Rahuman Sheriff is a Senior Project Leader (BioModels) at the European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, Cambridge, UK. He interests include mathematical modelling, development of novel tools and resources for building models, immune digital twin, quantitative imaging, single cell systems biology and chemoinformatics. He is one of the editors of Systems Biology Markup Language (SBML).
Projects: BioDynamics
Institutions: Universitat Politècnica de València
https://orcid.org/0000-0003-4144-3521Jesús Picó is Full Professor of Automatic Control at The Department of Systems Engineering and Control of the Universitat Politècnica de València (UPV). In 2013 he created the Laboratory of Synthetic Biology and Biosystems Control (SB2CLab) of the Institute of Automation and Industrial Informatics (ai2) at the UPV, the first multidisciplinary lab in Spain integrating systems and control engineers, bioinformatics and biotechnologists. His research interests are in the application of systems ...
Julio is the leader of the Computational Biology Lab at MBG-CSIC (Pontevedra, Spain), an institute of CSIC (Spanish National Research Council). More info at https://www.bangalab.org
Our research is focused in computational systems and synthetic biology.
We use mathematical modelling, simulation and optimization to understand complex biological systems and processes.
Current research topics include:
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Reverse engineering: systems identification (dynamic modelling) of biological networks
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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Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated material, Fusion-fission-mitophagy, Stochastics and bursting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: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2
Institutions: National Institute of Biology, tst
https://orcid.org/0000-0002-1669-6482Expertise: 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 and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)
Institutions: Latvia University of Agriculture
Expertise: Python, Systems Biology, Dynamic modelling, Mathematical modelling
Tools: COBRA toolbox, cobrapy toolbox, Python, SBML, Copasi, Computational Systems Biology
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.
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomington
https://orcid.org/0000-0002-7440-2905Expertise: Mathematical modelling, Data Management, Software Engineering, Python, standards, c++
Research Associate in the Macklin Lab, School of Informatics, Computing, and Engineering. Indiana University, Bloomington, IN USA.
Projects: SAFE-Aqua, Biomics Projects
Institutions: Institut Pasteur
https://orcid.org/0000-0001-6286-1138Projects: EmPowerPutida, COVID-19 Disease Map
Institutions: Wageningen University & Research, University Maastricht
https://orcid.org/0000-0003-3091-3962Expertise: Systems Biology, Mathematical modelling, Biotechnology, Synthetic Biology, Metabolic Engineering, metabolism, Metabolic Networks, SARS-CoV 2, COVID-19, Pathway Curation, Pathway Analysis, Network Analysis
Tools: Matlab, Computational Systems Biology, Flux balance analysis, omics analysis, Python, R, Constraint-based analysis
My research interest is in studying cellular and molecular pathways of COVID-19 disease.
Projects: EmPowerPutida
Institutions: LifeGlimmer GmbH
Expertise: Bioinformatics, Systems Biology, Transcriptomics, R, Genomics, Proteomics, Databases, Data Integration
Tools: Bioinformatics, Molecular Biology, Computational Systems Biology
Computational Biologist and App Designer @LifeGlimmer
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Institutions: National Institute of Biology, NewHorizon
https://orcid.org/0000-0001-7484-6031Projects: HUMET Startup, COVID-19 Disease Map
Institutions: Centro de Investigación Príncipe Felipe, Fundación Progreso y Salud
https://orcid.org/0000-0003-3318-120XExpertise: Bioinformatics, Data Management, Mathematical modelling, Genomics, Genetics, Transcriptomics, Systems Biology, Microarray analysis, Data Integration
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Genetics, Genomics, R, Systems Biology, Transcriptomics, Java
My scientific interests revolve around functional genomics, systems biology and the development of algorithms and software for the analysis of high-throughput data (mainly, but not restricted to, Next Generation Sequencing) and its application to the relationship between genotype and phenotype, mainly oriented to personalized and precision medicine. I am especially interested in the study of disease mechanisms and drug action mechanisms, drug repositioning and the definition of mechanism-based ...
Projects: FAIRDOM user meeting
Institutions: Peter MacCallum Cancer Centre
Expertise: Systems Biology, Transcriptomics, Genomics
Tools: Systems Biology, Transcriptomics, Computational Systems Biology, Bioinformatics, R
Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by ...
