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Web page: http://www.uva.nl
Country: Netherlands
City: Amsterdam
Address:
Nieuwe Achtergracht 166
1018WV
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Institutions: University of Amsterdam
Roles: Postdoc
Expertise: Microbiology, Biochemistry, Molecular Biology, Escherichia coli, HPLC
Tools: Biochemistry, Molecular Biology, Fermentation, Chromatography
Martijn Bekker (1979) was born in Amstelveen (The Netherlands). He started his studies in biology in 1997 at the University of Amsterdam, and graduated in 2003 with specializations in molecular microbiology and in immunology. The internships during his undergraduate studies were carried out in the labs of Prof. dr. B. Oudega (VU, Amsterdam, The Netherlands) and Prof. dr. F. Heffron (OHSU, Portland, Oregon, USA).
He continued with his graduate studies in 2003 in the Laboratory for Molecular Microbial
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Expertise: Metabolic Control Analaysis, Metabolomics, Metabolic Networks
Tools: Metabolomics, Transcriptomics
POSITION
Professor of Systems Medicine/Biology at the Academic Medical Center, Amsterdam and University Medical Center Groningen, Groningen, The Netherlands
RESEARCH
My major projects focus on understanding the etiology of metabolic syndrome and its comorbidities type2 diabetes and cardiovascular disease. To get grip on the sequence of events in disease progression we make use of longitidunal models and apply multiscal systems biology approaches.
PUBLICATIONS
My published work can be found at:
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Projects: SUMO
Institutions: University of Amsterdam
General microbiologist with specific interests in signal transduction mechanisms, biophysics and photobiology
Projects: SysMO-LAB, Sustainable co-production
Institutions: University of Amsterdam, Wageningen University & Research
Projects: HUMET Startup
Institutions: University of Amsterdam
Expertise: neuroanatomy, endocrinology, chronobiology
POSITION
Professor of Experimental Neuroendocrinology at the Academic Medical Center (AMC) and the Hypothalamic Integration Mechanisms group at the Netherlands Institute for Neuroscience (NIN), Amsterdam, The Netherlands
RESEARCH
My major projects focus on understanding how the hypothalamic biological clock controls hormonal rhythms and energy metabolism. For this we mainly use the rat as an animal model. Important techniques include blood sampling from and targeted brain infusions in awake and
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Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe, University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB)
Roles: Project Coordinator
I have modelling expertise in precise kinetic models of metabolism and signal transduction; metabolic control analysis, hierarchical regulation analysis, non-equilibrium dynamics, statistical mechanics, enzyme kinetics, flux balance analysis. Energy and carbohydrate metabolism in Archaea, Bacteria and human; ammonium assimilation in Bacteria; differential network-based drug design; cancer metabolic rewiring; cell cycle; genome wide metabolic map and inborn errors of metabolism; epigenetics.
Projects: SUMO
Institutions: University of Amsterdam
Institutions: University of Amsterdam
Professor Quantitative Microbial Physiology
Dept Mol Mic Phys
Swammerdam Inst Life Sc
University of Amsterdam
Projects: SUMO
Institutions: University of Amsterdam
Expertise: Transcriptomics, Bacillus subtilis, Escherichia coli, stress responses
Tools: Chemostats, HPLC, phage transduction
Projects: SUMO
Institutions: University of Amsterdam
Johan van Beilen University of Amsterdam j.w.a.vanbeilen@uva.nl;
Expertise: chromatin, Epigenetics, nuclear organisation, DNA repair
Tools: quantitative microscopy, Biochemistry, Systems Biology, Cell biology
POSITION
I am an emeritus professor in Biochemistry at the University of Amsterdam (retired 2010).
RESEARCH
My research focussed on the human chromatin in its natural environment, i.e. the nucleus of cultured living human cells.
Aspects, such as the dynamic folding of the chromatin fiber inside the nucleus and local chemical modification of histones and DNA at genetic loci, are the physical and chemical basis for epigenetic regulation of gene expression. In my group we worked parallel on human
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Projects: SysMO-LAB
Institutions: University of Amsterdam
Roles: Postdoc
Expertise: carbon metabolism, Biochemistry, Fermentation, Glycolysis, Microbiology
Tools: Chromatography, Fermentation, Biochemistry and protein analysis
POSITION
Prof. Dr. Natal van Riel is Professor in Computational Modelling at the Academic Medical Center - University of Amsterdam (AMC - UvA) and Associate Professor in Systems Biology and Metabolic Diseases at the Department of Biomedical Engineering of the Eindhoven University of Technology (TU/e).
RESEARCH
My research applies mathematical modelling and computation to study metabolic diseases, in particular Metabolic Syndrome and co-morbidities. Systems biology approaches are developed for
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Projects: SUMO
Institutions: University of Amsterdam
Started out in the field of environmental analytical chemistry and after a few years working in that field, switched to process analysis and chemometrics. Next during my PhD work I came into Life Sciences doing data analysis on microbial batch fermentations (Escherichia coli). During my PhD work my main task was to integrate prior knowledge into data analysis, so called grey modeling. Now my focus lies on white models (based on ordinary differential equations), more specifically building a detailed
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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
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, VU University Amsterdam, University of Amsterdam

Roles: Project Coordinator, Vice Coordinator
Expertise: Systems Biology, Thermodynamics
Tools: Computational Systems Biology, Dynamic modelling, Systems Biology, Biochemistry
Systems Biologist
University of Amsterdam
Free University Amsterdam
University of Manchester
Infrastructure Systems Biology.NL (ISBE.NL)
Modelling COVID-19 epidemics : the training course organized by ISBE-NL, ELIXIR-LU, and EOSC-Life
Programme: Independent Projects
Public web page: https://elixir-luxembourg.org/events/2020_11_30_COVID19_modelling_training
Start date: 30th Nov 2020
End date: 31st Jan 2021
Organisms: Not specified
Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that
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Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Start date: 1st Mar 2020
End date: 24th Mar 2023
Organisms: Homo sapiens
Glycon proposal preparation
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Organisms: Sulfobacillus thermosulfidooxidans
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Organisms: Homo sapiens
We are modelling ROS management and mitochondrial dysfunction. Mitochondria produce both energy and reactive oxygen species (ROS), and suffer from ROS. Experimental data from University Milan-Bicocca.
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Organisms: Homo sapiens
Aim of HUMET Startup Project is to make an inventory of expertise, research goals, resources etc. of the HUMET Coaliytion of the Willing.
Programme: HUMET
Public web page: Not specified
Organisms: Homo sapiens
Comparative Systems Biology: Lactic Acid Bacteria
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=57
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling
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Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
Organisms: Escherichia coli, Escherichia coli K-12
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus