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 kineticshttps://orcid.org/0000-0002-0443-6114
University of Amsterdam
Free University Amsterdam
University of Manchester
Infrastructure Systems Biology.NL (ISBE.NL)
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0003-4234-1172
Data Steward for the Plant Biology and Breeding Division of INRAe (https://www.inrae.fr/en/divisions/bap)
Projects: COVID-19 Disease Map
Institutions: University of Surreyhttps://orcid.org/0000-0001-5640-7422
Reader (Professor) of Systems Biology; Executive Director for the International Society of Systems Biology (ISSB); Editor-in-Chief of Current Opinion in Systems Biology (Elsevier).
Projects: COVID-19 Disease Map
Institutions: All India Institute of Medical Sciences, Kalyanihttps://orcid.org/0000-0002-8413-3454
Assistant Professor, Department of Biochemistry, All India Institute of Medical Sciences Kalyani
Tools: Biochemistry and protein analysis, Bioinformatics, Systems Biology, SBML, R, ODE, Molecular biology techniques (RNA/DNA/Protein), Genetics, Dynamic modelling, Computational and theoretical biology, CellDesigner, Parameter estimation
Institutions: Norwegian University of Science and Technologyhttps://orcid.org/0000-0002-0584-6748
Institutions: University of Stuttgarthttps://orcid.org/0000-0001-9119-1778
Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Institutions: Consiglio Nazionale delle Ricerchehttps://orcid.org/0000-0002-3399-7973
Institutions: Universidade de Santiago de Compostelahttps://orcid.org/0000-0002-7323-5439
Dr. Noelia Pérez-Rodríguez holds a PhD in Agro-Food Science and Technology and has over 6 years of expertise in the areas of Biomass Conversion and Bioprocess Technology with focus on the development of biorefinery strategies for total and sustainable conversion of biomass (lignocellulosic materials) into biobased products.
Dr. Pérez-Rodríguez’s research interests include: i) biomass pretreatment and hydrolysis using chemical, physico-chemical or biological methods; ii) biomass conversion by
Institutions: Beilstein Instituthttps://orcid.org/0000-0002-8697-6842
Project manager of STRENDA and MIRAGE @Beilstein-Institut
Projects: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, MIX-UP, CEPLAS – Cluster of Excellence on Plant Sciences, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study, NMTrypI - New Medicines for Trypanosomatidic Infections, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling, ModeleXchange initiative, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation, Mass spectrometry proteomics for biomarker discoveryhttps://orcid.org/0000-0002-9077-5664
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: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0003-2852-6648
I am performing research in biomarkers discovery, particularly regarding liver fibrosis in non-alcoholic fatty liver disease. My research activities involved the use of bioinformatic platforms, the analysis of biological protein-protein interaction networks and the experimental validation of candidates by ELISA.
Prof. Dr. Kathrin Thedieck
Leader WP8 – Project Coordination
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomingtonhttps://orcid.org/0000-0002-5901-1404
I am a multicell and multiscale modeler and member of the Biocomplexity group at Indiana University. The group produces and maintains the multicellular modelling package Compucell3D. I am also a voting member of the USA committee to the International Organization for Standards (ISO) working group on standards in biotechnology and the chairman of a sub-sub group on publishing standards.
Institutions: Wageningen University & Research
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0002-5293-5321
Biochemist currently keeping busy as: Research Data Manager (Vrije Universiteit Amsterdam), Software Engineer (Heidelberg University) and member of the SBML Development Team (Caltech).
Projects: Systems toxicology of Atlantic cod
Institutions: University of Bergenhttps://orcid.org/0000-0002-2484-9047
Institutions: University of Luxembourghttps://orcid.org/0000-0002-8071-7110
Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
I am an emeritus professor in Biochemistry at the University of Amsterdam (retired 2010).
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
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiativehttps://orcid.org/0000-0002-8683-7084
Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team.
Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and
Projects: SysMO-LAB, de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", MIX-UP, CEPLAS – Cluster of Excellence on Plant Sciences, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study
Within the de.NBI project my functions in the de.NBI-SysBio node comprise content curation, requirements elicitation, and community engagement for the users of biochemical reaction kinetics database SABIO-RK as well as of the data management platform SEEK.
