Connectionists: Three PhD/postdoc positions in “Systems modeling of Insulin Resistance”

[Volker Roth]

ETH Zurich / University of Basel (Switzerland): Three PhD/postdoc
Positions in “Systems modeling of Insulin Resistance”

Applications are invited for three PhD/postdoc positions in the
research program “LiverX: Systems Biology of Hepatic Insulin Resistance”
at the Competence Center for Systems Physiology and Metabolic Diseases
(CC-SPMD) (http://www.ccspmd.ethz.ch/), which is part of SystemsX,
the Swiss Initiative in Systems Biology (www.systemsx.ch).

The „LiverX“ Project is an approved SystemsX RTD project with 13
research groups from ETH Zurich, the University Basel and the University
Zurich working together towards understanding the mechanisms of insulin
resistance by systematically collecting and analyzing quantitative and
dynamic data of the involved hormonal and metabolic control networks at
the level of single cells, organs and whole organisms. Together with
clinical data of patients this knowledge will be used to develop
mathematical models of insulin resistance.

Within this Systems Biology Program, three positions are available for
PhD students/postdoctoral fellows working at the following departments:

  (i)  Computer Science Department, ETH Zurich (Prof. Joachim M. Buhmann);
  (ii) Department of Biosystems Science and Engineering, ETH Zurich
       (Prof. Jörg Stelling);
  (iii) Department of Computer Science, University of Basel (Prof. 
Volker Roth).
Together with the group of Prof. P. Bühlmann (Statistics Seminar, Math
Dept., ETH Zurich), these groups form the “modeling” subdivision within
the LiverX consortium. Close interaction with other scientists of the
LiverX research consortium of CC-SPMD is an attractive feature of the
project. The main focus of research concerns:

  1. Establishing a network of causal dependencies among genes in
     regulatory/metabolic networks. On the Machine Learning side, this
     task includes the development of probabilistic models for
     inferring network structures from data and for detecting causal
     dependencies in these networks. Particular emphasis will be put on
     perturbation experiments for validating the inferred network
     topology.
  2. Establishing a dynamical model for fatty acid subsystem in the
     liver. Based on dynamic measurements of key metabolites and
     metabolic fluxes, dynamic protein data and gene expression data,
     the goal is to identify a model for the dynamic control of the
     fatty acid synthesis. In a next step, this fatty acid model is
     planned to be extended to include causal dependencies relevant for
     the local control of lipid pools. Finally, the overall goal is a
     model for the whole-system dynamics of the liver system. On the
     modeling side, this approach will involve new developments of
     probabilistic methods for dynamic ODE-based biochemical networks.

  3. On a conceptual level, the project addresses the complicated
     question how complex dynamical models of biological systems can be
     estimated based on sparse, time dependent data. How can we
     quantify uncertainty in the model structure and the model
     parameters? How can we develop a working feedback loop from
     computational biology modeling to experimental design of
     experiments? Applicants with an interest in these model design
     questions are particularly encouraged to apply.
Candidates will have a Masters/PhD degree with background and
experience in computer science, applied mathematics, physics or
bioinformatics, interest to work in an interdisciplinary research
environment and very good communication skills (English).
For further inquiries, please contact

Joachim M. Buhmann: jbuhmann at inf.ethz.ch
Jörg Stelling: joerg.stelling at bsse.ethz.ch
Volker Roth: volker.roth at unibas.ch

Successful candidates will work in the international team and be
awarded a fellowship with a competitive salary (64000 CHF/year).
Applications with a full CV, list of publications, short statement of
research interests and names of at least one referee should be submitted
to:

Ms. Rita Klute,
ETH Zurich, Institute of Computational Science, CAB G 69.1,
Universitaetstrasse 6,
CH-8092 Zurich, Switzerland
email: rita.klute at inf.ethz.ch

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Volker Roth
Computer Science Dept.		     Tel.: +41-(0)61-2670549
University of Basel
Bernoullistr. 16,
CH-4056 Basel, Switzerland         email: volker.roth at unibas.ch         
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