Projects: Sustainable coproduction
Institutions: Wageningen University & Research
Roles: Postdoc
Expertise: Dynamic modelling, Mathematical Economics, Mathematics, Game Theory
Tools: Latex, Stata, Matlab, Mathematica
Expertise: Systems Biology, Mathematical modelling, parameter estimation
I studied Engineering Cybernetics at the University of Stuttgart and the University of Wisconsin, Madison. After my graduation, I started my PhD studies in systems biology for which I received a Ph.D. degree in 2013. A few months later I became team leader at the Institute of Computational Biology at the Helmholtz Zentrum München. Since August 2015, I lead an independent junior research group at the Helmholtz Zentrum München.
My research focuses on the development of methods for the datadriven
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Projects: INBioPharm
Institutions: Norwegian University of Science and Technology
Roles: Postdoc
Expertise: Mathematical modelling, parameter estimation, Systems Biology
Tools: Dynamic modelling, Matlab, ODE, parameter estimation
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.
Roles: PhD Student
Expertise: Fermentation, Analytical chemistry
Tools: Fermentation, HPLC, Biochemistry, Matlab
Projects: SBEpo  Systems Biology of Erythropoietin
Institutions: German Cancer Research Center (DKFZ)
orcid.org/0000000209712309Roles: PhD Student
Expertise: Mathematical modelling, Single Cell analysis, Cell biology, Molecular Biology
Tools: Biochemistry, Systems Biology, Matlab, R
Researcher at the European Institute for Systems Biology and Medicine, working on networkbased data analytics within the EU eTRIKS Project.
Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Projects: FAIRDOM user meeting
Institutions: SYSBIO  Centre of Systems Biology
orcid.org/0000000265662844Expertise: Bioinformatics, Data Management, Databases, Microarray analysis, Systems Biology
Roles: PhD Student
Expertise: Automation, Bioreactor cultivation, Corynebacterium glutamicum, Systems Biology, Stoichiometric modelling
Tools: Automation, Matlab, COBRA toolbox, Liquid handling systems
PhD student @ "Quantitative Microbial Phenotyping"
Institute of Bio and Geosciences, IBG1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
Expertise: Mathematical modelling, Biofilms, (Bio)Process Design
Tools: Numerical modells, Comsol, Matlab
Projects: SilicoTryp, SYSTERACT
Institutions: University of Glasgow, Chalmers University of Technology
orcid.org/0000000235935792Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: VU University Amsterdam
Expertise: Single Cell analysis, Image analysis
I am a beginning PhD student at the VU in Amsterdam and study the heterogeneity of yeast cells at near zero growth conditions. I have a versatile background in Biophysics and Systems Biology.
Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: Åbo Akademi University
Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: Institute for Experimental Internal Medicine
Expertise: Mathematical modelling, Image processing
Tools: Matlab, Copasi, c++, Mathematica
I am a PhD student in the field of Systems Biology. In my PhD project I apply mathematical modelling to understand the role of time delay in biological systems containing delayed negative feedbacks.
Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: University of Tübingen
Trained as a Computer Scientist at the University of Jena, Germany, my interests drifted more and more towards "computing life" during my PhD at Simon Fraser University and the University of British Columbia, Canada. On one hand, that term captures that I got fascinated by the idea to understand life as a form of computation and to describe, reprogram, and reassemble parts of cells as described in many brilliant experiments from a spectrum of disciplines ranging from DNA computing to Synthetic
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Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: Imperial College London
I am a PhD student in the Theoretical Systems Biology group, based at Imperial College London.
The aim of my PhD is to understand how noise can be the driving force of decisionmaking processes (differentiation, selfrenewal, apoptosis or tumorgenesis), and what are our chances to control them. So far I have been working on method development for stochastic models, a moment closure framework and a stochastic reachability method, to look into celltocellvariability.
Projects: FAIRDOM, ICYSB 2015  International Practical Course in Systems Biology, FAIRDOM user meeting
Institutions: University of Zürich, ETH Zurich, Manchester Centre for Integrative Systems Biology, University of Manchester
Expertise: Bioinformatics, Proteomics, Genomics
Tools: Perl, Python, Matlab, Microarray analysis, Data Management, Computational Systems Biology
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student,
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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, FAIRDOM Templates
Institutions: School of Computer Science, University of Manchester, Manchester Centre for Integrative Systems Biology, University of Manchester
orcid.org/0000000349580184Roles: 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: SUMO
Institutions: University of Stuttgart
Tools: Dynamic modelling, Matlab, Copasi, Flux balance analysis
I recently joined the Institute for System Dynamics as a PhD student. I'm currently working on a dynamic model of nitrate respiration in E. coli.
Projects: SUMO
Institutions: University of Stuttgart
Expertise: Systems Biology, parameter estimation, Data Management, Mathematical modelling
Tools: Matlab, Mathematica, SBML, ODE
Former:
PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMODB pals for SUMO.
Now:
Industrial affiliation
Projects: SUMO
Institutions: University of Stuttgart
I'm interested in the application and development of methods of systems theory in biology (systems biology). In particulary I work on the following topics:
Thermodynamic constraints on biochemical network; Model reduction; Modeling and Analysis of metabolic regulation.
