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Projects: SilicoTryp
Institutions: University of Glasgow
Projects: STREAM
Institutions: University of Groningen
Mathematical modeling, bioinformatics
Projects: SulfoSys, SulfoSys - Biotec
Institutions: Max-Planck-Institute for terrestrial Microbiology
Projects: SysMO DB
Institutions: University of Manchester - Department of Computer Science
Intern @ myGrid team
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: SysMO-LAB
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
Projects: COSMIC
Institutions: University of Rostock
Prof. Dr. Hubert Bahl Head, Division of Microbiology, Institute of Biological Sciences University of Rostock Albert-Einstein-Str. 3 D-18051 Rostock
Projects: SUMO
Institutions: University of Sheffield
I am a Professor in Medical Systems Biology and the University Medical Centre Groningen. The research in my lab is focused on complex regulation of mammalian lipid and carbohydrate metabolism, eventually aiming at network-based therapies. We combine dynamic computer simulations with quantitative metabolomics, 13C fluxomics, proteomics and transcriptome analysis, and in depth biochemical analysis. This allows to predict and understand ‘emergent’ properties, those properties that are counterintuitive ...
We are very interested in applying a systems approach (i.e. model-based 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
...
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: SilicoTryp
Institutions: University of Glasgow
Projects: BaCell-SysMO
Institutions: University of Erlangen-Nuernberg
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Institutions: University of Amsterdam
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 ...
Projects: SysMO-LAB
Institutions: VU University Amsterdam
Projects: Noisy-Strep
Institutions: University of Cologne
With a background in the statistical mechanics of disordered systems, my research focusses on the interface between statistical physics and molecular biology. At the centre is the relationship between fluctuations and noise in biological systems, the corresponding statistical ensembles, and biological function. This connection emerges at very different levels and timescales, from stochastic modeling of gene expression to the population dynamics of regulatory DNA.
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.
Projects: PSYSMO
Institutions: Queen's University Belfast
Projects: Noisy-Strep
Institutions: University of Cologne
I am a phd student working on statistical physics and complex systems and applying concepts from these fields to biology.
Projects: SulfoSys
Institutions: University of Bergen
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: PSYSMO
Institutions: University of Dortmund
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: MOSES
Institutions: VU University Amsterdam
Projects: KOSMOBAC
Institutions: University of Aberdeen
My research interests are in the physiology of bacteria subjected to stress. The focus of my recent research has been the structure and function of regulated transport systems and ion channels involved in cellular homeostasis. These transporters and channels respond to specific signals by a change in activity that either corrects the imposed stress or protects the cell during exposure to the stress. Our systems biology interests are in the interplay of different enzymes systems and transporters ...
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
Projects: SCaRAB, STREAM, SYSTERACT, INBioPharm
Institutions: SINTEF, Norwegian University of Science and Technology
Senior Research Scientist at SINTEF, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry
Projects: KOSMOBAC
Institutions: Max-Planck-Institute of Biochemistry Martinsried
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 ...
Projects: COSMIC
Institutions: University of Ulm
Phd student University of Ulm Institute of Microbiology and Biotechnology Albert-Einstein- Allee 11 89069 Ulm, Germany
Projects: STREAM, SilicoTryp
Institutions: University of Groningen
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 ...
Projects: BaCell-SysMO
Institutions: University of Marburg
Projects: STREAM, SCaRAB, WineSys, INBioPharm
Institutions: SINTEF, Norwegian University of Science and Technology
Projects: PSYSMO
Institutions: University of Dortmund
Projects: STREAM
Institutions: University of Warwick
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: STREAM
Institutions: University of Warwick
Projects: SilicoTryp
Institutions: University of Heidelberg
Projects: SysMO-LAB
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
- BSc in Physics and Chemistry at the West University Timisoara 1999 - graduated with a average grade of 9.57 (on a scale from 1.00 to 10.00)
- Accepted in the International MSc/PhD Program Molecular Biology - International Max Planck Research School, Goettingen, Germany in June 2000. For details about the program please consult http://www.gpmolbio.uni-goettingen.de/
- Master in Molecular Biology at the Georg-August Univ. Goettingen, Germany, August 2001 - graduated with a grade of 2.0 (on a scale ...
