Postdoc in the systems biology: Modelling pattern formation and morphogenesis

Postdoc Evolution and development and in systems biology: Modelling pattern formation and morphogenesis (Autonomous University of Barcelona, Helsinki University)

1.Job/ project description:

The main objectives of the PhD project is to:

a) Develop mathematical models of organ development (teeth, hair and wings).
The mathematical models include intracellular gene networks, cell signalling and extra-cellular signal diffusion, bio-mechanical interactions between large collectives of cells (all in 3D) (see above publications for orientative examples)

b) Develop models about the evolution of gene networks and embryonic development in general.

Since we want to understand the range of possible phenotypic variations in different animals' development we have decided to use modelling approaches. Our models take as inputs knwon or estimated gene networks and the initial distribution of cells in space (in a given stage in development) and provide as a result the final organ morphology and patterns of gene expression in a given organ (in a given, latter, stage of development). Each model is simply a mathematical implementation of a hypothesis about how an organ develops. We construct these hypotheses, based on experimental work from other groups, and implement them in a computational model. The advantage of computational models in respect to merely verbal arguments is that the models provide precise quantitative predictions that are more easily to unambigously compare with experimental results (from new experiments aimed at testing the hypothesis). Merely verbal arguments are more difficult to be proven wrong or right and get even difficult to express when the process under study involves a large number of cells in complex movement and communication between them (as it is often the case in development). These easily lead to largely unintuitive dynamics that are hard to analyze without quantitative models.

In addition, computational models allow to explore not only the wild-type but also, by variaton in the underlying gene network, the range of possible morphological variants (and how they change through development). The capacity to play with the parameters of the model allows us to actually understand its dynamics.

The biotechnology institute includes a range of
experimental biologitst working on several systems. The supervisor of the theoretical aspects will be Dr. Salazar-Ciudad but the PhD
would include close collaboration with Jukka Jernvall group and would include collaboration with developmental biologists,
bioinformaticians, paleontologists and other evolutionary and systems biologists. The work includes working in the Helsinki University and in the Autonomous University of Barcelona.
The modeling can focus on gene network regulation, cell-cell communication, cell mechanical interactions and developmental
mechanisms in general and, optionally, artifical in silico evolution.

2. Requirements:

The applicant should hold a PhD in either evolutionary biology, developmental biology, systems biology or theoretical biology.
Some knowledge of ecology, zoology, cell and molecular biology are also desirable.

Bioinformaticians, systems biologists or computer biologists that do not have a degree in biology or similar similar would not be considered
(this excludes Computer scientists, physicists and engineers).

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science, gene networks and evolution. A capacity for creative and
critical thinking is also desirable.

3. Description of the position:

The fellowship will be for a period of up to 4 years (100% research work: no teaching involved).

Salary according to Finnish postdoc salaries.

4. The application must include:

-Application letter including a statement of interests
-CV (summarizing degrees obtained, subjects included in degree and
grades, average grade)

-Application should be send to Isaac Salazar-Ciudad by email:

isaac.salazar en helsinki.fi

Foreign applicants are advised to attach an explanation of their
University's grading system. Please remember that all documents should
be in English (no official translation is required)

5. Examples of recent publications by Isaac Salazar-Ciudad group.

-Salazar-Ciudad I1, Marín-Riera M. Adaptive dynamics under development-based genotype-phenotype maps.
Nature. 2013 May 16;497(7449):361-4.

-Salazar-Ciudad I, Jernvall J. A computational model of teeth and the developmental origins of morphological variation. Nature 2010