygomycete Mucor spinosus and develop discrete models of two-dimensional filamental branching growth. The models are based on the hypothesis that the fungus secretes a regulatory substance that diffus...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02460715

    authors: Indermitte C,Liebling M,Clémençon H

    更新日期:1994-07-01 00:00:00

  • A mathematical model for the effects of HER2 over-expression on cell cycle progression in breast cancer.

    abstract::In this paper, we present a mathematical model predicting the fraction of proliferating cells in G1, S, and G2/M phases of the cell cycle as a function of EGFR and HER2. We show that it is possible to find parameters for the mathematical model so that its predictions agree with the experimental observations that HER2 ...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-011-9663-3

    authors: Eladdadi A,Isaacson D

    更新日期:2011-12-01 00:00:00

  • A Discrete Velocity Kinetic Model with Food Metric: Chemotaxis Traveling Waves.

    abstract::We introduce a mesoscopic scale chemotaxis model for traveling wave phenomena which is induced by food metric. The organisms of this simplified kinetic model have two discrete velocity modes, [Formula: see text] and a constant tumbling rate. The main feature of the model is that the speed of organisms is constant [For...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-016-0235-4

    authors: Choi SH,Kim YJ

    更新日期:2017-02-01 00:00:00

  • Least squares estimation in stochastic biochemical networks.

    abstract::The paper presents results on the asymptotic properties of the least-squares estimates (LSEs) of the reaction constants in mass-action, stochastic, biochemical network models. LSEs are assumed to be based on the longitudinal data from partially observed trajectories of a stochastic dynamical system, modeled as a conti...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-012-9744-y

    authors: Rempala GA

    更新日期:2012-08-01 00:00:00

  • Discussion: the Kermack-McKendrick epidemic threshold theorem.

    abstract::The paper reviews the work of Kermack and McKendrick on the development of simple mathematical models of the transmission dynamics of viral and bacterial infectious agents within population of hosts. The focus of attention is centred on the notion of a threshold density of susceptible hosts to trigger an epidemic and ...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0092-8240(05)80039-4

    authors: Anderson RM

    更新日期:1991-01-01 00:00:00

  • Mathematical insights in evaluating state dependent effectiveness of HIV prevention interventions.

    abstract::Mathematical models have been used to simulate HIV transmission and to study the use of preexposure prophylaxis (PrEP) for HIV prevention. Often a single intervention outcome over 10 years has been used to evaluate the effectiveness of PrEP interventions. However, different metrics express a wide variation over time a...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-013-9824-7

    authors: Zhao Y,Dimitrov DT,Liu H,Kuang Y

    更新日期:2013-04-01 00:00:00

  • A kinetic model of coronary reactive hyperemic response to transient ischemia.

    abstract::A kinetic model is proposed to delineate the factors that determine the coronary reactive hyperemic response (RHR) to transient ischemia. The model comprises of myocardial-interstitial (M) and vascular (V) compartments. Vasodilator metabolites (VM) are produced in the M compartment during the interval of coronary occl...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02458320

    authors: Wong AY

    更新日期:1995-01-01 00:00:00

  • Predicting Patient-Specific Radiotherapy Protocols Based on Mathematical Model Choice for Proliferation Saturation Index.

    abstract::Radiation is commonly used in cancer treatment. Over 50% of all cancer patients will undergo radiotherapy (RT) as part of cancer care. Scientific advances in RT have primarily focused on the physical characteristics of treatment including beam quality and delivery. Only recently have inroads been made into utilizing t...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-017-0279-0

    authors: Poleszczuk J,Walker R,Moros EG,Latifi K,Caudell JJ,Enderling H

    更新日期:2018-05-01 00:00:00

  • Tubuloglomerular feedback signal transduction in a short loop of henle.

    abstract::In previous studies, we used a mathematical model of the thick ascending limb (TAL) to investigate nonlinearities in the tubuloglomerular feedback (TGF) loop. That model does not represent other segments of the nephron, the water, and NaCl transport along which may impact fluid flow rate and NaCl transport along the T...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-009-9436-4

    authors: Layton AT,Edwards A

    更新日期:2010-01-01 00:00:00

  • Comparing approximations to spatio-temporal models for epidemics with local spread.

    abstract::Analytical methods for predicting and exploring the dynamics of stochastic, spatially interacting populations have proven to have useful application in epidemiology and ecology. An important development has been the increasing interest in spatially explicit models, which require more advanced analytical techniques tha...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1006/bulm.2001.0234

    authors: Filipe JA,Gibson GJ

    更新日期:2001-07-01 00:00:00

  • A Population Dynamics Model of Mosquito-Borne Disease Transmission, Focusing on Mosquitoes' Biased Distribution and Mosquito Repellent Use.