Projects: SCaRAB
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: SUMO
Institutions: University of Edinburgh
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: TRANSLUCENT
Institutions: University of Cordoba
Projects: SCaRAB
Institutions: University of Greifswald
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Projects: SysMO-LAB
Institutions: University of Heidelberg
I am working on the development of algorithms for Comparative Systems Biology.
Projects: BaCell-SysMO
Institutions: University of Groningen
Projects: PSYSMO, EmPowerPutida, SynBio4Flav
Institutions: CSIC Madrid, CSIC
Projects: COSMIC, SysMO-LAB, HUMET Startup
Institutions: Wageningen University & Research
Projects: SysMO-LAB
Institutions: Technical University of Denmark - Systems Biology
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: STREAM
Institutions: University of Groningen
Projects: COSMIC
Institutions: University of Goettingen
Projects: SulfoSys
Institutions: University of Groningen
Projects: SysMO DB
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: PSYSMO
Institutions: CSIC Madrid
Institutions: University of Ulm
Prof. Dr. Peter Dürre Head, Department of Microbiology and Biotechnology, University of Ulm 89069 Ulm, Germany
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: COSMIC
Institutions: University of Goettingen
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.
Projects: SulfoSys
Institutions: University of Bergen
Projects: STREAM, SCaRAB, INBioPharm, SYSTERACT
Institutions: SINTEF
Projects: SilicoTryp
Institutions: University of Heidelberg
Projects: SysMO-LAB
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Heidelberg
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: SysMO-LAB
Institutions: University of Rostock
Postdoc @ Institute of Medical Microbiology, University of Rostock
Projects: COSMIC
Institutions: University of Rostock
Projects: BaCell-SysMO
Institutions: University of Goettingen
I'm a PhD student at the lab of Prof. Dr. Jörg Stülke. My main interest is to analyze the central metabolism of Bacillus subtilis using systems biology software. I have developed an algorithm to find short pathways connecting sets of metabolites and I'm also involved in SubtiWiki, the wiki for all genes of Bacillus subtilis (http://subtiwiki.uni-goettingen.de)
Projects: PSYSMO
Institutions: University of Hannover
Projects: TRANSLUCENT
Institutions: University of Vienna
Projects: PSYSMO
Institutions: University of Duesseldorf
Projects: KOSMOBAC
Institutions: Ludwig-Maximilians University of Munich
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 ...
Projects: Noisy-Strep
Institutions: University of Groningen
Projects: KOSMOBAC
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: STREAM
Institutions: University of Warwick
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
Projects: SulfoSys
Institutions: University of Braunschweig
Projects: SCaRAB
Institutions: University of Greifswald
Projects: SilicoTryp
Institutions: University of Glasgow
Projects: MOSES
Institutions: Medical University Vienna
General Bioinformatics
Professor of Computer Science University of Manchester Co-Director of the FAIRDOM Initiative and co-leader of the SEEK4Science Platform Development Deputy Head of Node ELIXIR-UK Co-lead ELIXIR Interoperability Backbone Platform Lead ISBE WP Data and Model Management Data lead SynBioChem Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals
Projects: KOSMOBAC
Institutions: Max-Planck-Institute of Biochemistry Martinsried
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.
Projects: SCaRAB
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
https://orcid.org/0000-0001-6096-1354Process engineer, modeling biological systems since 1985.
Projects: SUMO
Institutions: University of Sheffield
Post-doctoral research associate working in Sheffield in the SUMO consortium.
Projects: TRANSLUCENT
Institutions: University of Vienna
Projects: SUMO
Institutions: University of Sheffield
The major theme of the research in my laboratory is bacterial gene regulation. We are interested in signal perception mechanisms (in particular oxygen); signal transduction (ligand induced protein confromational changes); interaction of transcription factors with the core transcription machinery; interactions between transcription factors to integrate multiple signals; and the influence of promoter architectures on these events. We are also interested in aome aspects of post-transcriptional ...
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: SilicoTryp, IMOMESIC
Institutions: University of Groningen, VU University Amsterdam
Projects: PSYSMO
Institutions: University of Braunschweig
Projects: SulfoSys
Institutions: University Duisburg-Essen
Projects: PSYSMO
Institutions: Queen's University Belfast
Projects: BaCell-SysMO
Institutions: University of Newcastle
Projects: BaCell-SysMO
Institutions: University of Newcastle
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, ...
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: COSMIC
Institutions: University of Rostock
biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock
Projects: BaCell-SysMO
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: COSMIC
Institutions: University of Nottingham
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.
