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.
I'm currently a Postdoc at the Institute of Technical Biochemistry in Stuttgart University. My project involves the experimental validation of the Indirect Enzymatic Dehydration Via Phosphorylation and Dephosphorylation of Isobutanol for Isobutene production.
Expertise: enzyme kinetics, enzymes, Enzymatic reactions, biochemical enzyme characterization, Biochemistry, molecular simulation, molecular modeling, Programming, Bioinformatics, Computational Biology
Tools: Gromacs, Python, Molecular Dynamics, bash, Biochemistry, Bioinformatics, Biochemistry and protein analysis, Enzyme assay, enzyme kinetics, isothermal titration calorimetry, dynamic light scattering, Spectrophotometry
Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
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
Institutions: University of Stuttgarthttps://orcid.org/0000-0002-5300-0915
Currently I focuse on the integration of data into multi-scale models with statistical methods and uncertainty tracking in the research unit QuaLiPerF.
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Web page: http://www.denbi.de
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒supercomplex and diverse PBPs in dinoflagellate Prorocentrum cordatum, icpm-kth, Catabolic network of the gut bacteria P. vulgatus, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG
Web page: Not specified
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Web page: http://sysmo.net/
The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.
Public web page: https://www.ist.uni-stuttgart.de/research/group-of-nicole-radde/
Start date: 11th Feb 2020
Organisms: Mus musculus
Exploiting native endowments by re-factoring, re-programming and implementing novel control loops in Pseudomonas putida for bespoke biocatalysis. The EmPowerPutida project aims to engineer the lifestyle of Pseudomonas putida to generate a tailored, re-factored chassis for the production of so far non-accessible biological compounds. Pseudomonas putida is a bacterium with a highly versatile metabolism, including the capability to degrade or produce organic chemicals.
BaCell-SysMO 2 Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.
Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying ...
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.
The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated ...
MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.