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.
I am a PhD student working the group of Zoya Ignatova. Cellular and extracellular changes like crowding and osmotic stress conditions play a major role in protein aggregation. A change in the cytoplasmic composition is the result of an interplay between high osmotic pressures outside the cell volume and the cellular response to it in terms of uptake of K+ and secondary organic osmolytes. My research focuses on elucidating the role of natural osmolytes (known also as chemical chaperones or compatible
I am a research technician at the Institute of Medical Science in Aberdeen, working for Prof. Ian Booth. The topic of our workpackage deals with K+ homostasis in Escherichia coli. I am working with the protein KefF, a regulatory subunit of the potassium channel KefC.
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 genome-wide scale. This may reveal various general mechanisms on control level of gene expression and folding efficiency regulation in different growth conditions.
Tools: Biochemistry and protein analysis, Spectroscopy and structural analysis, rtPCR, fluorescence spectroscopy, quantitative western blot analysis, Molecular biology techniques (RNA/DNA), Fluorescence and confocal microscopy FRAP/FLIP
The focus of our research is the protein biogenesis and how stress-related factors modulate it. Protein biogenesis in general comprises various processes, i.e., translation, protein folding, each of which responds differently to external stress stimuli. Using systems biology approaches we seek to understand the interplay between these processes in fine-tuning the protein pattern and proteins’ abundance under osmotic stress conditions.
Expertise: Gram positive bacteria (Bacillus, Lactococcus, Streptococcus), competence, sporulation, germination, antimicrobial peptides, phenotypic heterogeneity, bistability, C- and N- metabolism, gene regulation, stress responses, pathogens, virulence factors, metal ion homeostasis, protein secretion
Group leader Molecular Genetics
Tools: The Membrane Enzymology group focuses on the molecular mechanisms of transport and signalling across biological membranes. In other words: How do m..., engineering principles and approaches from molecular biology and synthetic chemistry are applied. Confocal microscopy and various spectroscopic met...
Bert Poolman is professor in biochemistry and program director of the Centre for Synthetic Biology. His research focuses on the elucidation of the mechanisms by which signals are transduced and small molecules are translocated across cellular membranes. Cells are reengineered for the production of correctly folded membrane proteins, and methods are developed to reconstitute complex molecular assemblies in synthetic membranes and to analyze their functional and structural properties. The in vitro
Tools: Genetics, Proteomics, Pharmacology and toxicology, Spectroscopy and structural analysis, Web services, PCR, Fluorescence and confocal microscopy, quantitative Western analyses), molecular biological techniques (RNA/DNA techniques, Proteomics (2D-PAGE), quantitative western blot analyses, Molecular biology techniques (RNA/DNA), transcriptional analysis (Northern blots
Postdoctoral Research fellow with experience in Genomics, transcriptomics, proteomics and metabolomics
Expertise: Mathematical modelling, Bacillus subtilis, Deterministic modelling of gene regulation networks, stress responses, Systems Biology, sensitivity analysis, Dynamics and Control of Biological Networks, Parameter estimation
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
I am postdoc in the group of Prof Ian Booth in Aberdeen working on the biochemical and biophysical characterisation of bacterial channels.
Expertise: Microbiology, Biochemistry, Mathematical modelling, Bacillus subtilis, Mathematical modelling of biosystems and bioprocesses, stress responses, Systems Biology, Nonlinear Dynamics, carbon metabolism, Signalling networks, Metabolic Networks
Tools: Computational and theoretical biology, ODE, Matlab, Mathematica, Fermentation, Chromatography, continuous cultivation, Enzyme assay, Computational Systems Biology, Deterministic models, Dynamic modelling, fed-batch cultivation
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.
Post-doctoral research associate working in Sheffield in the SUMO consortium.