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: KOSMOBAC
Institutions: Ludwig-Maximilians University of Munich
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, ...
Projects: SUMO
Institutions: University of Amsterdam
General microbiologist with specific interests in signal transduction mechanisms, biophysics and photobiology
Projects: TRANSLUCENT
Institutions: University of Leiden
Projects: SUMO
Institutions: University of Stuttgart
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 SysMO-DB pals for SUMO. Now: Industrial affiliation
Projects: SysMO-LAB
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Projects: SysMO-LAB
Institutions: University of Rostock
Projects: TRANSLUCENT
Institutions: University of Leiden
Projects: BaCell-SysMO
Institutions: University of Erlangen-Nuernberg
CURRICULUM VITAE
Wolfgang Hillen Full Professor and Chairman of Microbiology Lehrstuhl für Mikrobiologie Institut für Biologie Friedrich-Alexander Universität Erlangen-Nürnberg Staudtstr. 5 91058 Erlangen, Fed. Rep. of Germany
Date of Birth: April 24, 1948 Place of Birth: Osnabrück, FRG Nationality: German Status: Married Children: Hauke Sven Hillen - May 17, 1987
RESEARCH AND PROFESSIONAL EXPERIENCE
Present Full Professor and Chairman of Microbiology at the Institute of Biology, Friedrich-Alexander ...
Projects: STREAM
Institutions: University of Warwick
Projects: BaCell-SysMO
Institutions: University of Marburg
Projects: SUMO
Institutions: University of Sheffield
Professor of Computer Science, University of Sheffield. FBCS, FIMA, CEng, C.Math, CITP. I have been involved in the use of computational techniques for modelling biological systems since 1980. More recently I have developed a technique of agent-based modelling based on the framework FLAME which is the only such system that can be run on supercomputers. We have made significant new biological discoveries using this approach: The approach models the location and activity of millions of individual ...
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Projects: COSMIC
Institutions: Technical University of Munich
Projects: TRANSLUCENT
Institutions: University of Vienna
Projects: SysMO-LAB, Sustainable co-production
Institutions: University of Amsterdam, Wageningen University & Research
Projects: KOSMOBAC
Institutions: Max-Planck-Institute of Biochemistry Martinsried
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.
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 ...
Projects: PSYSMO
Institutions: University of Braunschweig
Projects: PSYSMO
Institutions: University of Duesseldorf
Projects: PSYSMO
Institutions: University of Braunschweig
Projects: STREAM
Institutions: University of Groningen
Projects: COSMIC
Institutions: University of Rostock
PhD University of Rostock, Germany Institute of Biological Sciences Division of Microbiology Albert-Einstein-Str. 3 18051 Rostock
Projects: SUMO
Institutions: University of Sheffield
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Projects: TRANSLUCENT
Institutions: University of Cordoba
Projects: KOSMOBAC
Institutions: Ludwig-Maximilians University of Munich
I have the chair for Microbiology at the Ludwig-Maximilians-Universität München since 2004. My lab has a long-standing interest in stress response and transmembrane signal transduction in E. coli and V. harveyi. Our work is focused on the molecular mechanisms of membrane-integrated receptors, and the systems biological analysis of regulatory circuits.
Projects: TRANSLUCENT
Institutions: University of Applied Sciences Koblenz, Rhein Ahr Campus
Grammar school until 1998 1998-99 Alternative civilian service 1999-2002 Professional education as male nurse 2002-2007 Study of Biomathematics 2007-... PhD student in TRANSLUCENT project
I'm a biologist working in the field of scientific datases as a biocurator.
Projects: COSMIC
Institutions: Wageningen University & Research
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.
