[SocBiN] Two postdoc positions at Computational Biomodeling Laboratory, Turku, Finland

Ion Petre ipetre at abo.fi
Mon Jul 1 14:50:18 CEST 2013


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 ipetre at abo.fi. 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 ipetre at abo.fi. 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 network’s 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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