Two postdoc openings are available at the Computational Biomodeling Laboratory, Turku Centre for Computer Science and Åbo Akademi University, Turku, Finland. The positions are funded by Academy of Finland. The deadline for applications is August 11. The positions can be filled in to start September 1 or soon after. For detailed information about each position see below.
With best regards, Ion Petre. ---------------------------------------------- Prof. Ion Petre Computational Biomodeling Laboratory Åbo Akademi University, Department of IT Turku 20520, Finland http://users.abo.fi/ipetre/ *************************************** Position 1: Quantitative model refinement Application and required skills Eligible applicants have a PhD in Computer Science, Mathematics, Computational Biology, or a closely related field, obtained not earlier than 2008. We are looking for candidates with a strong background in theoretical computer science and/or mathematics, with experience on modelling biological systems, demonstrated by a good publication record. Applicants should send an up to 3-page CV, their full list of publications, a letter of interest, and two recommendation letters to Prof. Ion Petre [email protected]. Quote in the subject of your email Application for postdoc: quantitative model refinement. Description We focus in this project on computational techniques allowing mathematical models in biology to be presented and used at different levels of detail. We aim to construct and investigate a computational framework for quantitative model refinement where details may be added to (or removed from) a model in a systematic way, while preserving its overall numerical behaviour. Our methodology addresses a major current challenge in computational systems biology, that of specifying a model at various levels of resolution while formally ensuring that once the model is quantitatively fit and validated at some level, it remains so at any other level. This approach provides the basis for creating and handling flexible hierarchical models, able to integrate data and processes across scales. The project is of a methodological nature, focusing on the development of a sound computational framework for quantitative model refinement; this framework is a quantitative development of earlier work done in connection to program specification and (qualitative) refinement, at the borderline between computer science and software engineering. We will test the applicability of our methodology on several biomodelling case studies. The project is funded by Academy of Finland. Duration The contract is for one year, with the possibility of extending it for another year. Salary The salary is in accordance with the pay scale at Finnish universities, in the bracket 2820-3616 eur/month before taxes, depending on the candidates skills and experience. Location The postdoc position will be hosted at the Computational Biomodeling Laboratory <http://combio.abo.fi/> , Turku Centre for Computer Science <http://tucs.fi/> and Åbo Akademi University <http://www.abo.fi/?lang=en> , Turku <http://www.turku.fi/Public/default.aspx?culture=en-US&contentlan=2&nodeid=2 3> , Finland. *************************************** Position 2: Network controllability Application and required skills Eligible applicants have a PhD in Computer Science, Mathematics, Computational Biology, or a closely related field, obtained not earlier than 2008. We are looking for candidates with a strong background in theoretical computer science and/or mathematics, with experience on modelling biological systems, demonstrated by a good publication record. Applicants should send an up to 3-page CV, their full list of publications, a letter of interest, and two recommendation letters to Prof. Ion Petre [email protected]. Quote in the subject of your email Application for postdoc: network controllability. Description The overall objective of the project is to better understand the fundamental principles of controllability of complex, biological networks, and how these control principles could be exploited to intervene in the network under analysis to change its dynamic behavior. Together with the consortium partners, we will consider two concrete case studies with important biotechnological and medical implications: (1) re-programming of prokaryote metabolism to enhance renewable and sustainable fuel production; and (2) finding druggable vulnerabilities of cancer networks for improved anticancer therapeutics. In our part of the project, we plan to formulate a novel mathematical formalism for analyzing complex biological networks and their controllability. This includes the ability to compute a networks degree of controllability when changing its architecture. The first step is finding new metrics for network controllability, considering different mathematical models of a network (graph, rule-based, Boolean), and thus gaining a quantitative assessment of how complex a network is with respect to its controllability. We plan to address partial controllability for biological networks; the focus here is on identifying the minimal set of driver/input nodes that controls at least a specified part (or proportion) of a network. In biological systems it is also crucial to determine the set of controlled nodes, given a set of controllable nodes. This information can further be used in two directions. First, one can gain insight on all the reachable nodes and in case the nodes of interest are in the set, reduce the control to the minimum set of nodes that affects all the nodes of interest. Second, one might find alternative sets of control nodes that span their action to a set of nodes of interest. The project is funded by Academy of Finland through the research program on Synthetic Biology (FinSynBio). The project will be carried out in collaboration with colleagues from University of Turku and Finnish Institute for Molecular Medicine. Duration The contract is for one year, with the possibility of extending it for another year. Salary The salary is in accordance with the pay scale at Finnish universities, in the bracket 2820-3616 eur/month before taxes, depending on the candidates skills and experience. Location The postdoc position will be hosted at the Computational Biomodeling Laboratory <http://combio.abo.fi/> , Turku Centre for Computer Science <http://tucs.fi/> and Åbo Akademi University <http://www.abo.fi/?lang=en> , Turku <http://www.turku.fi/Public/default.aspx?culture=en-US&contentlan=2&nodeid=2 3> , Finland.
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