Projects: SilicoTryp, SYSTERACT, SynBio4Flav
Institutions: University of Glasgow, Chalmers University of Technology
https://orcid.org/0000-0002-3593-5792Projects: STREAM
Institutions: University of Warwick
Projects: SilicoTryp
Institutions: University of Glasgow
Projects: COSMIC
Institutions: University of Nottingham
I am a mathematical modeller concerned primarily with applications in biology,
Projects: PSYSMO
Institutions: Imperial College London
Projects: MOSES
Institutions: University of Heidelberg
Projects: MOSES
Institutions: Medical University Vienna
Projects: SulfoSys
Institutions: eGene Biotechnologie GmbH
Projects: TRANSLUCENT, HUMET Startup
Institutions: Humboldt-Universität zu Berlin, Humboldt University Berlin
Projects: PSYSMO
Institutions: University of Hannover
Projects: SUMO
Institutions: University of Stuttgart
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: BaCell-SysMO
Institutions: University of Stuttgart
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: BaCell-SysMO
Institutions: University of Braunschweig
Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe, University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB)
I have modelling expertise in precise kinetic models of metabolism and signal transduction; metabolic control analysis, hierarchical regulation analysis, non-equilibrium dynamics, statistical mechanics, enzyme kinetics, flux balance analysis. Energy and carbohydrate metabolism in Archaea, Bacteria and human; ammonium assimilation in Bacteria; differential network-based drug design; cancer metabolic rewiring; cell cycle; genome wide metabolic map and inborn errors of metabolism; epigenetics.
Projects: SulfoSys, SulfoSys - Biotec, Glucose metabolism in cancer cell lines
Institutions: University Duisburg-Essen, Stellenbosch University
Projects: PSYSMO
Institutions: Imperial College London
Projects: STREAM
Institutions: University of London UCL
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
I created this for all SysMo Modellers
http://www.semanticsbml.org/aym Annotate Your Model
There you can annotate your non SBML models with biological terms (MIRIAM annotations). As a cool extra you can view you model source code with inserted biological infomation.
Together with this http://www.semanticsbml.org/semanticSBML you can serach for similar BioModels. The similarity search is based on MIRIAM annotations that are attached to you model. AYM also allows you to create annotations without ...
Projects: COSMIC
Institutions: University of Goettingen
I`m interested to investigate the Influence of the accumulation of reduction equivalents on solvent production
Projects: SilicoTryp
Institutions: University of Heidelberg
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
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, OLCIR: Optimization of Lung Cancer Therapy with Ionizing Radiation, 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), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP, BioCreative VII, MESI-STRAT Review, SDBV/HITS, MESI-Review 2024
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock, University of Innsbruck
https://orcid.org/0000-0003-3540-0402I 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 ...
Projects: SysMO-LAB
Institutions: University of Rostock
PD Dr. rer. nat. habil. Bernd Kreikemeyer is the head of a research group at the Inst. of Medical Microbiology and Hospital Hygiene focusing on the pathogenesis of the human LAB Streptococcus pyogenes, microbial biofilm biology, and oral microbiology. Streptococcus pyogenes research, which is the relevant part for this BMBF proposal, is focused on 1. Identification of GAS virulence factors, 2. Mechanisms of GAS host cell adherence, host cell internalization, cytotoxicity of GAS towards host cells ...
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: University of Applied Sciences Koblenz, Rhein Ahr Campus
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: MOSES
Institutions: Medical University Vienna
Projects: BaCell-SysMO
Institutions: University of Groningen
Group leader Molecular Genetics
Projects: COSMIC
Institutions: Wageningen University & Research
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.
Projects: SysMO-LAB, Kinetics on the move - Workshop 2016, de.NBI-SysBio
Institutions: University of Heidelberg
Ursula Kummer is heading the dept. "Modeling of Biological Processes" at the University of Heidelberg.
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
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: 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, text-mining, gene annotation via public databases)...
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Secretary
Projects: TRANSLUCENT
Institutions: University of Applied Sciences Koblenz, Rhein Ahr Campus
Projects: SilicoTryp
Institutions: University of Heidelberg
Projects: SysMO-LAB
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.
Projects: BaCell-SysMO
Institutions: University of Newcastle
The main component of research in my group is in the determination of macromolecular structures by X-ray crystallography. However, since not all proteins crystallize, every effort is made to complete our understanding of how proteins function by utilizing other methods, such as microbial genetics, monitoring protein:ligand interactions by biochemical and biophysical methods, electron microscopy and bioinformatics
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: BaCell-SysMO
Institutions: University of Rostock
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
Projects: SCaRAB
Institutions: Norwegian University of Science and Technology
Projects: SCaRAB
Institutions: University of Greifswald
Projects: PSYSMO
Institutions: Imperial College London
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: KOSMOBAC
Institutions: University of Aberdeen
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.
Projects: BaCell-SysMO
Institutions: University of Greifswald
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.
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: SUMO
Institutions: University of Sheffield
I am a research associate in the department of computer science at the University of Sheffield since January 2008. My research is primarily involved with using agent-based modelling techniques and mathematical modelling techniques to model Escherichia coli K-12 Respiratory Adaptation. My research interests also include, development of workflows to analyze Microarray Data.
