35 Result(s)
within
Edda Klipp
Life Sciences
English
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Article
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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Article
Open AccessModeling indicates degradation of mRNA and protein as a potential regulation mechanisms during cold acclimation
Plants are constantly exposed to temperature fluctuations, which have direct effects on all cellular reactions because temperature influences reaction likelihood and speed. Chloroplasts are crucial to temperat...
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Article
Open AccessPublisher Correction: MEMOTE for standardized genome-scale metabolic model testing
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
MEMOTE for standardized genome-scale metabolic model testing
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Article
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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Article
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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Article
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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Protocol
Using Confocal Microscopy and Computational Modeling to Investigate the Cell-Penetrating Properties of Antimicrobial Peptides
Antimicrobial peptides (AMPs) may display the ability to penetrate cells, which may be relevant for their antibiotic activity. To investigate the relevance of the penetrating activity for the antibiotic activi...
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Article
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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Article
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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Article
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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Article
Bridging the gaps in systems biology
Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding—the elucidation of the basic and ...
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Article
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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Article
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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Reference Work Entry In depth
Modeling Approaches of Cell Cycle Regulation by Signaling Pathways for External Stress
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Article
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs
Heat shock protein 90 (HSP90) is an essential, abundant and ubiquitous eukaryotic chaperone that plays crucial roles in the folding of its client proteins. Fun...
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Article
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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Chapter and Conference Paper
Zooming in on Yeast Osmoadaptation
Saccharomyces cerevisiae is considered as a model organism for the investigation of cellular and molecular processes and gene regulation. Specifically, the response of S. cerevisiae to increase in osmolarity of ...
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Article
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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Protocol
Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade
Cellular networks and processes can be mathematically described and analyzed in various ways. Here, the case example of a MAP kinase (MAPK) cascade is used to detail steps in the formulation of a system of ord...
