Projects: COVID-19 Disease Map
Institutions: Luxembourg Centre for Systems Biomedicine (LCSB)https://orcid.org/0000-0001-7403-181X
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: Norwegian University of Science and Technologyhttps://orcid.org/0000-0002-0672-0653
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0003-2971-5686
Professor- University Clermont Auyvergne (UCA) - Institute of Chemistry of Clermont-Ferrand (ICCF)
Institutions: University of Groningen
I work as a project manager for the Innovative Training Network PoLiMeR - Polymers in the LIver: Metabolism and Regulation funded by the EU. In addition I am a project manager for the UMCG Research BV where I support scientist in the pre-award phase with writing their proposals and in the post-award phase with managing their awarded projects.
Institutions: INSTITUTE FOR PLANT MOLECULAR AND CELL BIOLOGY (IBMCP)https://orcid.org/0000-0001-8589-7002
Institutions: Leibniz Institute for Farm Animal Biology (FBN)https://orcid.org/0000-0002-7968-3152
Institutions: UNIBI: Bielefeld Universityhttps://orcid.org/0000-0002-6100-9135
Institutions: National Institute of Biologyhttps://orcid.org/0000-0002-1669-6482
Roles: PhD Student
Expertise: Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming, Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Visualization, Data Integration, Computational Biology
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology, Data Integration
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
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.
Institutions: National Institute of Biologyhttps://orcid.org/0000-0003-4776-7164
Institutions: National Institute of Biologyhttps://orcid.org/0000-0003-3644-7827
Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0001-8357-2159
Expertise: Biochemical analysis, protein extraction, protein purification, ELISA, Immunoblots, Immunoassays, oral food challenge, Data analysis, Mass spectrometry (LC-MS/MS), food allergy, peanut and treenut allergy, Molecular Biology, Microbiology
Tools: Biochemistry and protein analysis, molecular biology techniques, 1D and 2D SDSPAGE, immunoblot, ELISA Techniques, Immunological techniques, oral food challenge matrix preparation for food allergy research, data analysis and data management, Mass spectrometry, protein purification, food allergen characterisation
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburghhttps://orcid.org/0000-0003-1756-3654
Institutions: Wageningen University & Research
Institutions: Wageningen University & Researchhttps://orcid.org/0000-0001-7049-5334
I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
Projects: Systems toxicology of Atlantic cod
Institutions: University of Bergenhttps://orcid.org/0000-0002-2484-9047
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0002-4790-7377
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0002-6586-717X
Research scientist in multi-Omics, molecular (cell)biology and bioinformatics.
Projects: Not specified
Institutions: Not specified
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0003-2727-9518
I am had of the Research Group PiDOMICS which aims at the identification of human biomarkers for fungal infection using omics-data. Moreover, I am PI Infrastructure project of the Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction - FungiNet. Thereby my expertise is the implementation and usage of pipeline for OMICS (genome, transcriptome, protoem) data analysis, as well as data-warehouses for visualizing these data.
Scientific Project Manager at Luxembourg Centre for Systems Biomedicine, University of Luxembourg
I got my Master’s Degree in Biomathematics, Bioinformatics, and Computational Biology 2007 at Novosibirsk State University (NSU). I am working at Computer Proteomics Laboratory, Institute of Cytology and Genetics SB RAS. We develope computer system to analyze the coding features of functional sites by taking into account the exon structure of the gene, to detect the exons involved in shuffling in protein
evolution, also to design protein-engineering experiments. Tools developed - SitEx http://www-bionet
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", Working Group Nicole Radde, MIX-UP, CEPLAS – Cluster of Excellence on Plant Sciences, COVID-19 Disease Map, ERNEST Training school
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.
My research is intended to contribute to the elucidation of the physiological and molecular processes involved in the biofilm formation of acidophilic leaching bacteria with emphasis in their cell-cell communication mechanisms.
In SysMetEx, our role is to understand biofilm formation at a microscopical and OMICS levels, in order to optimize it.
Institutions: Institute of Pathology
I am a postdoc at the Technical University in Munich. When I studied nutritional science I got more and more interested in molecular cancer research. My PhD thesis was in the field of molecular cancer research. In our lab we are interested in molecular basic research on cell culture level, especially regarding gastric cancer.