    abstract::We present an improved mathematical model of population dynamics of mosquito-borne disease transmission. Our model considers the effect of mosquito repellent use and the mosquito's behavior or attraction to the infected human, which cause mosquitoes' biased distribution around the human population. Our analysis of the...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-019-00666-1

    authors: Aldila D,Seno H

    更新日期:2019-12-01 00:00:00

  • Global stability for a class of virus models with cytotoxic T lymphocyte immune response and antigenic variation.

    abstract::We study the global stability of a class of models for in-vivo virus dynamics that take into account the Cytotoxic T Lymphocyte immune response and display antigenic variation. This class includes a number of models that have been extensively used to model HIV dynamics. We show that models in this class are globally a...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-010-9543-2

    authors: Souza MO,Zubelli JP

    更新日期:2011-03-01 00:00:00

  • A stochastic version of the Eigen model.

    abstract::We exhibit a stochastic discrete time model that produces the Eigen model (Naturwissenschaften 58:465-523, 1971) in the deterministic and continuous time limits. The model is based on the competition among individuals differing in terms of fecundity but with the same viability. We explicitly write down the Markov matr...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-010-9525-4

    authors: Musso F

    更新日期:2011-01-01 00:00:00

  • A maximum likelihood approach to correlation dimension and entropy estimation.

    abstract::To obtain the correlation dimension and entropy from an experimental time series we derive estimators for these quantities together with expressions for their variances using a maximum likelihood approach. The validity of these expressions is supported by Monte Carlo simulations. We illustrate the use of the estimator...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02458619

    authors: Olofsen E,Degoede J,Heijungs R

    更新日期:1992-01-01 00:00:00

  • Modeling the Transmission Dynamics of Rabies for Dog, Chinese Ferret Badger and Human Interactions in Zhejiang Province, China.

    abstract::Human rabies is one of the major public health problems in China with an average of 1977 cases per year. It is estimated that 95% of these human rabies cases are due to dog bites. In recent years, the number of wildlife-associated human rabies cases has increased, particularly in the southeast and northeast regions of...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-018-00537-1

    authors: Huang J,Ruan S,Shu Y,Wu X

    更新日期:2019-04-01 00:00:00

  • Seasonal population dynamics of ticks, and its influence on infection transmission: a semi-discrete approach.

    abstract::In this paper, a simple semi-discrete (ticks' feeding is assumed to occur only during the summers of each year) model for tick population dynamics is presented. Conditions for existence, uniqueness, and stability of a positive equilibrium are found; the system is then studied numerically using parameter estimates cali...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1016/j.bulm.2004.03.007

    authors: Ghosh M,Pugliese A

    更新日期:2004-11-01 00:00:00

  • The mathematics of radiation target analyses.

    abstract::Radiation target theory has been extended to complex biochemical systems. Mathematical analyses are presented for multiple forms of biological active proteins, for the presence of large inhibitors or activators, for compounds which regulate rate or affinity and for multiple-step reactions. Several predictions of these...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02458298

    authors: Kempner ES

    更新日期:1995-11-01 00:00:00

  • Statistical evaluation of dendritic growth models.

    abstract::A mathematical model (Kliemann, W. 1987. Bull. math. Biol. 49, 135-152.) that predicts the quantitative branching pattern of dendritic tree was evaluated using the apical and basal dendrites of rat hippocampal neurons. The Wald statistic for chi 2-test was developed for the branching pattern of dendritic trees and for...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02458630

    authors: Carriquiry AL,Ireland WP,Kliemann W,Uemura E

    更新日期:1991-01-01 00:00:00

  • Integrin activation--the importance of a positive feedback.

    abstract::Integrins mediate cell adhesion and are essential receptors for the development and functioning of multicellular organisms. Integrin activation is known to require both ligand and talin binding and to correlate with cluster formation but the activation mechanism and precise roles of these processes are not yet resolve...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-005-9049-5

    authors: Iber D,Campbell ID

    更新日期:2006-05-01 00:00:00

  • The mutation process in colored coalescent theory.

    abstract::The mutation process is introduced into the colored coalescent theory. The mutation process can be viewed as an independent Poisson process running on the colored genealogical random tree generated by the colored coalescent process, with the edge lengths of the random tree serving as the time scale for the mutation pr...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-009-9428-4

    authors: Tian JP,Lin XS

    更新日期:2009-11-01 00:00:00

  • Disease Extinction Versus Persistence in Discrete-Time Epidemic Models.

