16 Result(s)
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Open Accesskboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models
Computational models of cell signaling networks are extremely useful tools for the exploration of underlying system behavior and prediction of response to various perturbations. By representing signaling casca...
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Open AccessOsmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae
Cell growth is well described at the population level, but precisely how nutrient and water uptake and cell wall expansion drive the growth of single cells is poorly understood. Supported by measurements of si...
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Open AccessTranscriptional timing and noise of yeast cell cycle regulators—a single cell and single molecule approach
Gene expression is a stochastic process and its appropriate regulation is critical for cell cycle progression. Cellular stress response necessitates expression reprogramming and cell cycle arrest. While previo...
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Open AccessA Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle
Precise timing of cell division is achieved by coupling waves of cyclin-dependent kinase (Cdk) activity with a transcriptional oscillator throughout cell cycle progression. Although details of transcription of...
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Open AccessThe game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression
The fungal pathogen Candida albicans colonizes the gastrointestinal (GI) tract of mammalian hosts as a benign commensal. However, in an immunocompromised host, the fungus is capable of causing life-threatening in...
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Open AccessNetwork reconstruction and validation of the Snf1/AMPK pathway in baker’s yeast based on a comprehensive literature review
The SNF1/AMPK protein kinase has a central role in energy homeostasis in eukaryotic cells. It is activated by energy depletion and stimulates processes leading to the production of ATP while it downregulates A...
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Open AccessStochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks
Cellular decision-making is governed by molecular networks that are highly complex. An integrative understanding of these networks on a genome wide level is essential to understand cellular health and disease....
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Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system
Cellular signaling is key for organisms to survive immediate stresses from fluctuating environments as well as relaying important information about external stimuli. Effective mechanisms have evolved to ensure...
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Open AccessGlobal dynamic optimization approach to predict activation in metabolic pathways
During the last decade, a number of authors have shown that the genetic regulation of metabolic networks may follow optimality principles. Optimal control theory has been succesfully used to compute optimal en...
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Open AccessReaction-contingency based bipartite Boolean modelling
Intracellular signalling systems are highly complex, rendering mathematical modelling of large signalling networks infeasible or impractical. Boolean modelling provides one feasible approach to whole-network m...
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Open AccessPropagating semantic information in biochemical network models
To enable automatic searches, alignments, and model combination, the elements of systems biology models need to be compared and matched across models. Elements can be identified by machine-readable biological ...
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Open AccessSTSE: Spatio-Temporal Simulation Environment Dedicated to Biology
Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in...
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Open AccessTIde: a software for the systematic scanning of drug targets in kinetic network models
During the stages of the development of a potent drug candidate compounds can fail for several reasons. One of them, the efficacy of a candidate, can be estimated in silico if an appropriate ordinary differential...
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Open AccessTowards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation
The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G0/G1 phase, a point called the restric...
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Open AccessMonte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network
Gene Regulatory Networks (GRNs) control the differentiation, specification and function of cells at the genomic level. The levels of interactions within large GRNs are of enormous depth and complexity. Details...
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Open AccessSBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for ...
