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Graduate position for a PhD in systems biology in evolution and development open

1.Job/ project description:


The main objectives of the PhD project is to:


Develop computational models of organ development (morphogenesis and pattern formation) and their evolution in mammalian teeth, hair or Drosophila wing.


The research will take place in the Center of Excellence in Experimental and computational developmental biology of the Biotechnology Institute of the Helsinki University under the supervision of Isaac Salazar-Ciudad.

Embryonic development is one of the most amazing phenomena in life. During development a single cell transforms into a complex functional organism made of many cells, different cell types and a specific spatial distribution of those in space. How embryos organize themselves so that each cell ends up located in a specific position in the body is the central question of pattern formation and morphogenesis. This process involves the interaction of many genes in complex networks and the interaction of those with cells' and tissue's mechanical properties. In addition, this process is now widely acknowledged to be crucial to understand evolution since any change in the phenotype in evolution (e.g. morphology) would be first a change in the developmental process by which this phenotype is produced. Understanding development, thus, would allows us to understand which phenotypic variation can arise in populations due to genetic mutation (the so called genotype-phenotype map) and that, together with natural selection, would determine the direction of evolution. Understanding this link between development and evolution is a central aspect of the research in Salazar-Ciudad group.


Computational models are important tools to understand how gene networks interact with cell and tissue mechanical properties in development. There is currently a huge amount of data on how genes interact during development but data alone do not directly lead to understanding. The large number of genes involved, the complexity of the gene networks and cell and tissue mechanics in development require the building of precise quantitative hypotheses, the building of mathematical models to explore the consequences of these hypotheses and the comparison between models' predictions and well designed quantitative experiments. The center of experimental and computational developmental biology is a pioneering center combining models and experiments with this approach. In that sense the PhD will include collaborating with experimental developmental biologists, bioinformaticians, populational and quantitative geneticists, systems biologists, mathematicians, paleontologists and other evolutionary biologists.


The modeling will focus on integrating gene network regulation, cell-cell communication, cell mechanical interactions and developmental mechanisms in general and, optionally, artifical in silico evolution.


2. Requirements:


The applicant must be a biologists preferably with a strong background in either evolutionary biology, developmental 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 a strong background in biology will not be considered (e.g. no engineers or computer scientists).


Programming skills or a willingness to acquire them is required.


The most important requirement is a strong interest and motivation on science, embryonic development and evolution. A capacity for creative and critical thinking is also required.


3. Description of the position:


The fellowship will be for a period of up to 3-4 years (100% research work: no teaching involved).


The purpose of the fellowship is research training leading to the successful completion of a PhD degree.


Salary according to Finnish PhD student 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 sent to Isaac Salazar-Ciudad by email:

isaac.salazar @ helsinki.fi


Foreign applicants are advised to attach an explanation of their university's grading system. No official documents are required for the application first stage but these may be required latter on.


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

Mar 25;464(7288):583-6.


6. Interested candidates should check our group webpage:


http://www.biocenter.helsinki.fi/salazar/index.html


The selected candidates will start as soon as an agreement is reached.

Isaac Salazar-Ciudad: isaac.salazar@helsinki.fi

posted 2017.03.27