Projects: SulfoSys
Institutions: University of Vienna
Projects: PSYSMO
Institutions: Imperial College London
Projects: BaCell-SysMO
Institutions: University of Groningen
PhD student. Analyzing CcpA affinity to cre boxes (catabolite responsive elements) and response of B. subtilis to membrane protein overproduction stress.
Projects: BaCell-SysMO
Institutions: University of Groningen
Projects: STREAM
Institutions: INBIOTEC Leon
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
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
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 ...
Projects: SilicoTryp
Institutions: University of Edinburgh
Projects: SilicoTryp
Institutions: University of Edinburgh
Projects: PSYSMO
Institutions: University of Essex
Wet Lab experimentalist. Solute stress in Pseudomonas putida, group 12 in the PSYSMO consortium under Terry McGenity at the University of Essex. A PSYSMO PAL.
Projects: PSYSMO
Institutions: University of Essex
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
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: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: MOSES
Institutions: VU University Amsterdam
Projects: STREAM
Institutions: University of Groningen
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: BaCell-SysMO
Institutions: University of Goettingen
Projects: KOSMOBAC
Institutions: University of Groningen
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
Projects: COSMIC, BaCell-SysMO
Institutions: University of Rostock
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Projects: KOSMOBAC
Institutions: University of Aberdeen
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 ...
Projects: COSMIC
Institutions: University of Nottingham
A molecular microbiologist with a passion for Clostridia! Interested in the development of more effective countermeasures (diagnosis, prevention & treatment) against pathogens, specifically Clostridium difficile and Clostridium botulinum as well as the exploitation of the medical and industrial properties of beneficial strains, specifically in cancer therapy and biofuel production
Projects: STREAM
Institutions: University of Warwick
Systems Biologist specialising in data integration, high-throughput sequence analysis, and evolutionary and comparative analyses.
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: KOSMOBAC
Institutions: University of Aberdeen
Physicist, working on the modelling side.
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, BioCreative VII, SDBV ephemeral data exchanges, The BeeProject, SDBV/HITS, MESI-STRAT Review, MESI-Review 2024
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-4980-3512I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
Projects: SysMO-LAB
Institutions: Wageningen University & Research
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).
Projects: BaCell-SysMO
Institutions: University of Greifswald
I am pursuing my PhD at Prof. Volker's Lab in the Department of Functional Genomics, EMA Universitat Greifswald, Germany. I am working on the general stress responses mediated by SigB and the prediction of SigB regulon members using the Random forest algorithm.
Projects: TRANSLUCENT
Institutions: University of Cordoba
PhD Student
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Professor in biotechnology at the Dept. Chemistry, Biotechnology and Food Science. I am heading "Laboratory of microbial gene technology and food microbiology" that consists of approximately 20 members (staff members, technicians,and students). During the last 20 years my research has been focused on lactica acid bacteria with a focus on bacteriocins of lactic acid bacteria.These studies have included purification and chemical and genetic characterization of such peptides followed by biosynthesis ...
Projects: BaCell-SysMO
Institutions: University of Newcastle
I am a postdoc in the lab of Rick Lewis working on the biophysical characterization of protein-protein complexes involved in central carbon metabolism.
Software developer for FAIRDOM
Projects: SCaRAB, SysMilk, IMOMESIC
Institutions: Chalmers University of Technology
Institutions: University of Tuebingen, University of Tübingen
Projects: BaCell-SysMO
Institutions: University of Erlangen-Nuernberg
Projects: SCaRAB
Institutions: Norwegian University of Science and Technology
Projects: COSMIC
Institutions: University of Ulm
Postdoc University of Ulm/Dept. Microbiology and Biotechnology
Projects: PSYSMO, SynBio4Flav
Institutions: CSIC Madrid, CSIC
Projects: SUMO
Institutions: University of Stuttgart
Projects: TRANSLUCENT
Institutions: University of Vienna
Projects: SUMO
Institutions: University of Sheffield
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.
Projects: STREAM
Institutions: University of Warwick
Postdoctoral Research fellow with experience in Genomics, transcriptomics, proteomics and metabolomics
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting, FAIRDOM Community Workers
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-2130-0865Senior Research Software Engineer and Architect working at the University of Manchester within the FAIRDOM team.
