Projects: EmPowerPutida
Institutions: Wageningen University & Research
Disciplines: Not specified
Roles: PhD Student
Expertise: Metabolic Engineering, metabolism, metabolic networks, Biotechnology, Synthetic Biology, Systems Biology, Mathematical modelling
Tools: Flux balance analysis, COBRA toolbox, Matlab, Computational Systems Biology
I'm currently a PhD student in Laboratory of Systems and Synthetic Biology in Wageningen University & Research. My project involves using genome scale metabolic modelling to understand and improve chemical production capacities of microorganism.
Projects: EmPowerPutida
Institutions: Wageningen University & Research
Disciplines: Not specified
Roles: Not specified
Expertise: Molecular Biology, Metabolic Engineering, Metabolic modelling, Fermentation
Tools: model prediction testing, Microbiology, Molecular Biology
Institutions: University of Rostock

Disciplines: Not specified
Roles: Postdoc
Expertise: plant biotechnology, Molecular Biology, recombinant protein production, protein expression, Metabolic Engineering
Projects: BioZEment 2.0, BESTER
Institutions: SINTEF
Disciplines: Not specified
Roles: Not specified
Expertise: Molecular Biology, Molecular microbiology, Microbiology, Genetics, Genomics
Tools: Biochemistry and protein analysis, Metabolic Engineering, Molecular Biology, Microbiology, Biochemistry, Genetic modification
Projects: INBioPharm
Institutions: Norwegian University of Science and Technology
Disciplines: Experimentalist
Roles: Not specified
Expertise: Fermentation, Metabolomics, Metabolic Engineering, Mathematical modelling, Microbiology
Tools: Flow cytometry, Fermentation, Metabolomics, Metabolic Engineering, Matlab, Microbiology
Disciplines: Experimentalist
Roles: Postdoc
Expertise: Molecular Biology, Metabolic Engineering, Saccharomyces cerevisiae, Genetics
Tools: Genetics, Metabolic Engineering, Molecular Biology, Fermentation, Genetic modification
Projects: WURSynBio
Institutions: Wageningen University & Research
Disciplines: Not specified
Roles: Project Coordinator
Expertise: Microbiology, Molecular Biology, Fermentation, Metabolic Engineering
Tools: Molecular Biology, Metabolic Engineering, Fermentation, Genetic modification, Transcriptomics, Microbiology
Projects: WURSynBio
Institutions: Wageningen University & Research
Disciplines: Experimentalist
Roles: Not specified
Expertise: Plant biology, Biochemistry, Molecular Biology, plant metabolism, Metabolic Engineering, secondary metabolites, terpenes, aromatic compounds
Tools: Biochemistry and protein analysis, Enzyme assay, molecular biological techniques (RNA/DNA techniques, Metabolomics, Metabolic Engineering
Projects: EmPowerPutida
Institutions: University of Stuttgart
Disciplines: Not specified
Roles: PhD Student
Expertise: Molecular Biology, Metabolic Engineering
Tools: Not specified
PhD student, Institute of Biochemical Engineering at the University of Stuttgart
Disciplines: Modeller, Bioinformatician
Roles: Not specified
Expertise: Metabolic Engineering, Kinetic modelling, dynamics and control of biological networks, Bioinformatics, Databases, Mathematical modelling, Molecular Biology, Systems Biology
Tools: SBML, Python, Petri Nets, Snoopy, Marcie, Charlie, Matlab, Jupyter, FBA, MySQL, HTML, Javascript, PHP, CSS
Projects: SYSTERACT
Institutions: University of Tübingen
Disciplines: Not specified
Roles: Not specified
Expertise: Microbiology, Molecular Biology, Genetics, Transcriptomics, Metabolic Engineering, nitrogen metabolism, Streptomyces coelicolor, Actinobacteria, antibiotic production
Tools: Fermentation, Genetic modification, Molecular biology techniques (RNA/DNA/Protein), Proteomics, Transcriptomics, Biochemistry and protein analysis
Disciplines: Not specified
Roles: Postdoc
Expertise: Genetics, Microbiology, Metabolic Engineering
Tools: antiSMASH, CloneManager, artemis
Disciplines: Modeller, Experimentalist
Roles: Project Coordinator
Expertise: Systems Biology, Metabolic Engineering, Synthetic Biology, Proteomics, Metabolomics, Fluxomics
Tools: Mass spectrometry (LC-MS/MS), 13C-MFA, High-throughput phenotyping, Integrative modeling
Team leader "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
Disciplines: Experimentalist
Roles: Not specified
Expertise: Microbiology, genetic engineering, Fermentation, Cell biology, Metabolic Engineering
Tools: Not specified
Research Scientist in the Biotechnology and Nanomedicine department at the non-profit research institution, SINTEF, in Norway.
Projects: SilicoTryp, SYSTERACT
Institutions: University of Glasgow, Chalmers University of Technology