    abstract::We focus on discrete-time infectious disease models in populations that are governed by constant, geometric, Beverton-Holt or Ricker demographic equations, and give a method for computing the basic reproduction number, [Formula: see text]. When [Formula: see text] and the demographic population dynamics are asymptotic...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-018-0426-2

    authors: van den Driessche P,Yakubu AA

    更新日期:2019-11-01 00:00:00

  • Estimating microbial inactivation parameters from survival curves obtained under varying conditions--the linear case.

    abstract::When the isothermal semi-logarithmic survival curves of heat inactivated microbial cells or spores are known to be linear it is possible to calculate their survival parameters from curves obtained under nonisothermal conditions, provided that the temperature history ('profile') satisfies certain simple mathematical re...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1016/S0092-8240(02)00097-6

    authors: Peleg M,Normand MD,Campanella OH

    更新日期:2003-03-01 00:00:00

  • Continuous probabilistic analysis to evolutionary game dynamics in finite populations.

    abstract::Evolutionary game dynamics of two strategies in finite population is studied by continuous probabilistic approach. Besides frequency dependent selection, mutation was also included in this study. The equilibrium probability density functions of abundance, expected time to extinction or fixation were derived and their ...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-009-9397-7

    authors: Gao M

    更新日期:2009-07-01 00:00:00

  • Estimating the selective advantage of mutant p53 tumour cells to repeated rounds of hypoxia.

    abstract::The tumour suppressor gene, p53, plays an important role in tumour development. Under low levels of oxygen (hypoxia), cells expressing wild-type p53 undergo programmed cell death (apoptosis), whereas cells expressing mutations in the p53 gene may survive and express angiogenic growth factors that stimulate tumour vasc...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1006/bulm.2000.0210

    authors: Gammack D,Byrne HM,Lewis CE

    更新日期:2001-01-01 00:00:00

  • Checkpoint method for choice recovery in dynamic programming.

    abstract::Many dynamic programming algorithms consist of a 'forward pass' computation to optimize a cost function, followed by a 'choice recovery' computation to construct a configuration that optimizes the cost function. 'Checkpointing' is a method to perform choice recovery using limited storage. During a forward pass, checkp...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1016/j.bulm.2004.10.002

    authors: Bax E

    更新日期:2005-07-01 00:00:00

  • Evolution of dispersal toward fitness.

    abstract::It is widely believed that the slowest dispersal strategy is selected in the evolutional if the environment is temporally invariant but spatially heterogeneous. Authors claim in this paper that this belief is true only if random dispersals with constant motility are considered. However, if a dispersal strategy with fi...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-013-9904-8

    authors: Kim YJ,Kwon O,Li F

    更新日期:2013-12-01 00:00:00

  • Oscillations and waves of cyclic AMP in Dictyostelium: a prototype for spatio-temporal organization and pulsatile intercellular communication.

    abstract::The amoebae Dictyostelium discoideum aggregate after starvation in a wavelike manner in response to periodic pulses of cyclic AMP (cAMP) secreted by cells which behave as aggregation centers. In addition to autonomous oscillations, the cAMP signaling system that controls aggregation is also capable of excitable behavi...

    journal_title:Bulletin of mathematical biology

    pub_type: 历史文章,杂志文章

    doi:10.1007/s11538-006-9090-z

    authors: Goldbeter A

    更新日期:2006-07-01 00:00:00

  • A semi-empirical model for flow or blood and other particulate suspensions through narrow tubes.

    abstract::A semi-empirical model applicable to the flow of blood and other particulate suspensions through narrow tubes has been developed. It envisages a central core of blood surrounded by a wall layer of reduced hematocrit. With the help of this model the wall layer thickness and extent of plug flow may be calculated using p...

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/BF02459514

    authors: Das RN,Seshadri V

    更新日期:1975-10-01 00:00:00

  • Temperature- and Turbidity-Dependent Competitive Interactions Between Invasive Freshwater Mussels.

    abstract::We develop a staged-structured population model that describes the competitive dynamics of two functionally similar, congeneric invasive species: zebra mussels and quagga mussels. The model assumes that the population survival rates are functions of temperature and turbidity, and that the two species compete for food....

    journal_title:Bulletin of mathematical biology

    pub_type: 杂志文章

    doi:10.1007/s11538-016-0146-4

    authors: Huang Q,Wang H,Ricciardi A,Lewis MA

    更新日期:2016-03-01 00:00:00