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Showing papers in "Journal of Theoretical Biology in 2006"


Journal ArticleDOI
TL;DR: A comprehensive and flexible framework for detecting and interpreting gene-gene interactions that utilizes advances in information theory for selecting interesting single-nucleotide polymorphisms (SNPs), MDR for constructive induction, machine learning methods for classification, and finally graphical models for interpretation is described.

603 citations


Journal ArticleDOI
TL;DR: In situations for which neither chemotherapy nor immunotherapy alone are sufficient to control tumor growth, but in combination the therapies are able to eliminate the entire tumor, a mathematical model governing cancer growth on a cell population level is developed and analyzed.

495 citations


Journal ArticleDOI
TL;DR: A differential equation is derived which describes how the average frequency of each strategy on the graph changes over time, and is a replicator equation with a transformed payoff matrix, which results in a transformation of the payoff matrix.

421 citations


Journal ArticleDOI
TL;DR: It is demonstrated that a simple time lag model provides a general, parsimonious explanation of the extensive variation in the dN/dS ratio seen when comparing closely related bacterial genomes, and a role for hitch-hiking in the accumulation of non-synonymous mutations is suggested.

402 citations


Journal ArticleDOI
TL;DR: A mathematical model which simultaneously couples vessel growth with blood flow through the vessels--dynamic adaptive tumour-induced angiogenesis (DATIA), used to examine the effects of changing various physical and biological model parameters on the developing vascular architecture and the delivery of chemotherapeutic drugs to the tumour.

377 citations


Journal ArticleDOI
TL;DR: The keys to the success in indirect reciprocity are to be nice (maintenance of cooperation among themselves), retaliatory (detection of defectors, punishment, and justification of punishment), apologetic, and forgiving.

373 citations


Journal ArticleDOI
TL;DR: A new continuous mathematical model of cell-cell adhesion is developed by considering the movement of cells in response to the adhesive forces generated through binding, and it is demonstrated that this model predicts the aggregation behaviour of a disassociated adhesive cell population.

349 citations


Journal ArticleDOI
TL;DR: An approach is proposed that allows the determination of material models from uniaxial tests and histostructural data including fiber orientation of the tissue including Fung-type strain-energy functions providing strict local convexity and preferred fiber orientations.

336 citations


Journal ArticleDOI
TL;DR: This framework provides the first unifying approach to model cooperation in different kinds of social dilemmas and recovers the four basic scenarios of evolutionary dynamics given by dominating defection, coexistence of defectors and cooperators, dominating cooperation and bi-stability.

316 citations


Journal ArticleDOI
TL;DR: Methods from percolation theory are used to develop a mathematical framework for predicting disease transmission through semi-directed contact networks in which some contacts are undirected-the probability of transmission is symmetric between individuals-and others are directed-transmission is possible only in one direction.

305 citations


Journal ArticleDOI
TL;DR: The epidemic model agrees well with the observed epidemic data and finds that effective isolation measures in hospital clinics at best would only ensure control with probability 0.87 while reducing the transmission rate by >76.5% guarantees stopping an epidemic.

Journal ArticleDOI
TL;DR: A mathematical model is constructed in order to test the hypothesis that periv vascular drainage of interstitial fluid and solutes out of brain tissue is driven by pulsations of the blood vessel walls, and it is shown that successful drainage may depend upon some attachment of solutes to the lining of the perivascular space, although an alternative without this requirement is also postulated.

Journal ArticleDOI
Alan Grafen1
TL;DR: The first fully explicit argument is given that broadly supports a widespread belief among whole-organism biologists that natural selection tends to lead to organisms acting as if maximizing their inclusive fitness, and is incorporated into the formal Darwinism project.

Journal ArticleDOI
TL;DR: This work derives a reduced conceptual model for the acute inflammatory response to infection, built up from consideration of direct interactions of fundamental effectors, to explore the importance of dynamic anti-inflammation in promoting resolution of infection and homeostasis.