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiative, SDBV/HITS, EDITH (Ecosystem Digital Twins in Health) test project
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-8683-7084Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team. Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and ...
Projects: de.NBI-SysBio, GenoSysFat, Kinetics on the move - Workshop 2016, Example use cases, COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Institutions: University of Rostock, University of Greifswald, University Medicine of Greifswald
https://orcid.org/0000-0002-5886-5563I am a computer scientist by training with a specialisation on database and information systems. Since December 2018 I am professor of Medical Informatics at the University Medicine in Greifswald, Germany, at the Institute of Community Medicine. My lab focuses on research data management in biomedicine, data integration across health care providers, and provenance of clinical research data items within clinical information systems. Furthermore, I am actively involved in COMBINE standardisation ...
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Institute of Cytology and Genetics
I am a biomodeler, PhD student. Actually, I've graduated from Novosibirsk State University on two specialities: my bachelor diploma is done in computer science and the master thesis is defended in information biology. So, I'm kind of drifting towards biology. I am a part of the Haploid Evolutionary Constructor project. Our research group studies are dedicated to the simulation of prokaryotic communities. Personally, I am involved into the simulation of spatially distributed bacterial communities ...
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Imperial College London
I am a PhD student in the Theoretical Systems Biology group, based at Imperial College London. The aim of my PhD is to understand how noise can be the driving force of decision-making processes (differentiation, self-renewal, apoptosis or tumorgenesis), and what are our chances to control them. So far I have been working on method development for stochastic models, a moment closure framework and a stochastic reachability method, to look into cell-to-cell-variability.
Projects: FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, FAIRDOM user meeting
Institutions: University of Zürich, ETH Zurich, Manchester Centre for Integrative Systems Biology, University of Manchester
Expertise: Bioinformatics, Proteomics, Genomics
Tools: Matlab, Microarray analysis, Data Management, Computational Systems Biology, Perl, Python
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student, ...
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
Expertise: Microbiology, Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, Biotechnology
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 ...
Expertise: Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, sensitivity analysis, Dynamic optimization., Dynamics and Control of Biological Networks, Parameter estimation
Tools: ODE, Partial differential equations, Matlab, differential algebraic equations, Stochastic models, Computational Systems Biology, Deterministic models, Dynamic modelling, Parameter estimation
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: 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: COSMIC, BaCell-SysMO
Institutions: University of Rostock
Expertise: Mathematical modelling, dynamics of biological networks, Physics, bistability, Systems Biology, Data analysis, Statistical Physics, Dynamics and Control of Biological Networks
Tools: Computational and theoretical biology, ODE, Matlab, Mathematica, differential algebraic equations, Stochastic models, C programming, Computational Systems Biology, Dynamic modelling, Data Modelling
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Projects: BaCell-SysMO
Institutions: University of Stuttgart
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.
Projects: PSYSMO, MOSES, COSMIC, BaCell-SysMO
Institutions: University of Stuttgart
Expertise: Reactor models, rapid sampling experiments, Systems Biology, Mathematical modeling, Regulatory Networks, Dynamics and Control of Biological Networks
Tools: Fermentation, stimulus response experiments, evaluation of process dynamics, continuous cultivation, Computational Systems Biology, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Dynamic modelling, In silico Metabolic Network Analysis, fed-batch cultivation
Professor for Biochemcial Engineering, University Stuttgart
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: 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: STREAM, SilicoTryp
Institutions: University of Groningen
Expertise: Transcriptomics, Metabolomics, Systems Biology
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 ...
Expertise: Mathematical modelling, Statistically and biologically inspired optimization algorithms, Mathematical modelling of biosystems and bioprocesses, Dynamics and Control of Biological Networks, Parameter estimation
Tools: Computational and theoretical biology, ODE, Partial differential equations, Matlab, Mathematica, Computational Systems Biology, including: - Dynamic modelling - Parameter estimation - Optimal experimental design - Dynamic optimization
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
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Projects: KOSMOBAC
Institutions: University of Aberdeen
Expertise: Mathematical modelling, Mathematical modelling of biosystems and bioprocesses
Tools: Computational and theoretical biology, ODE, linux, data modeling, enzymatic analyses, Stochastic models, C programming, Computational Systems Biology, Deterministic models, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization
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 ...