Projects: BaCellSysMO
Institutions: University of Stuttgart
Expertise: carbon metabolism, Signalling networks, metabolic networks, Nonlinear Dynamics, Systems Biology, stress responses, Mathematical modelling of biosystems and bioprocesses, Bacillus subtilis, Mathematical modelling, Biochemistry, Microbiology
Tools: fedbatch cultivation, Dynamic modelling, Computational Systems Biology, Deterministic models, continuous cultivation, Enzyme assay, Chromatography, Fermentation, Matlab, Mathematica, ODE, Computational and theoretical biology
I am a biologist in the lab of Prof. Reuss at the University of Stuttgart and I am working in the field of biotechnology and mathematical modelling.
Projects: SUMO
Institutions: University of Stuttgart
Expertise: Nonlinear Dynamics, parameter estimation, Mathematical modelling
PI of the SUMO work package "Detailed kinetic modelling, identification and analysis of the citric acid cycle and respiratory chains of E. coli". Director of the Institute for System Dynamics, Universität Stuttgart, Germany.
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunscheig
I am an engineer with a PhD degree in Chemical Engineering and had been working on dynamic modeling of mammalian cell culture fermentation in London for three years before moving into simulation of microbial systems. In this PSYSMO project I am mainly involved in modeling of PHAs synthesis. I am also a PAL since May 2009  2011 to coordinate data management and general communication among all 17 partners.
Projects: SysMOLAB
Institutions: University of Heidelberg
I am working on a kinetic model of the central metabolism as well as on a genome wide model of Streptococcus pyogenes.
Institutions: University of Stavanger
Expertise: biophysical chemistry, kinetics
Tools: fortran, madonna, enzyme kinetics, quantitative western blot analyses, Matlab, Perl
Physical chemist with expertise in experimental kinetics, molecular biology, and mathematical modeling.
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems.
I am a PAL and I am looking forward to communication with other SYSMO members.
Projects: STREAM
Institutions: University of Warwick
Research fellow in Bioinformatics at the Warwick Systems Biology Centre, University of Warwick.
Working on high throughput data analysis (microarray data, next generation sequencing) and data integration (database management, textmining, gene annotation via public databases)...
Projects: TRANSLUCENT
Institutions: University of Applied Sciences Koblenz, Rhein Ahr Campus
Expertise: Ma
Tools: Thermodynamics, Machine Learning, Biophysics, R, Matlab, Computational and theoretical biology
I am working in the mathematical modeling of potassium homeostasis. In addition, we are developing tools and methods for the statistical analysis of biological data.
Projects: NoisyStrep
Institutions: University of Cologne
Expertise: Statistical Physics, Mathematical modelling
Tools: fortran, stochastic methods, Stochastic models, Mathematica, Matlab, Python
I am a phd student working on statistical physics and complex systems and applying concepts from these fields to biology.
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: TRANSLUCENT
Institutions: University of Applied Sciences Koblenz, Rhein Ahr Campus
Grammar school until 1998
199899 Alternative civilian service
19992002 Professional education as male nurse
20022007 Study of Biomathematics
2007... PhD student in TRANSLUCENT project
Projects: SysMOLAB
Institutions: Wageningen University & Research
Expertise: Reactor models, dynamics of biological networks., Mathematical modelling, Bioinformatics
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 SysMOLAB 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 (genomescale modeling, qualitative modeling).
Projects: KOSMOBAC
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: MOSES, ExtremoPharm, ZucAt, GenoSysFat, DigiSal, EraCoBiotech 2 nd call proposal preparation, FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: University of Stuttgart, University of Hohenheim, Norwegian University of Life Sciences, Norwegian University of Science and Technology
orcid.org/0000000279739902Roles: Postdoc
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 (LCMS/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 postdoc 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 “stimulusresponse” methodology for the unraveling the dynamic structure of the network and to
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Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
orcid.org/0000000160961354Roles: Project Coordinator
Expertise: Nonlinear Dynamics, Data integration, Dynamic optimization., Optimal experimental design, bioreactor models, dynamics of biological networks, parameter estimation, coupling metabolome and environome, rapid sampling experiments, Data Management, Mathematical modelling
Tools: Dynamic modelling, evaluation of process dynamics, continuous cultivation, Material balance based modeling, stimulus response experiments, Fermentation, Matlab, SBML
Process engineer, modeling biological systems since 1985.
Expertise: Mathematical and statistical modeling, bioreactor models, dynamics of biological networks, dynamics and control of biological networks, parameter estimation, Reactor models, Mathematical modelling, Bioinformatics, Molecular Biology
Tools: evaluation of process dynamics, continuous cultivation, DIVA, differential algebraic equations, linux, Material balance based modeling, stimulus response experiments, Microarray analysis, Matlab, Linear equations, ODE, Model organisms, Single Cell analysis, SBML, Transcriptomics, Computational and theoretical biology, Bioinformatics
I'm an engineer at the MPI Magdeburg and I'm working in the field of mathematical modeling, model verification, parameter identification, model analysis and experimental design. I'm involved in two projects, KOsmoBac and PSYSMO.
