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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 AccessA comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae
Understanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with c...
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Article
Open AccessA transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle
Oscillating gene expression is crucial for correct timing and progression through cell cycle. In Saccharomyces cerevisiae, G1 cyclins Cln1–3 are essential drivers of the cell cycle and have an important role for ...
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Article
Open AccessGeneral solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks
Multimodality is a phenomenon which complicates the analysis of statistical data based exclusively on mean and variance. Here, we present criteria for multimodality in hierarchic first-order reaction networks,...
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Article
Open AccessAlterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations
Metabolic reprogramming is as a hallmark of cancer, and several studies have reported that BRAF and KRAS tumors may be accompanied by a deregulation of cellular metabolism. We investigated how BRAFV600E and KRASG...
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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
Monitoring cytochrome P450 activity in living hepatocytes by chromogenic substrates in response to drug treatment or during cell maturation
The metabolic activity of hepatocytes is a central prerequisite for drug activity and a key element in drug–drug interaction. This central role in metabolism largely depends on the activity of the cytochrome P...
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Article
Open AccessEstimation of immune cell content in tumour tissue using single-cell RNA-seq data
As interactions between the immune system and tumour cells are governed by a complex network of cell–cell interactions, knowing the specific immune cell composition of a solid tumour may be essential to predic...
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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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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 AccessSystems Level Analysis of the Yeast Osmo-Stat
Adaptation is an important property of living organisms enabling them to cope with environmental stress and maintaining homeostasis. Adaptation is mediated by signaling pathways responding to different stimuli...
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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
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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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 ...