Leads the development of FAIRDOM SEEK and RightField.
Projects: KOSMOBAC
Institutions: University of Aberdeen
I am final year PhD student in Prof Ian Booth's lab and a microbiologist by trade. I am interested in how enteric bacteria cope with stress and what systems they employ to increase their chances of survival, in particular upon methylglyoxal stress.
Projects: STREAM
Institutions: University of Groningen
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: SysMO Funders
Institutions: BBSRC
Projects: TRANSLUCENT
Institutions: Institute of Physiology Academy of Sciences
Translucent
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University of Sheffield
Projects: PSYSMO
Institutions: Imperial College London
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Projects: SUMO
Institutions: University of Sheffield
Work in my laboratory is focussed on microbial physiology - the study of how bacteria and other microorganisms work. Although rooted in the tradition of bacterial growth and intermediary metabolism, microbial physiology now embraces molecular biology, genetics, biochemistry, and indeed any discipline that can shed light on bacterial function. Much of our experimental work is conducted with Escherichia coli, the pre-eminent ‘model’ organism with unrivalled ease of genetic and physiological ...
Projects: KOSMOBAC
Institutions: University of Groningen
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 ...
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
PSYSMO project manager
Projects: COSMIC
Institutions: Wageningen University & Research
Projects: TRANSLUCENT
Institutions: University of Cordoba
Professor of Microbiology
Projects: PSYSMO
Institutions: CSIC Granada
Projects: STREAM
Institutions: University of Warwick
Projects: KOSMOBAC
Institutions: University of Aberdeen
I am postdoc in the group of Prof Ian Booth in Aberdeen working on the biochemical and biophysical characterisation of bacterial channels.
Projects: PSYSMO, MOSES, COSMIC, BaCell-SysMO
Institutions: University of Stuttgart
Professor for Biochemcial Engineering, University Stuttgart
Projects: STREAM
Institutions: University of Tuebingen
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, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study, CC-TOP, SABIO-VIS, SDBV/HITS
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
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.
Projects: KOSMOBAC
Institutions: University of Aberdeen
My background is physics engineering & biomedical engineering. I did my PhD in Surrey on the modelling of response of mammalian cells to radiation of different qualities. I have been working at the University of Aberdeen since November 2007 as a theoreticien research fellow of the KOSMOBAC project. We are investigating the homeostasis of ions in bacteria E. coli. I have been working at a model of the buffering capacity of the cytopplasm, arising from the presence of weak acids and bases. We ...
Projects: COSMIC
Institutions: University of Ulm
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 diffusion-reaction systems
Projects: STREAM
Institutions: INBIOTEC Leon
Projects: PSYSMO
Institutions: CSIC Madrid
Projects: SilicoTryp
Institutions: University of Edinburgh
I am a Postdoc at Keith Matthews lab in the Institute of Immunology and Infection Research, Edinburgh University. As part of the SilicoTryp project we are in charge of performing Targeted disruption and Overexpression of critical enzymes of Trypanosoma brucei redox metabolism enzymes and developmental perturbations to provide part of the necessary data for the construction of the model. Also generate consistent samples, so that data can be integrated and quantification results are guarateed to ...
Projects: SUMO
Institutions: University of Sheffield
I am a post-doctoral research associate working in Sheffield in the SUMO consortium. My research focuses on transcriptional regulation in E. coli, with particular emaphasis on the transcriptomic analysis of steady-state chemostat cultures using both microarray and qRT-PCR approaches.
Previous experience, especially that gained during my PhD, involved work on Salmonella physiology and lag phase growth, focusing particularly on gene-expression and transcriptional regulation. Other techniques used ...
Projects: KOSMOBAC
Institutions: University of Aberdeen
physicist
Projects: PSYSMO
Institutions: University of Dortmund
Projects: SysMO Funders
Institutions: Forschungszentrum Jülich
Working for Project Management Jülich, I am responsible for the SysMO-Office. This implies the coordination of communication between funding organisations (i.e. the Steering Committee), the Scientific Advisory Board, the Data Management Group, the PALs and the research groups.
Additionally, I am one of the administrative contacts for all German groups at Project Management Jülich.
Before I came to Jülich, my research focus was modelling and simulation in marine ecosystems.
Institutions: University of Stavanger
Physical chemist with expertise in experimental kinetics, molecular biology, and mathematical modeling.
