Systems Biology studies the properties and phenotypes that emerge from the interaction of biomolecules where such properties are not obvious from those of the individual molecules. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and eventually of whole cells and organisms are generated as tools for research. ICYSB will provide a hands-on experience in integrating experimentation and mathematical modelling with an emphasis on kinetic modelling of cellular pathways. The course focuses on yeast because the development of the emerging field of Systems Biology requires suitable model systems for data generation.
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Institutions: Humboldt-Universität zu Berlin
I am working at the boundary of wet-labs and mathematical modeling, trying to understand the regulation of the eukaryotic cell cycle. I started working with yeast in a group of Systems Biology (Prof. Edda Klipp, Humboldt University, Berlin). Before that I studied biology, engineering and did research on the nuclear pore complex.
Institutions: Universität Konstanz
I studied Life Science (which is similar to chemical biology) at the University of Konstanz and became interested in Bioinformatics, Systems Biology and quantitative analyses during my Master's. In my PhD project I combine experimental analyses with modeling and parameter estimation approaches to quantitatively analyse regulation of apoptosis at the level of the Bcl-2 protein family.
Institutions: University of Tübingen
Trained as a Computer Scientist at the University of Jena, Germany, my interests drifted more and more towards "computing life" during my PhD at Simon Fraser University and the University of British Columbia, Canada. On one hand, that term captures that I got fascinated by the idea to understand life as a form of computation and to describe, reprogram, and reassemble parts of cells as described in many brilliant experiments from a spectrum of disciplines ranging from DNA computing to Synthetic
Institutions: Åbo Akademi University
Institutions: Institute of Pathology
I am a postdoc at the Technical University in Munich. When I studied nutritional science I got more and more interested in molecular cancer research. My PhD thesis was in the field of molecular cancer research. In our lab we are interested in molecular basic research on cell culture level, especially regarding gastric cancer.
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: 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, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, 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)https://orcid.org/0000-0003-3540-0402
I 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 project
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,
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.
Institutions: Institute for Experimental Internal Medicine
I am a PhD student in the field of Systems Biology. In my PhD project I apply mathematical modelling to understand the role of time delay in biological systems containing delayed negative feedbacks.
Institutions: Imperial College London
I am a first year PhD student at Imperial College London. My undergraduate degree was in Chemistry with a focus in medicinal Chemistry. My PhD project focuses on using chemical proteomics to obtain time resolved data of hypothesized signalling networks in cancer. More specifically, I study the roles of the KLK Activome in prostate cancer progression. My future research goals include developing a deterministic kinetic model of the KLK Activome that will aid in the discovery of novel therapeutics
Butanol producing iNS142, redesigned using RobOKoD.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Model type: Metabolic network
Model format: SBML
Organism: Not specified
Investigations: Designing a new way to predict engineering stra...
Modelling analyses: RobOKoD applied to e.coli for butanol production.
Authors: J. Schaber, R. Baltanas, A. Bush, E. Klipp, A. Colman-Lerner
Date Published: 15th Nov 2012
Publication Type: Not specified
PubMed ID: 23149687
Citation: Mol Syst Biol. 2012;8:622. doi: 10.1038/msb.2012.53.
Authors: J. Schaber, A. Lapytsko, D. Flockerzi
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 24307567
Citation: J R Soc Interface. 2013 Dec 4;11(91):20130971. doi: 10.1098/rsif.2013.0971. Print 2014 Feb 6.