Projects: COVID-19 Disease Map
Institutions: University of Tübingen

Expertise: Systems Biology, Computational Systems Biology, Databases, Dynamic modelling, Java, Mathematical modelling, Metabolic Engineering, Disease Maps, Curation, Modeling, Data Integration, Constraint-based Modelling, Parameter estimation
Tools: SBML, SBGN, SBGNML, JSBML, Jupyter, Python, cobrapy toolbox, SBSCL, InSilico, Kinetic Modeling
Andreas Dräger is the assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tübingen in Germany. His group aims to combat the spreading antibiotics resistances by using mathematical modeling and computer simulation of bacterial systems up to entire microbiomes and host-pathogen interactions. In doing so, his group actively contributes to the advancement of various COMBINE standards.
Projects: COVID-19 Disease Map
Institutions: Barcelona Supercomputing Center

I completed my BSc in Biology and MSc in Cell Biology by the University of Valencia. During my last undergrad year I participated in synthetic biology’s iGEM competition where I dove in the use of models in Biology, which pushed me to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia.
My research on Metabolic Engineering of hydrogen in cyanobacteria led me to be visiting researcher at Uppsala University, Denmark Technical University and EMBL Heidelberg.
...
I'm currently a Postdoc at the Institute of Technical Biochemistry in Stuttgart University. My project involves the experimental validation of the Indirect Enzymatic Dehydration Via Phosphorylation and Dephosphorylation of Isobutanol for Isobutene production.
Projects: EmPowerPutida
Institutions: Wageningen University & Research

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
Projects: BioZEment 2.0, BESTER, Auromega, C1Pro
Institutions: SINTEF
Projects: INBioPharm
Institutions: Norwegian University of Science and Technology
Roles: Postdoc
Expertise: Molecular Biology, Metabolic Engineering, Saccharomyces cerevisiae, Genetics
Tools: Genetic modification, Genetics, Metabolic Engineering, Molecular Biology, Fermentation
Projects: WURSynBio
Institutions: Wageningen University & Research
Projects: WURSynBio, INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
Projects: EmPowerPutida
Institutions: University of Stuttgart
Roles: PhD Student
Expertise: Molecular Biology, Metabolic Engineering
PhD student, Institute of Biochemical Engineering at the University of Stuttgart
Projects: SYSTERACT
Institutions: University of Tübingen
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
Roles: Postdoc
Expertise: Genetics, Microbiology, Metabolic Engineering
Tools: antiSMASH, CloneManager, artemis
Team leader "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
Expertise: Microbiology, genetic engineering, Fermentation, Cell biology, Metabolic Engineering
Research Scientist in the Biotechnology and Nanomedicine department at the non-profit research institution, SINTEF, in Norway.
Projects: SilicoTryp, SYSTERACT, SynBio4Flav
Institutions: University of Glasgow, Chalmers University of Technology

Projects: MetApp, LEANPROT, C1Pro
Institutions: SINTEF, Norwegian University of Science and Technology
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
...
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, FAIRDOM Templates
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

Roles: Postdoc
Expertise: Systems Biology, Metabolic Engineering, Stoichiometric modelling, Kinetic modelling, Data Management, Metabolic Networks
Tools: Python, Copasi, Matlab, COBRA toolbox
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
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
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 &
...
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
Roles: Project Coordinator
Expertise: Microbiology, Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, Biotechnology
Tools: Bioinformatics, Genetic modification, Proteomics, Fermentation, Microarray analysis, Computational Systems Biology, Metabolic Engineering, microbiology techniques, reverse engineering, computational platform development, metabolic netwlrk visualization
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
...
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: COSMIC
Institutions: Wageningen University & Research
Expertise: Microbiology, Genetics, Molecular Biology, Systems Biology, Anaerobic Microbiology, Clostridial Genetics, Metabolic Engineering, Synthetic Biology, bacterial metabolism, carbon metabolism, Clostridium
Tools: Microbiology, Molecular Biology, Chromatography, Molecular biology techniques (RNA/DNA/Protein)
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).
Submitter: 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.
First draft of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) .
Creators: David San León Granado, Juan Nogales, Álvaro Gargantilla Becerra
Submitter: David San León Granado
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Organism: Pseudomonas putida
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
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
...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Modelling analyses: Flux Balance Analysis of multi-compartment meta... and 1 hidden item