Investigations

75 Investigations visible to you, out of a total of 110

Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation

Studies: Figure 2: Model calibration with time-resolved quantitative immunoblot d...

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

One of these activities is antibiotic production and is widespread in streptomycetes
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Studies: ScoCyc metabolic pathway curation, Timeseries 1

Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.

Studies: Comparison of S. solfataricus grown on l-fucose and d-glucose

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Full name of the project: "Control of Engineered Metabolism by Flowering and Temperature Triggered Plant Regulatory Networks".
This is a project within ERA-net on Synthetic Biology: www.erasynbio.eu funded in its second call (https://www.erasynbio.eu/joint-calls/2nd-call).

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Optimisation of kinetic models by global stochastic methods is hardly predictable and therefore complicated to automate. We attempt to explore different ways to utilise optimisation methods, termination and other criteria to make it automatic and simple to use.

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Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and
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Studies: Experimental study for hands on session

The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.

Studies: Model analysis, Model construction, Model validation

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Studies: Hands-On: Tyson1991 - Cell Cycle 6 var

Tool and work flow development for computational biology.

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Gene expression study is a part of Salmon genome paper. The work was carried out in 2014/2015. This work is published in Nature 533, 200–205 (12 May 2016) titled "The Atlantic salmon genome provides insights into rediploidization"

Studies: Sally RNA Sequencing, Sally whole genome sequencing

This investigation contains spreadsheet templates and examples for SEEK users to download and use for structuring experimental data. These templates were developed by the SysMO-DB team and the SysMO PALs

Studies: Creating Templates for Proteomics, Creating Templates for Transcriptomics, Creating template for metabolomics data

Files used in the presentation on data and model management in systems biology.

Studies: Studying the increased affinity of calmodulin for calcium

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Studies: Figure 2B: Transcriptional response to a sudden increase in extracellul...

Basically extending SYSMO-LAB 1st phase into second with addition of fourth species, Lb. plantarum. The main focus is amino acid metabolism. primary metabolisms, like glycolysis is also interest.

Studies: Arginine and Glutamine metabolism in S. pyogenes, Determination of essential amino acids for Streptococcus pyogenes

Here SYSMO-LAB put all there pre-liminary data files or models ordered per person and project

Studies: Pre-liminary data from Martijn Bekker, Pyruvate formate-lyase (PFL), allosteric regulation of pyruvate kinase

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped
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Studies: Analysis of central carbon and energy metabolisms of growing Arabidopsis...

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range

Studies: Figure 3A: Model calibration with experimental data of JAK2-STAT5 signal...

ExtremoPharm project is dedicated to a poorly investigated fundamental problem of antagonistic interactions between extremophilic microorganisms in their communities, namely, to the investigation of the ability of extremophiles to produce secondary metabolites displaying biocidic and cytotoxic activities. This project has also an important application potential, since nowadays, the search of novel secondary metabolites with antimicrobial, cytotoxic, antineoplastic and other properties is one of
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