Projects: TRANSLUCENT
Institutions: HumboldtUniversität zu Berlin
Projects: COSMIC
Institutions: University of Nottingham
I am a Birmingham and MRC Fellow in mathematical biology. Specialising in the modelling of gene regulation networks using both numerical and analytical approaches, my work spans a range of biological applications, from drug development to bioenergy to understanding bacterial behaviour. My MRC fellowship gave me the opportunity to gain experimental training in order to generate the complementary data required to adopt a truly interdisciplinary approach to mathematical modelling in biology.
I worked
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Projects: COSMIC, BaCellSysMO
Institutions: University of Rostock
Roles: Postdoc
Expertise: Statistical Physics, Data analysis, Systems Biology, bistability, Physics, dynamics of biological networks, dynamics and control of biological networks, Mathematical modelling
Tools: data modelling, Dynamic modelling, Computational Systems Biology, Stochastic models, C programming, differential algebraic equations, Mathematica, Matlab, ODE, Computational and theoretical biology
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Projects: COSMIC, BaCellSysMO, SYSTERACT, HUMET Startup, INCOME, BESTER, iRhythmics
Institutions: University of Rostock
Expertise: Data analysis Mathematical modelling Bioinformatics Systems biology, dynamics of biological networks, dynamics and control of biological networks
Tools: quantitative western blot analysis, Stochastic models, quantitative western blot analyses, differential algebraic equations, stimulus response experiments, Mathematica, Matlab, ODE, Computational and theoretical biology
Projects: COSMIC
Institutions: University of Rostock
biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock
Projects: PSYSMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Expertise: Mathematical modelling of biosystems and bioprocesses, Statistically and biologically inspired optimization algorithms, dynamics and control of biological networks, parameter estimation, Mathematical modelling
Tools: including:  Dynamic modelling  Parameter estimation  Optimal experimental design  Dynamic optimization, Computational Systems Biology, Mathematica, Matlab, Partial differential equations, ODE, Computational and theoretical biology
We are very interested in applying a systems approach (i.e. modelbased concepts and related computational tools) to problems from the biological domain. In particular, we are doing research in computational systems biology, targetting the following topics:
 Parameter estimation (inverse problems, model calibration) in biochemical pathways
 Optimal experimental design (optimal dynamic experiments) for Systems Biology
 Dynamic optimization (optimal control) of biosystems and bioprocesses

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Projects: KOSMOBAC
Institutions: MaxPlanckInstitute of Biochemistry Martinsried
Expertise: sequencing, Mathematical modelling, Bioinformatics, Molecular Biology, Biochemistry, Microbiology
Tools: Transcriptomics, qPCR, molecular biological techniques (RNA/DNA techniques, rtPCR, Fermentation, Matlab, Biochemistry and protein analysis, Bioinformatics, Molecular Biology, Microbiology
Professor in Jinan University, Guangzhou, China.
My research interest is in the modeling of translation. Connecting various processes in translation, we can investigate the impact of different factors on protein biosynthesis and biogenesis in genomewide scale. This may reveal various general mechanisms on control level of gene expression and folding efficiency regulation in different growth conditions.
Expertise: sensitivity analysis, Dynamic optimization., Systems Biology, Optimal experimental design, Mathematical modelling of biosystems and bioprocesses, dynamics and control of biological networks, parameter estimation
Tools: Dynamic modelling, Computational Systems Biology, Deterministic models, Stochastic models, parameter estimation, differential algebraic equations, Matlab, Partial differential equations, ODE
I am a postdoctoral researcher in the group of Julio Banga. My research is focused on computational systems biology with particular attention to the mathematical modelling of biosystems and bioprocesses. Some of the topics we address are:
 Parameter estimation
 Model identifiability
 Global sensitivity analysis
 Optimal experimental design
 Dynamic optimization
 Robust control of diffusionreaction systems
Projects: BaCellSysMO
Institutions: University of Rostock
Expertise: sensitivity analysis, Systems Biology, stress responses, Deterministic modelling of gene regulation networks, dynamics and control of biological networks, parameter estimation, Bacillus subtilis, Mathematical modelling
Tools: Dynamic modelling, Deterministic models, Stochastic models, linux, Matlab, ODE, Computational and theoretical biology, Biochemistry
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
call
ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
 automated integration of transcriptomic and reactome data to differential equations
 structure of the paths is maintained
 continuous fermentation model in standard format for data integration, two component model (cell and fermenter)
call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example
where
model_map is the desired mapping of species,
reaction_compounds_final.csv is the entire network,
extracellular.txt is a manual
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Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
The model presents a multicompartmental (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 lightgrowth 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 multicompartment meta...
Abstract (Expand)
Authors: Matthew Rolfe, Jeff Green, Guido Sanguinetti, Asif H M Shahzad,Lawrence Neil D,Rattray Magnus
Date Published: 24th Aug 2010
Journal: Bioinformatics
PubMed ID: 20739311
Citation: