I am a Researcher at the National Laboratory of Scientific Computing (LNCC). I am a bioinformatician and my research interests are in data integration and analyses. I use scientific workflows technologies to integrate and analyse data in systems biology, phylogenomics, and functional genomics.
Post Doc (2010 – 2015) of the Department of Computer Science at the COPPE Institute of the Federal University of Rio de Janeiro (Brazil) and was supported by a FAPERJ’s grant “Post-Doc Note 10” (2013 –
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0002-3671-895X
Researcher at the European Institute for Systems Biology and Medicine, working on network-based data analytics within the EU eTRIKS Project.
Institutions: National Institute of Biologyhttps://orcid.org/0000-0002-1669-6482
Roles: PhD Student
Expertise: Data Management, Visualization, Data analysis, Data analysisMathematical modellingBioinformaticsSystems biology, Data integration, Molecular Biology, Mathematical and statistical modeling, Statistics, Programming, computational biology, Bioinformatics
Tools: Computational and theoretical biology, Data Management, Molecular Biology, Systems Biology, Computational Systems Biology, Databases, Python, Bioinformatics, Data integration, Dynamic modelling, R
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Projects: Not specified
Institutions: Not specifiedhttps://orcid.org/0000-0003-2852-6648
I am performing research in biomarkers discovery, particularly regarding liver fibrosis in non-alcoholic fatty liver disease. My research activities involved the use of bioinformatic platforms, the analysis of biological protein-protein interaction networks and the experimental validation of candidates by ELISA.
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomingtonhttps://orcid.org/0000-0002-7440-2905
Research Associate in the Macklin Lab, School of Informatics, Computing, and Engineering. Indiana University, Bloomington, IN USA.
Institutions: National Institute of Biologyhttps://orcid.org/0000-0003-0913-2715
Institutions: Wageningen University & Researchhttps://orcid.org/0000-0003-3091-3962
I'm currently a PhD student in Laboratory of Systems and Synthetic Biology in Wageningen University & Research. My project involves using genome scale metabolic modelling to understand and improve chemical production capacities of microorganism.
Institutions: National Institute of Biologyhttps://orcid.org/0000-0001-7484-6031
Projects: HUMET Startup
Institutions: Centro de Investigación Príncipe Felipehttps://orcid.org/0000-0003-3318-120X
Tools: Computational and theoretical biology, Databases, Genomics, Transcriptomics, Computational Systems Biology, Dynamic modelling, R, Java, Bioinformatics, Data Management, Genetics, Systems Biology
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
Institutions: Norwegian University of Life Scienceshttps://orcid.org/0000-0002-7778-4515
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 Workershttps://orcid.org/0000-0002-8683-7084
Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team.
Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and
Projects: 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"https://orcid.org/0000-0002-5886-5563
I 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
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
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.
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,
Expertise: Systems Biology, sensitivity analysis, Dynamic optimization., Optimal experimental design, Mathematical modelling of biosystems and bioprocesses, parameter estimation, dynamics and control of biological networks
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
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
Tools: data modelling, Dynamic modelling, Computational Systems Biology, Stochastic models, C programming, differential algebraic equations, Mathematica, Matlab, ODE, Computational and theoretical biology
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Expertise: metabolic networks, carbon metabolism, Signalling networks, Nonlinear Dynamics, Systems Biology, stress responses, Mathematical modelling of biosystems and bioprocesses, Bacillus subtilis, Mathematical modelling, Biochemistry, Microbiology
Tools: fed-batch cultivation, Dynamic modelling, Computational Systems Biology, Deterministic models, Enzyme assay, continuous cultivation, Chromatography, Fermentation, Matlab, Mathematica, ODE, Computational and theoretical biology
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.
Tools: fed-batch cultivation, In silico Metabolic Network Analysis, Dynamic modelling, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Computational Systems Biology, evaluation of process dynamics, continuous cultivation, stimulus response experiments, Fermentation
Professor for Biochemcial Engineering, University Stuttgart
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: 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: metabolic netwlrk visualization, reverse engineering, computational platform development, microbiology techniques, Metabolic Engineering, Computational Systems Biology, Microarray analysis, Fermentation, Proteomics, Genetic modification, Bioinformatics
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 am working on a kinetic model of the central metabolism as well as on a genome wide model of Streptococcus pyogenes.
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 of biosystems and bioprocesses, Statistically and biologically inspired optimization algorithms, dynamics and control of biological networks, parameter estimation, Mathematical modelling
Tools: including: - Dynamic modelling - Parameter estimation - Optimal experimental design - Dynamic optimization, Computational Systems Biology, Mathematica, Matlab, Partial differential equations, ODE, Computational and theoretical biology
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
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
Tools: Deterministic models, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Computational Systems Biology, Stochastic models, C programming, enzymatic analyses, data modeling, linux, ODE, Computational and theoretical biology