Wednesday, October 7, 2009

Master, PhD, Postdoc Open Positions on Mechanistic aspects and spatial effects in cell signalling

Mechanistic aspects and spatial effects in cell signalling, within TEAM Programme sponsored by Foundation for Polish Science.

Concepts and objectives
The leading aim of the project is to identify and study the turning points in molecular pathways of immune response and cancer, in which the single cell fate, understood as a choice between apoptosis, senescence, proliferation, differentiation or cell cycle arrest, is decided. As a model molecular pathways we will consider these related to innate and adaptive immune response and cancer, in which we have expertise. The project will be realized both by means of numerical simulations and theoretical analysis.

We have the open positions for undergraduate students (with the third year finished), PhD students and postdoctoral researchers

The following topics will be financed:

For MSc (undegraduate, after third year) students:

1. Stochastic gene expression: numerical simulations and mathematical analysis.
2. Stochastic numerical simulations of complex regulatory pathways: development of new simulation tools.
3. Evolution and co-evolution of genes (and their regulatory regions) related to p53 and NF-kappaB pathways: From yeast to human.
4. Mutations of p53 pathways genes in various types of cancer.

For PhD students:

1. Calcium signalling, calcium travelling waves, spatial organization of kinase cascades, stochastic and deterministic reaction-diffusion equations.
2. Mathematical aspects of regulatory pathways: Markov processes, bifurcation theory for stochastic systems.
3. Integration of signalling pathways of transcription factors: NF-kappaB, p53 and IRF3/IRF7.

For postdoctoral researchers:

1. Formation and signalling in nanoclusters and receptor complexes, B-cell receptor signalling.
2. DNA regulation and dynamics (formation of cruciforms, Z-DNA and other noncanonical DNA) in the context of gene expression.

Stipends/salaries (netto)

* For MSc students – 1000 PLN/month
* For PhD students – about 3000 PLN/month
* For postdoctoral researchers – about 7000 PLN/month

Criteria for the candidates selection

(1) Scientific achievements of the candidate (30 points)

(2) Evaluation of the candidate (15 points)

* for MSc candidates: average of the marks obtained during the studies
* for PhD candidates: average of the marks obtained during the MSc studies, the mark of the final exam, the mark of MSc thesis
* for postdoc candidate: average of the marks obtained during the PhD studies, the mark of the final exam, the mark of PhD thesis

(3) Experience in scientific activity (20 points)

(4) Scientific stipends and stays at foreign scientific institutions (20 points)

(5) Presentations at conferences and workshops (15 points)

The PhD candidates should have background in

* computational biology and/or
* applied mathematics and/or
* physics

The candidate for the postdoc position should have experience in systems biology, computer methods and have good background in applied mathematics.

Persons interested in applying for the positions should contact Dr. T. Lipniacki ( and present by October 16, 2009, covering letter, scientific CV (including list of publications, conferences, stays at scientific institutions, etc.) and all the necessary documents concerning criterion (2). Please e-mail covering letter and CV to and send the documents to

Dr. Tomasz Lipniacki,
Institute of Fundamental Technological Research
Pawinskiego 5B, 02-106 Warsaw, Poland

The final stage of the selection will be the qualification interview in English (held between October 19-23, 2009). PhD position holders will be enrolled for the doctoral studies in the Institute of the Fundamental Technological Research.

For inquieries, please contact Dr. Tomasz Lipniacki (

Team members:

* Tomasz Lipniacki – principal investigator (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)
* Bogdan Kazmierczak (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)
* Aleksandra Nowicka (Institute of Theoretical Physics, PAS, Warsaw, Poland).

External collaborators:

* Prof. Mark Alber (Notre Dame University, US),
* Prof. Allan R. Brasier (UTMB Galveston, TX, US),
* Assoc. Prof. James R. Faeder (University of Pittsburgh School of Medicine, US),
* Assoc. Prof. William S. Hlavacek (Los Alamos National Laboratories, US),
* Prof. Marek Kimmel (Rice University and MD Anderson Cancer Center, Houston, TX, US),
* Prof. Vitaly Volpert (Universite Claude Bernard – Lyon 1, France),
* Prof. Michael R.H. White (Liverpool University, UK).

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