Projects: SysMO-LAB, MOSES, PSYSMO, SulfoSys, SulfoSys - Biotec, EraCoBiotech 2 nd call proposal preparation, Make Me My Model, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, Xenophiles Systems Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated materialhttps://orcid.org/0000-0002-0443-6114
Systems Biologist University of Amsterdam Free University Amsterdam University of Manchester Infrastructure Systems Biology.NL (ISBE.NL) Systems Biology Amsterdam
Projects: SYSTERACT, Kinetics on the move - Workshop 2016, BESTER, iRhythmics, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke
Institutions: University of Rostockhttps://orcid.org/0000-0002-1678-0051
Projects: COVID-19 Disease Map
Institutions: University of Tübingenhttps://orcid.org/0000-0002-1240-5553
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
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 Centerhttps://orcid.org/0000-0002-7696-1241
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. ...
Institutions: UNIBI: Bielefeld Universityhttps://orcid.org/0000-0002-6100-9135
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.
Expertise: Systems Biology, Mathematical modelling, Biotechnology, Synthetic Biology, Metabolic Engineering, metabolism, Metabolic Networks, SARS-CoV 2, COVID-19, Pathway Curation, Pathway Analysis, Network Analysis
My research interest is in studying cellular and molecular pathways of COVID-19 disease.
Institutions: Wageningen University & Research
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0002-4790-7377
Team leader "Quantitative Microbial Phenotyping" Institute of Bio- and Geosciences, IBG-1: Biotechnology Forschungszentrum Jülich GmbH 52425 Jülich, Germany
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 Templateshttps://orcid.org/0000-0003-4958-0184
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
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
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
Roles: Project Coordinator
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 ...
Expertise: Microbiology, Genetics, Molecular Biology, Systems Biology, Anaerobic Microbiology, Clostridial Genetics, Metabolic Engineering, Synthetic Biology, bacterial metabolism, carbon metabolism, Clostridium
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
Investigation: Designing a new way to predict engineering stra...
Organisms: No organisms
Data files: FBA result of RobOKoD designed e.coli strain.
Snapshots: No snapshots
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) .
Submitter: David San León Granado
Model type: Metabolic network
Model format: SBML
Organism: Pseudomonas putida
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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 ...
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
Assays: Flux Balance Analysis of multi-compartment meta... and 1 hidden item