Journal of Theoretical Biology
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Journal of Theoretical Biology 359:IFC (2014)
Journal of Theoretical Biology 354:IFC (2014)
Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network mod...
We have developed a robust, accurate and high throughput computational model using two discrete sample representation methods Pseudo amino acid composition (PseAAC) and split amino acid composition. Various classification algorithms including probabilistic neural network (PNN), K-nearest neighbor, d...
Analysis of an epidemic model with awareness decay on regular random networks.
We interpret the dynamics of the system in this region and prove that the existence of bifurcation for this second epidemic threshold crucially depends on the absence of awareness decay. We show that the continuum of equilibria that characterizes the slow die-out dynamics collapses into a unique equ...
Maximizing yields of virulent phage: the T4/Escherichia coli system as a test case.
A hybrid mathematical model was devised to obtain optimal values for bacterial doubling time and initial phage/bacteria multiplicity of infection for the purpose of reaching the highest possible phage titers in steady-state exponentially growing cultures. The computational model consists of an initi...
Nonlinearity in cytoplasm viscosity can generate an essential symmetry breaking in cellular behaviors.
We investigated how the nonlinearity infers the cellular behaviors and whether nonlinearity-specific behaviors exist. We modeled the developed plasmodium of the slime mold Physarum polycephalum as a network of branching tubes and examined the linear and nonlinear viscous cytoplasm flows in the tubes...
Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts.
We show that both methods in fact yield identical estimators for the correlation coefficient and regression gradient of correlated traits, indicating that reconstructed ancestral states are a valid source of information about correlated evolution. We show that the independent contrast associated wit...
Species radiation by DNA replication that systematically exchanges nucleotides?
RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the...
Core and specific network markers of carcinogenesis from multiple cancer samples.
Cancer is the leading cause of death worldwide and is generally caused by mutations in multiple proteins or the dysregulation of pathways. Understanding the causes and the underlying carcinogenic mechanisms can help fight this disease. In this study, a systems biology approach was used to construct...
Stochastic evolution of staying together.
We analyze the fixation probability of a mutant that has the ability to stay together. We assume that the size of the complex affects the reproductive rate of its units and the probability of staying together. We examine the combined effect of natural selection and random drift on the emergence of s...