Disciplines: Modeller, Experimentalist
Roles: Not specified
Expertise: genome-scale modeling, Kinetic modelling, metabolism, Data integration, Metabolomics, Metabolic Engineering, Transcriptomics, Microbiology
Tools: COBRA toolbox, Copasi, RNAseq, Bioreactor experiments, Metabolomics, Dynamic modelling, R, Matlab
Institutions: SINTEF, Norwegian University of Science and Technology
Disciplines: Not specified
Roles: Project Coordinator
Expertise: Microbiology Biochemistry Molecular biology Genetics Enzymology Synthetic biology Regulatory metabolic networks, Metabolic Engineering
Tools: Not specified
Since 1st of January 2015 I am Professor in synthetic biology at the Norwegian University of Science and Technology (NTNU) institute of biotechnology. Before that I was research director in the non-profit research institution SINTEF. My major research activities are within microbial molecular biology, mainly combining metabolic engineering, synthetic biology and systems biology to develop microbial cell factories, and focusing both on the products and on the raw materials. The research includes
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Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Institutions: School of Computer Science, University of Manchester, Manchester Centre for Integrative Systems Biology, University of Manchester

Disciplines: Modeller
Roles: Postdoc
Expertise: Data Management, Stoichiometric modelling, Kinetic modelling, Systems Biology, Metabolic Engineering, metabolic networks
Tools: COBRA toolbox, Python, Copasi, Matlab
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: COSMIC
Institutions: University of Nottingham
Disciplines: Not specified
Roles: Not specified
Expertise: Anaerobic Microbiology, Clostridial Genetics, Pathogenesis, Metabolic Engineering, Synthetic Biology, gene regulation
Tools: Transcriptomics, Genetic modification, Molecular Biology
A molecular microbiologist with a passion for Clostridia! Interested in the development of more effective countermeasures (diagnosis, prevention & treatment) against pathogens, specifically Clostridium difficile and Clostridium botulinum as well as the exploitation of the medical and industrial properties of beneficial strains, specifically in cancer therapy and biofuel production
Projects: BaCell-SysMO
Institutions: University of Braunschweig
Disciplines: Not specified
Roles: Not specified
Expertise: yeast, fungi, Metabolic Pathway Analysis and Engineering Microbial Physiology Modeling of Biological Networks Industrial Systems Biotechnology White Biotech...
Tools: In silico Metabolic Network Analysis, Fluxomics, Metabolic Engineering, Fermentation, Metabolomics
University Education: 1987-1993, Biotechnology (Diploma), Technische Universität Braunschweig, Germany.
Dissertation: 1993-1996, Disseration German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany.
Habiliation: 2006, Saarland University, Saarbrücken, Germany.
Positions
1993-1996: Research Assistant, German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany.
1997-1998: Post-doc at Department of Applied Chemistry &
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Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua
Institutions: Helmholtz Centre for Infection Research Braunscheig, Wageningen University & Research
Disciplines: Not specified
Roles: Project Coordinator
Expertise: Biotechnology, Systems Biology, Optimal experimental design, Mathematical modelling of biosystems and bioprocesses, Microbiology
Tools: reverse engineering, computational platform development, metabolic netwlrk visualization, microbiology techniques, Metabolic Engineering, Computational Systems Biology, Microarray analysis, Fermentation, Proteomics, Genetic modification, Bioinformatics
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological
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Projects: BaCell-SysMO
Institutions: University of Greifswald
Disciplines: Experimentalist
Roles: Not specified
Expertise: Metabolic Engineering, Metabolomics, Molecular Biology
Tools: NMR, HPLC, GC and LC analysis of metabolites, GC and LC analysis of metabolites | Analysis of signal molecules | Handling of anaerobic bacteria |, Molecular Biology, Microbiology
Projects: COSMIC
Institutions: Wageningen University & Research
Disciplines: Experimentalist
Roles: Not specified
Expertise: Clostridium, carbon metabolism, bacterial metabolism, Anaerobic Microbiology, Clostridial Genetics, Metabolic Engineering, Synthetic Biology, Systems Biology, Molecular Biology, Genetics, Microbiology
Tools: Molecular biology techniques (RNA/DNA/Protein), Chromatography, Molecular Biology, Microbiology
I'm an experimentalist 'Pre-doc' (I still have to finish my PhD thesis) and my work on the COSMIC project will focus on setting up a metabolomic analysis method for Clostridium acetobutylicum.
In the past I have worked on metabolic engineering of the same organism by disrupting genes to asses their impact on acid and solvent formation.
I'm looking forward to joining the COSMIC web-community. It hopefully will all us to stay in touch and update each other on advances in the (computer)lab.
RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).
Contributor: Natalie Stanford
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Designing a new way to predict engineering stra...
Study: Predicting engineering strategies for overprodu...
Organisms: No organisms
Models: iNS142 RobOKoD Redesigned Butanol Producing.
SOPs: RobOKoD SOP for Redesigning Butanol Producing S...
Data files: FBA result of RobOKoD designed e.coli strain.
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
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Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Contributor: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl...
Studies: Analysis of central carbon and energy metabolis...
Modelling analyses: Flux Balance Analysis of multi-compartment meta...