Projects: PSYSMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: SUMO
Institutions: University of Edinburgh
Projects: BaCell-SysMO
Institutions: University of Greifswald
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.
Projects: SUMO
Institutions: University of Stuttgart
From 2005 to 2008 I was group leader at the Institute for System Dynamics at the University of Stuttgart. Since 2008 I am now Professor of Systems Biology at the University of Luxembourg.
The research of the Systems Biology Group at the University of Luxembourg is focussed in the area of experimental and theoretical systems biology. We are applying different modelling techniques (mainly ODE and logical) to biological systems to develop suitable computational models. The analysis of these models ...
Projects: SUMO
Institutions: University of Stuttgart
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: COSMIC
Institutions: University of Ulm
Dr. Bettina Schiel-Bengelsdorf Senior Scientist Department of Microbiology and Biotechnology University of Ulm 89069 Ulm, Germany
Projects: SulfoSys
Institutions: University of Vienna
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).
Projects: PSYSMO
Institutions: University of Dortmund
Projects: SCaRAB
Institutions: University of Greifswald
Projects: PSYSMO
Institutions: University of Braunschweig
Projects: SulfoSys, PSYSMO, SulfoSys - Biotec, EbN1 Systems Biology
Institutions: University of Braunschweig
Projects: PSYSMO, SulfoSys, SulfoSys - Biotec
Institutions: University of Braunschweig
Projects: TRANSLUCENT
Institutions: University of Bonn
Projects: COSMIC
Institutions: Wageningen University & Research
PostDoc at Wageningen University, Laboratory of Microbiology
Projects: TRANSLUCENT
Institutions: University of Vienna
Projects: BaCell-SysMO
Institutions: University of Erlangen-Nuernberg
I studied chemistry in Erlangen and started research on carbon catabolite regulation in Bacillus megaterium in my diploma thesis. During my PhD thesis I was concerned with quantitative analyses of protein-protein and protein-DNA interactions of CcpA, in vivo- and in vitro-characterization of point mutants of CcpA and coeffectors and I contributed to the structural analysis of different CcpA complexes. During a postdoctoral appointment I focused on interaction analyses of PrfA, a regulator of ...
Projects: Noisy-Strep
Institutions: University of Groningen
Projects: MOSES, PSYSMO, SysMO-LAB, SulfoSys
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: SUMO
Institutions: University of Amsterdam
Projects: SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers
Institutions: University Duisburg-Essen, Universitity Duisburg-Essen
https://orcid.org/0000-0002-9905-541XHead 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 ...
Projects: SysMO-LAB
Institutions: University of Rostock
Projects: PSYSMO
Institutions: University of Stuttgart
Projects: SulfoSys
Institutions: Wageningen University & Research
Projects: STREAM
Institutions: University of Aberdeen
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, Project Coordination, WP 3: Drug release kinetics study, Glucose metabolism in cancer cell lines
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University
Projects: SysMO-LAB
Institutions: Norwegian University of Life Sciences
Projects: Noisy-Strep
Institutions: University of Groningen
Projects: SUMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
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
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: BaCell-SysMO
Institutions: University of Greifswald
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 ...
Projects: BaCell-SysMO
Institutions: University of Erlangen-Nuernberg
Projects: SUMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: BaCell-SysMO
Institutions: University of Newcastle
Projects: BaCell-SysMO
Institutions: University of Goettingen
Projects: SCaRAB
Institutions: Norwegian University of Science and Technology
Projects: STREAM
Institutions: University of Groningen
Projects: TRANSLUCENT
Institutions: Institute of Physiology Academy of Sciences
biochemistry, molecular biology and physiology of lower eukaryotes, characterization of cell membrane transporters
Projects: STREAM
Institutions: University of Groningen
Institutions: University of Amsterdam
Professor Quantitative Microbial Physiology Dept Mol Mic Phys Swammerdam Inst Life Sc University of Amsterdam
Projects: SUMO
Institutions: University of Amsterdam
Projects: SysMO-LAB, SysMilk, IMOMESIC
Institutions: Wageningen University & Research, VU University Amsterdam
https://orcid.org/0000-0003-3929-0423Since 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.
