Institutions: UNIBI: Bielefeld Universityorcid.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.
Institutions: Wageningen University & Research
Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Projects: HUMET Startup
Institutions: Leiden University Medical Centerorcid.org/0000-0002-2172-7394
Professor in genetics and systems biology of the metabolic syndrome
Professor of Systems Medicine/Biology at the Academic Medical Center, Amsterdam and University Medical Center Groningen, Groningen, The Netherlands
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.
My published work can be found at:
Team leader "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
Expertise: yeast, fungi, Metabolomics, Proteomics, Stoichiometric modelling, carbon metabolism, Systems Biology, dynamics and control of biological networks, coupling metabolome and environome, rapid sampling experiments, Biochemistry
Tools: parameter estimation, ODE, HPLC, GC and LC/MS analysis of metabolites, Mass spectrometry (LC-MS/MS), continuous cultivation, Enzyme assay, Material balance based modeling, stimulus response experiments, Chromatography, Fermentation, Matlab, Metabolomics, Biochemistry and protein analysis
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
Institutions: University of Milano-Bicocca
I am a PostDoc working on yeast metabolomics. During my PhD I studied the interplay between metabolism, cell cycle and signalling, mainly focusing on the Snf1/AMPK pathway. I am currently interested in studying metabolic rewiring caused by different nutrients, generating high-throughput data suitable for modelling.
Tools: SQL, Material balance based modeling, Mathematica, Matlab, Copasi, JWS Online, Algebraic equations, Linear equations, ODE, Partial differential equations, SBML, Metabolomics, Model organisms, Cell biology, Computational and theoretical biology, Molecular Biology
I'm a modeller, specialized in kinetic modeling of biochemical networks. My focus in the SysMO-LAB consortium is on creating models of Lactococcus lactis glycolysis and couple this to other related lactic acid bacteria like Streptococcus pyogenes and Enterococcus faecalis. Besides kinetic modeling, I'm also interested in combining various modeling techniques (genome-scale modeling, qualitative modeling).
I am assistant professor at the Laboratory of Microbiology and my interest is in the area of molecular microbiology. Research focuses on the analysis of the metabolism of anaerobic fermentative bacteria and archaea, especially with respect to biofuel production (hydrogen, butanol). Within SysMo our tasks concern the effect of butanol stress, using metabolomics and transcriptomics.
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.
1993-1996: Research Assistant, German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany.
1997-1998: Post-doc at Department of Applied Chemistry &
PostDoc at Wageningen University, Laboratory of Microbiology
Roles: Vice Coordinator
Expertise: genome-scale modeling, enzyme kinetics, Metabolic Pathway Analysis and Engineering Microbial Physiology Modeling of Biological Networks Industrial Systems Biotechnology White Biotech..., dynamics and control of biological networks
Since August 2008 I am professor in Systems Biology at the VU University Amsterdam. My Systems Bioinformatics group focusses on systems biology with a special focus on integrative bioinformatics. It aims at forming bridges between the classical bottom-up approaches in systems biology and the more data-driven approaches in classical bioinformatics. We combine experimental, modeling and theoretical approaches to study cellular physiology, with an emphasis on metabolic networks.
I am currently Professor of Systems Biology at the University of Manchester. My research interests focus on the development of innovative computational approaches for post-genomic systems biology, statistical methods for high-throughput biological experimentation and the dynamic modelling of cellular systems. This work is highly interdisciplinary and usually involves close collaboration with experimental biologists and clinicians. A recurrently theme is the study of complex cellular networks at
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
Contributor: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Snapshots: No snapshots
Investigation: Metabolic analysis of effects of sucrose transl...
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: ZucAt: FBA constraints for dark conditions, ZucAt: FBA constraints for light conditions, ZucAt: FBA solution of the model under dark gro..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: The compound database, ZucAt: The gene database, ZucAt: The stoichiometric matrix of the model, ZucAt: The transformers database, ZucAt: the model documentation
Contributor: Theresa Kouril
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Organisms: Sulfolobus solfataricus (batch)
SOPs: No SOPs
Data files: Metabolomics L-fuc vs D-glc
Master file, aggregates metabolite concentrations inside and outside the cell, protein copy number and flux estimates for metabolites in the core model. Based on all internal metabolite concentrations, external metabolite concentrations from growth curve data, flux of glucose, lactate and acetate based on growth curve data and protein copy number data for enzyme concentrations. Combines absolute and relative measurements and metabolomics measurements from different experiment to get an as complete
Intracellular metabolome analysis of S. solfataricus P2 grown on caseinhydrolysate or D-glucose as sole carbon source.
Samples were analyzed with GC-MS. CoA derivatives were analyzed with LC-MS.
Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS
intracellular metabolites measured by LC/MS
Investigations: Multiomics study of Bacillus subtilis under osm...
Assays: intracellular metabolites
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
Contributor: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl...
Modelling analyses: Flux Balance Analysis of multi-compartment meta...
Date Published: 1st Dec 2016
Journal: BMC Plant Biol
Citation: BMC Plant Biol 16(1) : e00669
Date Published: 1st Apr 2015
Citation: Metabolomics 11(2) : 286
Date Published: 1st Aug 2015
Journal: Journal of Thermal Biology
Citation: Journal of Thermal Biology 52 : 117
Authors: Maksim Zakhartsev, Bock Christian
Date Published: 1st Feb 2010
Journal: Analytical Biochemistry
Date Published: 1st Dec 2011
Journal: Journal of Chromatography B