Tools: Genetics, Biochemistry and protein analysis, Fermentation, Chromatography, Membrane protein biochemistry, molecular biological techniques (RNA/DNA techniques), spectroscopy, site-directed and random mutagenesis, plasmon resonance spectroscopy, reporter gene analyses
I am a PhD student of the microbiology department at the Ludwig-Maximilians Universität München. I work at the chair of Prof. Kirsten Jung. The topic of our workpackage deals with "K+ homeostasis in Escherichia coli". In special I'm working on the sensor kinase KdpD that controls together with the response regulator KdpE the expression of the high-affinity K+ uptake system KdpFABC. The yet not fully understood molecular mechanism of stimulus perception and signal transduction is of particular
Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.
Archaea possess many novel enzymes and pathways and our aim is
I'm a biologist working in the field of scientific datases as a biocurator.
I obtained my PhD in 1989 at the Free University (Amsterdam) on a research project in which microbial physiology, biochemistry, and molecular biology were combined. Subsequently I spent 3 years abroad, 2.5 years of which as EMBO fellow at the EMBL (Heidelberg, Germany) where I worked on protein engineering and protein crystallization. I returned to Amsterdam as KNAW fellow for 3 years, during which I worked on protein analysis and pathway engineering. In 1995 I was appointed as group leader
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
Professor of Biochemistry at the Centre of Biochemistry of Heidelberg University, teaching biochemistry for medical and biology students
Research focus is the trypanothione redox metabolism of African trypanosomes (Trypanosoma brucei).
The work is funded within the Collaborative Research Centre 544 on "Control of Tropical Infectious Diseases" of the German Research Foundation
Roles: Project Coordinator
The Veening lab is interested in phenotypic bi-stability in Streptococcus pneumoniae and its importance in virulence of this human pathogen.
Institutions: University of Leidenhttps://orcid.org/0000-0002-1279-5133
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
I started to work with B. subtilis during my diploma thesis in Marburg, analyzing the gene expression pattern during sporulation and their control by the four sporulation sigma factors. This work was continued during my PhD thesis in Greifswald. In collaboration with Prof. Bremer and Prof. Marahiel in Marburg we also studied additional adaptation processes of B. subtilis, like the adaptation to low temperatur and high osmolarity.
I am now working as a staff scientist in Prof. Völkers lab in
Expertise: Biochemistry, coupling metabolome and environome, rapid sampling experiments, Systems Biology, carbon metabolism, Stoichiometric modelling, Proteomics, Metabolomics, yeast, fungi, Dynamics and Control of Biological Networks
Tools: Biochemistry and protein analysis, Metabolomics, Matlab, Fermentation, Chromatography, Material balance based modeling, stimulus response experiments, continuous cultivation, Enzyme assay, Mass spectrometry (LC-MS/MS), HPLC, GC and LC/MS analysis of metabolites, ODE, Parameter estimation
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
Kosmobac, WP3, looking at diffusion of macromolecules in vivo (in E.coli cells) and cell responses to osmotic shock using confocal (fluorescence) microscopy especially pulsed - FRAP
Tools: Protein chemical methods (protein overproduction, purification, enzymatic analyses, quantitative Western analyses), molecular biological techniques (RNA/DNA techniques, qPCR, Northern analyses), Proteomics (2D-PAGE), mutant strain generation, Fluorecence based reporter gene analyses/single cell analyses
I am research assistant in the microbiology department at the Ludwig-Maximilians Universität in Munich (München), working at the chair of Prof. Kirsten Jung. In our SysMO consortium we generate biological data and work in close cooperation with the workgroup of Dr. Andreas Kremling of the Max-Planck-Institut für Dynamik komplexer technischer Systeme in Magdeburg who performs mathematical modeling. The topic of our workpackage deals with "K+ homeostasis in Escherichia coli", wherby the K+ transporters,
Tools: Biochemistry and protein analysis, mutant strain generation, Fluorecence based reporter gene analyses/single cell analyses, molecular biological techniques (RNA/DNA techniques analyses of transport across cell membranes heterologous expression of transporters
biochemistry, molecular biology and physiology of lower eukaryotes,
characterization of cell membrane transporters
Professor of Microbiology