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: STREAM
Institutions: University of Aberdeen
Quantitative proteomics
Projects: COSMIC
Institutions: University of Nottingham
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Projects: PSYSMO
Institutions: University of Hannover
Projects: PSYSMO
Institutions: Helmholtz Centre for Infection Research Braunschweig
Projects: MOSES
Institutions: Medical University Vienna
Projects: PSYSMO, COVID-19 Disease Map
Institutions: CSIC Madrid
Projects: SCaRAB
Institutions: Norwegian University of Science and Technology
Projects: TRANSLUCENT
Institutions: Autonomous University of Barcelona
Projects: SUMO
Institutions: University of Amsterdam
Johan van Beilen University of Amsterdam j.w.a.vanbeilen@uva.nl;
Projects: SulfoSys
Institutions: Wageningen University & Research
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 ...
Projects: BaCell-SysMO
Institutions: University Medical Centre Groningen
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 ...
Projects: SysMO-LAB
Institutions: University of Amsterdam
Projects: Noisy-Strep
Institutions: University of Groningen
The Veening lab is interested in phenotypic bi-stability in Streptococcus pneumoniae and its importance in virulence of this human pathogen.
Projects: SysMO-LAB
Institutions: University of Heidelberg
Projects: MOSES, SysMO-LAB, BaCell-SysMO
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
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 ...
Projects: SCaRAB, BaCell-SysMO
Institutions: University of Greifswald
By training I am a molecular microbiologist with a particular interest in bacterial stress adaptation reactions. Since the early 90ies we have used functional genomics technologies, particularly proteomics, to investigate the response of Bacillus subtilis to environmental challenges. I am currently Head of the Functional Genomics Department of the Interfaculty Institute of Genetics and Functional Genomics at the Ernst-Moritz-Arndt-University Greifswald. Within the Department we are applying ...
Projects: COSMIC
Institutions: University of Rostock
Projects: SulfoSys
Institutions: eGene Biotechnologie GmbH
Group Leader, Molecular and Cellular Modeling Group, EML Research, Heidelberg
Projects: STREAM
Institutions: University of Warwick
Projects: STREAM, SYSTERACT, INBioPharm, BioZEment 2.0, OXYMOD, BESTER, AquaHealth (ERA-BlueBio)
Institutions: SINTEF
https://orcid.org/0000-0002-9420-1959Projects: 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 material, Fusion-fission-mitophagy, Stochastics and bursting
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, VU University Amsterdam, University of Amsterdam, Systems Biology Amsterdam
https://orcid.org/0000-0002-0443-6114Systems Biologist at University of Amsterdam, Free University Amsterdam, University of Manchester, Infrastructure Systems Biology.NL (ISBE.NL), Systems Biology Amsterdam.
Projects: SulfoSys
Institutions: University of Braunschweig
Projects: STREAM
Institutions: University of Warwick
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: COSMIC
Institutions: University of Nottingham
A microbiologist with interest in microbial physiology and metabolism. Current research focuses on the biology of pathogenic and non-pathogenic clostridia, in particluar in vivo metabolism and cell-to-cell communication. Also active in metabolic engineering, using both systems and synthetic biology approaches.
Projects: BaCell-SysMO
Institutions: University of Braunschweig
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.
Positions 1993-1996: Research Assistant, German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany. 1997-1998: Post-doc at Department of Applied Chemistry & ...
Institutions: University of Tuebingen, University of Tübingen
Projects: MOSES, ExtremoPharm
Institutions: University of Heidelberg
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.
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University of Sheffield
I am the foundation Professor of Systems Biology and Engineering within the Department of Chemical and Process Engineering (CPE), at The University of Sheffield. My research philosophy is centred on a mechanistic systems biology approach to solve biochemical reaction engineered processes. I wish to pursue issues involved in the effective utilisation of biological resources. The approach is specifically targeted at the conjunction of chemical engineering (metabolic engineering and synthetic biology), ...
Projects: BaCell-SysMO
Institutions: DSM Nutritional Products Ltd.
Projects: Noisy-Strep
Institutions: University of Newcastle
Projects: TRANSLUCENT
Institutions: Institute of Physiology Academy of Sciences
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
https://orcid.org/0000-0002-7973-9902I'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 ...
Projects: SulfoSys
Institutions: University Duisburg-Essen
Projects: BaCell-SysMO
Institutions: University of Marburg
Projects: Noisy-Strep
Institutions: University of Newcastle
Projects: SysMO-LAB
Institutions: University of Rostock
Projects: COSMIC
Institutions: University of Nottingham
Projects: KOSMOBAC
Institutions: Ludwig-Maximilians University of Munich