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54 Result(s)
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Chapter
MicroRNA-Regulated Networks: The Perfect Storm for Classical Molecular Biology, the Ideal Scenario for Systems Biology
MicroRNAs (miRNAs) are involved in many regulatory pathways some of which are complex networks enriched in regulatory motifs like positive or negative feedback loops or coherent and incoherent feedforward loop...
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Chapter
Reproducibility of Model-Based Results in Systems Biology
Science requires that results are reproducible. This is naturally expected for wet-lab experiments and it is equally important for model-based results published in the literature. Reproducibility, in general, ...
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Article
Diagrams as locality aids for explanation and model construction in cell biology
Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically t...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Multi-compartmental modeling of SORLA’s influence on amyloidogenic processing in Alzheimer’s disease
Proteolytic breakdown of the amyloid precursor protein (APP) by secretases is a complex cellular process that results in formation of neurotoxic Aβ peptides, causative of neurodegeneration in Alzheimer’s disea...
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Protocol
Modeling miRNA Regulation in Cancer Signaling Systems: miR-34a Regulation of the p53/Sirt1 Signaling Module
MicroRNAs (miRNAs) are a family of small regulatory RNAs whose function is to regulate the activity and stability of specific messenger RNA targets through posttranscriptional regulatory mechanisms. Most of th...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Modeling the Calvin-Benson cycle
Modeling the Calvin-Benson cycle has a history in the field of theoretical biology. Anyone who intends to model this system will look at existing models to adapt, refine and improve them. With the goal to stud...
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Article
Systems medicine and integrated care to combat chronic noncommunicable diseases
We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disor...
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Article
A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks
In this paper we present and discuss a model-based approach to link miRNA translational control with cell signalling networks. MicroRNAs are small regulatory RNAs that are able to regulate the activity and the...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Studies on mechanisms of interferon-gamma action in pancreatic cancer using a data-driven and model-based approach
Interferon-gamma (IFNγ) is a multifunctional cytokine with antifibrotic and antiproliferative efficiency. We previously found that pancreatic stellate cells (PSC), the main effector cells in cancer-associated ...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture
Clostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly efficient biofuel. Fo...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
A stem cell niche dominance theorem
Multilevelness is a defining characteristic of complex systems. For example, in the intestinal tissue the epithelial lining is organized into crypts that are maintained by a niche of stem cells. The behavior o...
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Book
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Chapter
The 2MA Cell Cycle Model
In this chapter we take the Tyson–Novák model [108] for the fission yeast cell cycle as a case study [159]. This deterministic model is a practical example using nonelementary reactions and relative concentrat...
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Chapter
Wet-Lab Experiments and Noise
In this chapter we review selected publications on noise and stochastic modeling that are linked to experimental studies. Due to the wide range of experimental technologies used to generate data, and because t...
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Chapter
Hybrid Markov Processes
Our focus so far has been on continuous-time, discrete-state-space Markov jump processes. These stochastic processes are conceptually suitable to biochemical reaction networks because the reaction events occur...
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Chapter
Introduction
All known living systems are made up of one basic structural and functional unit: the cell. Populations of interacting cells can form higher levels of structural and functional organization. Take, for example,...
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Chapter
Randomness
This chapter is intended to provide an informal introduction to concepts that are necessary for stochastic modeling. The goal is to prepare readers unfamiliar with probability theory for the next chapter, whic...
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Chapter
Stochastic Modeling of Biochemical Networks
In this chapter, we present a stochastic framework for modeling subcellular biochemical reaction networks. In particular, we make an effort to show how the notion of propensity, the chemical master equation (C...
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Chapter
Biochemical Reaction Networks
This chapter is a basic introduction to chemical reactions and chemical species. Different ways of quantifying the abundance of molecules lead to the notions of concentration. Similarly, a deterministic quanti...
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Chapter
Probability and Random Variables
The previous chapter provided an informal introduction to concepts that are necessary for stochastic modeling. So the readers who are happy with that material may skip this chapter on first reading and return ...