Journal ArticleDOI
TL;DR: A hybrid cellular automata-partial differential equation model of moderate complexity is presented to describe the interactions between a growing tumor next to a nutrient source and the immune system of the host organism.

Journal ArticleDOI
TL;DR: A simple relationship is found that characterizes those linking dynamics which allow natural selection to favour cooperation over defection, and conditions for evolutionary stability are outlined.

Journal ArticleDOI
TL;DR: Using the mass conservation law, this work introduces two explicit time delays and proposes a more robust alternative model for better understanding the glucose-insulin endocrine metabolic regulatory system and the ultradian insulin secretory oscillations for the cases of continuous enteral nutrition and constant glucose infusion.

Journal ArticleDOI
TL;DR: The phylogenetically informative spacers, in concert with the previously identified single nucleotide mutations and chromosomal deletions, can be used to identify a series of clades in the RD9 deleted lineage each with a separate host preference, and it is suggested that the M. tuberculosis complex may best be described as aseries of host-adapted ecotypes.

Journal ArticleDOI
TL;DR: Simulation results showed that fitted coefficient estimates from simulated data sets appeared accurate, as well as fitted rates of VFA production, although the model accounted for only a small fraction (maximally 45%) of the variation in VFA molar proportions.

Journal ArticleDOI
TL;DR: Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance the understanding of the role of natural selection in the evolution by gene duplication.

Journal ArticleDOI
TL;DR: The LogitBoost, one of the boosting algorithms developed recently, is introduced for predicting protein structural classes using a regression scheme as the base learner, which can handle multi-class problems and is particularly superior in coping with noisy data.

Journal ArticleDOI
TL;DR: The hypothesis that endotoxin tolerance and other related phenomena can be considered as dynamic manifestations of a unified acute inflammatory response, and offer specific predictions related to the dynamics of this response to endotoxin, is supported.

Journal ArticleDOI
TL;DR: A model predictive control based method for determining optimal treatment interruption schedules for this purpose and provides a clinically implementable framework for calculating interruption schedules that are robust to errors due to measurement and patient variations.

Journal ArticleDOI
TL;DR: In this paper, based on the concept of representing protein samples in terms of their pseudo-amino acid composition, the fuzzy K-nearest neighbors (KNN) algorithm has been introduced to predict membrane protein types, and high success rates were observed.

Journal ArticleDOI
Chao Chen1, Yuan-Xin Tian1, Xiaoyong Zou1, Peixiang Cai1, Jinyuan Mo1 
TL;DR: A novel predictor is developed for predicting protein structural class by employing a support vector machine learning system and using a different pseudo-amino acid composition (PseAA), indicating that the current predictor featured with the PseAA may play an important complementary role to the elegant covariant discriminant predictor and other existing algorithms.

Journal ArticleDOI
TL;DR: A novel approach called "stacked generalization" or "stacking" has been introduced, which can combine several different types of classifiers through a meta-classifier to maximize the generalization accuracy.

Journal ArticleDOI
TL;DR: The evolution of a nervous system not only changed the way that information was transmitted between cells and profoundly altered the nature of the individuals in which it was present, it also led to a new type of heredity-social and cultural heredite based on the transmission of behaviourally acquired information.

Journal ArticleDOI
TL;DR: In this approach, the ordinary differential equations with a stochastic component for mRNA and protein levels in a single cells yield a system of first-order partial differential equations (PDEs) for two-dimensional probability density functions (pdf).

Journal ArticleDOI
TL;DR: It is argued that the evolution of germ-soma specialization and the emergence of individuality at a new higher level during the transition from unicellular to multicellular organisms are also consequences of trade-offs between the two components of fitness-survival and reproduction.

Journal ArticleDOI
TL;DR: The model is used to explain experimental observations of the opposite effects of raising cytosolic Ca(2+)in low and high glucose, and to predict the effects of a mutation in the mitochondrial enzyme nicotinamide nucleotide transhydrogenase in pancreatic beta-cells.