Institutions: Universität Konstanz
I studied Life Science (which is similar to chemical biology) at the University of Konstanz and became interested in Bioinformatics, Systems Biology and quantitative analyses during my Master's. In my PhD project I combine experimental analyses with modeling and parameter estimation approaches to quantitatively analyse regulation of apoptosis at the level of the Bcl-2 protein family.
Institutions: Radboud University Nijmegen
I am a first year graduate student in the lab of Prof. Wilhelm Huck at the Radboud University Nijmegen. I am working on a project to create an artificial cell. This involves implementing complex genetic networks in cell-free systems which are far from equilibrium. My project involves designing, quantifying, modeling such networks. I am a molecular biologist by training and have basic modeling skills. I am looking to expand my skill-set to include microscopy, microfluidics and a little bit of
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 PostDoc in prof. Brautaset's lab at NTNU in Trondheim, Norway. During my Ph studies D, Irla was involved in two ERA projects; SynMet and MetAPP (PAL) and currently in I am active in C1Pro project (Asset housekeeper). I have been working with methylotrophic Bacillus methanolicus since 2012, in that time I have been involved in engineering of that bacterium for production of different value-added products (amino acids and their derivatives, vitamins, and others). Furthermore, I have improved
Roles: Project Coordinator
The Veening lab is interested in phenotypic bi-stability in Streptococcus pneumoniae and its importance in virulence of this human pathogen.
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
I have a permanent position at the department of microbiology at the TU-München. As a microbiologist I am interested in the regulation of central metabolism in prokaryotic organisms with different types of energy metabolism such as Clostridia, Bacilli and acetic acid bacteria. Furthermore I worked as a software developer for several years in a bioinformatics company and I am very interested in bioinformatics and handling of large amounts of data.
Expertise: Microbiology, Molecular Biology, Bacillus subtilis, regulation of gene expression, carbon metabolism, Clostridium, carbon catabolite regulation in Gram positive bacteria, mRNA, overflow metabolism in Bacillus
Tools: Genetic modification, cultivation, northern blot analysis, Molecular biology techniques (RNA/DNA), Optimal experimental design, absolute quantification, qRT-PCR, reporter gene analyses, Western blot analyses, microbiology techniques
Geneticist and Microbiologist with research focus on Archaea. Professor of Genetics in Ecology (Faculty of Life Sciences/University of Vienna, Austria) and associate professor of the Center of Geobiology (University of Bergen/Norway).
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
Tools: Microbiology, Molecular Biology, Biochemistry and protein analysis, Cell biology, Genetic analysis, Genomics, Transcriptomics, Proteomics, Model organisms, Proteomics (2D-PAGE), gene regulation, DNA technology RNA technology Protein analysis Fermentation Mutagenesis, molecular biological techniques (RNA/DNA techniques), protein interaction studies
Optimisation of Bacillus subtilis for the secretion of heterologous proteins Therapeutic proteins (including those required for experimental purposes and clinical trials) are major products of biomanufacturing processes and considerable time and expense are expended to maximise the yield and quality of proteins produced in heterologous hosts. The production host of choice is the Gram-negative bacterium Escherichia coli for which many strains and expression systems have been developed. However,
Post-doctoral research associate working in Sheffield in the SUMO consortium.
PostDoc at Wageningen University, Laboratory of Microbiology
University of Ulm
Institute of Microbiology and Biotechnology
Albert-Einstein- Allee 11
89069 Ulm, Germany
Expertise: Molecular Biology, Bacillus subtilis, functional protein expression, protein-protein interactions, microscopy, Bacterial Cell Biology, carbon catabolite regulation in Gram positive bacteria
Tools: Chromatography, Fluorescence and confocal microscopy, Protein chemical methods (protein overproduction, quantitative western blot analysis, Dynamic modelling, 2-D Gel Electrphoresis, Immunofluorescence, Cell culture, Western blot analyses, interaction analysis techniques especially SPR measurements
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.
I am interested in the coupling of global regulation and metabolism in E. coli. To analyze this I construct and analyze defined mutant strains. These strains are characterized in bioreactor experiments of different types (batch, conti, pulse ...) and measurements on the level of metabolites, mRNA, and protein are applied. For all projects there are cooperation partners that use the data in modeling approaches either from the MPI Magdeburg or from the SUMO consortium.
