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Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated materialhttps://orcid.org/0000-0002-0443-6114
Systems Biologist University of Amsterdam Free University Amsterdam University of Manchester Infrastructure Systems Biology.NL (ISBE.NL) Systems Biology Amsterdam
I am a biochemist & bio-informatician working in phytobacteriology at the Plant Sciences Unit of ILVO, the Flanders Research Institute for Agricultural, Fisheries and Food Research. The focus is on genomics-based research and diagnostics for Plant Health.
My expertise is 'wet-lab' work (microbiology, sequencing, molecular biology, design & validation of diagnostics assays using qPCR/LAMP, automatisation) and 'dry-lab' work such as bio-informatics/data analysis (e.g. scripting analysis ...
Institutions: University of Freiburghttps://orcid.org/0000-0002-5340-3423
Projects: COVID-19 Disease Map
Institutions: Golestan University of Medical Scienceshttps://orcid.org/0000-0002-0773-1610
I would like to collaborate on the COVID-19 projects. I am currently a faculty member of the Infectious Diseases research center, at the Golestan University of Medical Sciences, Iran, and studying clinical information of patients with COVID-19. I am a microbiologist and can help other teams to evaluate the data obtained from COVID-19 cases.
Institutions: Consiglio Nazionale delle Ricerchehttps://orcid.org/0000-0002-3399-7973
Institutions: INSTITUTE FOR PLANT MOLECULAR AND CELL BIOLOGY (IBMCP)https://orcid.org/0000-0001-8589-7002
Projects: SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layershttps://orcid.org/0000-0002-9905-541X
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 ...
Institutions: UNIBI: Bielefeld Universityhttps://orcid.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.
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: HUMET Startup
Institutions: Université catholique de Louvainhttps://orcid.org/0000-0003-2040-2448
Tools: Animal models, Genetic modification, Microbiology, Integrative physiology, Glucose metabolism, Lipid metabolism, Molecular biology techniques (RNA/DNA/Protein), LPS measurments, Gut microbiota analysis
Professor Patrice D. Cani is researcher from the Belgian Fund for Scientific Research and group leader in the Metabolism and Nutrition lab at the Louvain Drug Research Institute from the UCL, Brussels, Belgium. He is WELBIO investigator and recipient of an ERC Starting Grant 2013 and a PoC ERC Grant 2016. He is laureate of the Baillet-Latour grant for medical research and the international prize of Physiology Lucien Dautrebande. His main research interests are the investigation of interactions ...
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.
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: 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 ...
Post doc. in the SysMO-LAB2 project from August 2010. I work at Nofima and the Norwegian University of Life Sciences (UMB) at Ås, Norway. My focus in SysMO-LAB2 will be on four Lactobacillus plantarum strains, diversity analysis, omics-technologies, genome scale modelling.
Background: Ph.D. in Molecular Microbiology June 2010, where I worked with Lactobacillus sakei, metabolism and diversity studies.
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Roles: Project Coordinator
Tools: Bioinformatics, Genetic modification, Proteomics, Fermentation, Microarray analysis, Computational Systems Biology, Metabolic Engineering, microbiology techniques, reverse engineering, computational platform development, metabolic netwlrk visualization
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological ...
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 ...
Roles: Project Coordinator
Expertise: Microbiology, Transcriptomics, regulation of gene expression, bacterial gene regulation, Molecular microbiology, Microarray experiments with prokaryotes, Protein-DNA-interaction, Streptomyces, genetic engineering
Tools: Microbiology, Genetic modification, Transcriptomics, PCR, Microarray analysis, Chip-chip, Northern analyses), Bioconductor Packages in R, Molecular biology techniques (RNA/DNA/Protein), Mutant and Strain Construction, site-directed and random mutagenesis, reporter gene analyses, microbiology techniques, analysis of functional genomics data, transcription analysis
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 ...
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.
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: 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'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.
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, ...
The main area of my expertise concerns protein sorting and secretion in Gram-positive bacteria, such as Bacillus subtilis and Staphylococcus aureus.
The Gram-positive bacterium B. subtilis is well known for its high capacity to secrete proteins into the extracellular milieu, which has led to its exploitation as a "cell factory" for secreted proteins. Nevertheless, the secretion of heterologous proteins of pharmaceutical importance is frequently inefficient. This applied problem has been a major ...
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.
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.
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.
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 ...
I am a first year PhD student, working with Professor Robert Poole (University of Sheffield), Professor Jeff Green (University of Sheffield) and Dr Jamie Wood (University of York) using a systems biology approach to study respiration in Escherichia coli.
PostDoc at Wageningen University, Laboratory of Microbiology
Dr. Bettina Schiel-Bengelsdorf Senior Scientist Department of Microbiology and Biotechnology University of Ulm 89069 Ulm, Germany
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.
Phd student University of Ulm Institute of Microbiology and Biotechnology Albert-Einstein- Allee 11 89069 Ulm, Germany
PhD University of Rostock, Germany Institute of Biological Sciences Division of Microbiology Albert-Einstein-Str. 3 18051 Rostock
I`m interested to investigate the Influence of the accumulation of reduction equivalents on solvent production
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
Expertise: Bacillus subtilis, functional protein expression, bacterial metabolism, carbon metabolism, Bacterial Cell Biology, Protein-DNA-interaction, Microbiology/ Protein chemistry/ Molecular Biology, Cell physiology, regulation of gene expression, quantative biology
Tools: Microbiology, Biochemistry and protein analysis, Cell biology, Model organisms, Chromatography, Molecular biology techniques (RNA/DNA/Protein), DNA, surface plasmon resonance spectroscopy, reporter gene analysis
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 ...
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
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 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.
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.
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: 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: 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: 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