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**** EDIT The position has now been filled and I'm no longer taking applications ****
Having got my Estonian Science Foundation grant funded recently, I have an open PhD position available! See below.
Dr Atkinson’s research addresses protein functional evolution, using bioinformatic approaches and primarily focusing on the ancient families of proteins involved in translation of mRNA to protein. Members of these families are often essential for life and predate the last common ancestor of all life on earth. Thus by studying these proteins we can gain understanding of the fundamental processes of life, and how these processes have evolved over billions of years.
The PhD project will take advantage of the thousands of whole genome sequences now available for the study of evolution of protein families from the origin of life to the present day. Work will involve sensitive sequence searching to identify the presence and absence of particular proteins across genomes, phylogenetic analyses to reconstruct their emergence and evolution, and sequence analyses to link domain- and site-specific patterns of amino acid substitution with molecular function. Specifically, the proposed PhD project will target the ABC superfamily of ATP-binding enzymes found in all domains of life. This superfamily comprises enigmatic proteins of diverse, and often unknown functions. Several ABC enzymes have recently been found to have important roles in regulation of translation such as ribosome recycling protein Rli1/ABCE1, yeast-specific elongation factor eEF3 and starvation response enzymes Gcn1 and Gcn20.
From the results of the PhD, it is expected that enzymes with novel roles in protein synthesis will come to light as interesting targets for subsequent experimental study. Dr Atkinson collaborates with the lab Dr Vasili Hauryliuk, also in Prof Tenson’s group, for biochemical and genetic validation of in silico results. If the candidate so wishes, there is an opportunity to gain practical lab experience in Dr Hauryliuk’s lab.
The candidate should have:
Estonia has a rich culture and beautiful natural environment, with unspoiled forests, meadows and coastlines. Enjoying warm summers and cold winters, the historical city of Tartu is the intellectual capital of Estonia, and its university is the leading research and development institution in the country. The Institute of Technology is a lively, modern centre for biological and technological research.
The PhD will be funded by a monthly stipend, with additional monies available for regular attendance at international conferences and workshops, and for visiting labs abroad. Information on funding is available by request.
Applications should contain:
The candidate is expected to start at the latest September 2012. Please send applications and informal enquiries to gemma.atkinson@ut.ee
Gemma Atkinson
University of Tartu,
Institute of Technology
Nooruse 1, 50411 Tartu, Estonia
More information about the research of Dr Atkinson can be found here:
http://lepo.it.da.ut.ee/~atkinson/gem_mac/gemma_c_atkinson.html
Having got my Estonian Science Foundation grant funded recently, I have an open PhD position available! See below.
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We are seeking a highly motivated PhD candidate to be supervised by Dr Gemma Atkinson within the group of Prof Tanel Tenson in the Institute of Technology, University of Tartu, Estonia.Dr Atkinson’s research addresses protein functional evolution, using bioinformatic approaches and primarily focusing on the ancient families of proteins involved in translation of mRNA to protein. Members of these families are often essential for life and predate the last common ancestor of all life on earth. Thus by studying these proteins we can gain understanding of the fundamental processes of life, and how these processes have evolved over billions of years.
The PhD project will take advantage of the thousands of whole genome sequences now available for the study of evolution of protein families from the origin of life to the present day. Work will involve sensitive sequence searching to identify the presence and absence of particular proteins across genomes, phylogenetic analyses to reconstruct their emergence and evolution, and sequence analyses to link domain- and site-specific patterns of amino acid substitution with molecular function. Specifically, the proposed PhD project will target the ABC superfamily of ATP-binding enzymes found in all domains of life. This superfamily comprises enigmatic proteins of diverse, and often unknown functions. Several ABC enzymes have recently been found to have important roles in regulation of translation such as ribosome recycling protein Rli1/ABCE1, yeast-specific elongation factor eEF3 and starvation response enzymes Gcn1 and Gcn20.
From the results of the PhD, it is expected that enzymes with novel roles in protein synthesis will come to light as interesting targets for subsequent experimental study. Dr Atkinson collaborates with the lab Dr Vasili Hauryliuk, also in Prof Tenson’s group, for biochemical and genetic validation of in silico results. If the candidate so wishes, there is an opportunity to gain practical lab experience in Dr Hauryliuk’s lab.
The candidate should have:
- a Masters degree in a biological or computational discipline
- a strong interest in, and enthusiasm for molecular evolution
- familiarity with basic sequence and phylogenetic analyses
- experience in using a programming language such as Python, Perl, Java etc
- fluency in spoken and written English
Estonia has a rich culture and beautiful natural environment, with unspoiled forests, meadows and coastlines. Enjoying warm summers and cold winters, the historical city of Tartu is the intellectual capital of Estonia, and its university is the leading research and development institution in the country. The Institute of Technology is a lively, modern centre for biological and technological research.
The PhD will be funded by a monthly stipend, with additional monies available for regular attendance at international conferences and workshops, and for visiting labs abroad. Information on funding is available by request.
Applications should contain:
- a full CV with detailed description of previous relevant experience
- a statement of academic interests
- an electronic version of the Masters thesis
- the names and contact details of at least 2 referees
The candidate is expected to start at the latest September 2012. Please send applications and informal enquiries to gemma.atkinson@ut.ee
Gemma Atkinson
University of Tartu,
Institute of Technology
Nooruse 1, 50411 Tartu, Estonia
More information about the research of Dr Atkinson can be found here:
http://lepo.it.da.ut.ee/~atkinson/gem_mac/gemma_c_atkinson.html