Dr. Bettina Schiel-Bengelsdorf
Department of Microbiology and Biotechnology
University of Ulm
89069 Ulm, Germany
I`m interested to investigate the Influence of the accumulation of reduction equivalents on solvent production
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
I am PhD student at Prof.Uwe Voelker lab in Department of Functional Genomics. My area of research is microbial functional genomics in particular analysing the whole transcriptome(by microarray and other molecular biolology methods) of B.subtilis under various stress conditions.
I use QconCAT strategy for absolute quantification of carbon metabolic enzymes via MRM(multiple reaction monitoring) by LC-MS/MS.
I also perofrm experiments for understanding of dynamics of SigmaB network for modelling.
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,
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
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: 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
I'm Post-Doc in the lab of Prof. Becher at the University of Greifswald. I'm working on the relative and absolute protein quantitation using gel-based and mass-spectrometric methods.
Expertise: Molecular Biology, Bioinformatics, Mathematical modelling, Reactor models, dynamics of biological networks, Mathematical and statistical modeling, bioreactor models, Dynamics and Control of Biological Networks, Parameter estimation
Tools: Bioinformatics, Computational and theoretical biology, Transcriptomics, Model organisms, Single Cell analysis, SBML, ODE, Linear equations, Matlab, Microarray analysis, linux, Material balance based modeling, stimulus response experiments, DIVA, differential algebraic equations, evaluation of process dynamics, continuous cultivation
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.
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
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.
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: Microbiology, Genetics, Molecular Biology, Bacillus subtilis, translational control of gene expression, sporulation, phenotypic heterogeneity, bistability, gene regulation, stress responses, Signal transduction in Gram-negative bacteria; Synthetic Microbiology; Single cell gene expression; Regulatory networks; biochemistry; histidine ki..., regulation of gene expression, Systems Biology
Tools: Microbiology, Genetics, Molecular Biology, Genetic analysis, Genetic modification, Model organisms, Single Cell analysis, PCR, Fluorecence based reporter gene analyses/single cell analyses, Molecular biology techniques (RNA/DNA), time lapse microscopy, Time-lapse fluorescence microscopy Flow cytometry
Expertise: Genetics, Molecular Biology, Microarray analysis, Bacillus subtilis, phenotypic heterogeneity, gene regulation, stress responses, protein secretion, functional protein expression, microscopy, fluorescence protein fusions (transcriptional and translational), localisation studies
Tools: Genetic modification, Transcriptomics, Microarray analysis, Fluorecence based reporter gene analyses/single cell analyses, Site-directed mutagenesis, Fluorescence microscopy, Flow cytometry, Immunofluorescence, transposon mutagenesis, Molecular biology techniques (RNA/DNA/Protein), DNA affinity chromatography, EMSA
PhD student. Analyzing CcpA affinity to cre boxes (catabolite responsive elements) and response of B. subtilis to membrane protein overproduction stress.
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio)https://orcid.org/0000-0003-3540-0402
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project
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.
I'm an 'experimentalist' (molecular microbiologist) Postdoc working on regulation and peptide signaling in Clostridium acetobutylicum.
I'm also a SysMO-DB PAL (Product Application Liason) for COSMIC, working on data management including standards and integration with SysMO SEEK.
Tools: Microbiology, Molecular Biology, Biochemistry of substrate transport. molecular biological techniques (RNA/DNA techniques analyses of transport across cell membranes heterologous e..., Membrane protein biochemistry, Chemical cross-linking, Site-directed mutagenesis
I am a biologist by training. My research career is focussed on the structure-function relationships of membrane transport systems in Escherichia coli. I am interested in understanding the mechanism of ion and solute transport across the membrane and how this influences bacterial cell survival. My work mainly focusses on the ligand-gated potassium efflux systems which are crucial for cell survival during electrophile exposure and the mechanosensitive channels involved in hypoosmotic stress
Tools: Microbiology, Molecular Biology, Biochemistry and protein analysis, Genetic analysis, Genetic modification, Proteomics (2D-PAGE), mutant strain generation, Chemical cross-linking, SubtiWiki, SPINE, bacterial two-hybrid system
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