[Socbin] PhD position in evolutionary systems biology (Ref. No. DBB 7-12), apply by February 29

[Lukasz Huminiecki]

GOOD PROJECT!
GOOD ATMOSPHERE!
GOOD SUPERVISION!
GOOD PLACE TO LIVE!
GOOD PLACE TO WORK!
GOOD CAREER PROSPECTS!




Fully-funded PhD position in EVOLUTIONARY SYSTEMS BIOLOGY!!!
Please, quote "Ref. No. DBB 7-12" in the email subject line when applying
The application should be labelled with "Ref. No. DBB 7-12", and should be received no later than February 29, 2012 by the department.
email: haidi at dbb.su.se<mailto:haidi at dbb.su.se> (please combine all your documents into a single pdf file)
cc: Lukasz.Huminiecki at ki.se<mailto:Lukasz.Huminiecki at ki.se>




!!! quote "Ref. No. DBB 7-12" in the email subject line !!!




COMPUTATIONAL ANALYSIS OF GLOBAL PATTERNS OF GENE AND GENOME DUPLICATIONS IN VERTEBRATES
We are looking for an exceptionally talented and motivated PhD student in evolutionary systems biology to work and study under joint supervision of Dr. Lukasz Huminiecki and Prof. Arne Elofsson at the Department of Biochemistry and Biophysics, Stockholm University.

You will live in STOCKHOLM, a beautiful and international city with high standard of life and social services, the Home of the Nobel Prize, offering a vibrant scientific environment and rich opportunities for collaborations, postdoctoral fellowships, or employment in the technology sector. You will work within the newly created bioinformatics and computational biology cluster at the Science for Life Lab, a joint venture between Sweden's three top research universities: Karolinska Institutet, KTH Royal Institute of Technology, and Stockholm's University.

The project focuses on computational analysis of global patterns of gene and genome duplications in vertebrates, and their consequences for signal transduction, and microRNA (miRNA) network evolution, as well as expression pattern evolution. We will use pathway databases and freely available genomic, expression, and miRNA datasets, to infer architectural changes of the animal signal transduction and miRNA networks after small scale duplications (SSDs) and whole genome duplications (WGDs). Quantification of the patterns of nonfunctionalization, subfunctionalization, and neofunctionalization will enhance our understanding of the evolutionary forces driving duplicate retention. The identification of the shared animal developmental toolkit is one of the most significant and fundamental discoveries in biology, and we designate the toolkit to be a focus area investigated besides the global perspective.

The methodological toolkit necessary for the project will consist of phylogenetics and other molecular evolution methods, R statistical package, Bioconductor, MySQL, and Perl. Unix or Linux experience is highly desired. Candidates will have undergraduate degree background in biology, biotechnology, biophysics, molecular biology, mathematical biology, bioinformatics, mathematics, or computer science. Good command of English is required. This is not a pipeline bioinformatics project: the chosen candidate will have a natural aptitude to flexibly and creatively tackle complex and abstract problems, using a dynamic mixture of procedural programming, SQL, statistics, bioinformatics, and evolutionary theory.

REFERENCES:
2R and remodeling of vertebrate signal transduction engine. Huminiecki L, Heldin CH. BMC Biol. 2010 Dec 13;8:146.

Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. Huminiecki L, Goldovsky L, Freilich S, Moustakas A, Ouzounis C, Heldin CH. BMC Evol Biol. 2009 Feb 3;9:28.

Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Huminiecki L, Wolfe KH. Genome Res. 2004 Oct;14(10A):1870-9.




APPLICATION
The application should contain a letter of intent (one to two pages that explain why you are
interested in working on this project, why you are interested in studying for a PhD, what you
hope to accomplish during your PhD studies, and what skills you can bring to this project),
curriculum vitae, copies of degree certificates and transcripts of academic records, a list of
two persons who may act as referees (with telephone numbers and e-mail addresses), and one
copy of your undergraduate thesis and articles, if any.




About the Department of Biochemistry and Biophysics, Stockholm University
More than 20 research groups are active at the Department of Biochemistry and Biophysics.
The research projects span across a broad range of topics covering various aspects of
structure and function of biological systems. A major fraction of these topics are centered
on biological membranes, where many groups working within this area are part of the
Center for Biomembrane Research, which is hosted by the department. Also the Stockholm
Bioinformatics Centre and the Science for Life Laboratory are closely linked to the
department. The combination of the highly interdisciplinary expertise and research projects
at the department is unique in Sweden and also at an international level. This expertise
ranges across cell biology, biochemistry, biophysics and theory. Some specific topics that
are addressed include membrane protein biogenesis, membrane protein topology &
assembly, mitochondria & chloroplasts, protein structure & function, protein folding &
trafficking, lipid biosynthesis & function, energy conversion, biochemical toxicology, DNARNA-
PNA interactions, biological nitrogen fixation, viral membrane glycoproteins, protein
structure & disease, bioinformatics, computational structural biology and development of
theoretical tools. The experimental studies are performed on a wide range of organisms and
are also combined with the use of a wide range of advanced biochemical and biophysical
techniques. For more information about the department, see www.dbb.su.se<http://www.dbb.su.se/>.




Further information on the web:
Stockholm University: www.su.se/english<http://www.su.se/english>
Faculty of Science: www.science.su.se<http://www.science.su.se/>
The Department of Biochemistry and Biophysics: www.dbb.su.se<http://www.dbb.su.se/>
The handbook for postgraduate students: www.doktorandhandboken.nu/english<http://www.doktorandhandboken.nu/english>




Terms of employment
Economic support is guaranteed during the agreed time in the individual study syllabus
(study plan) for the graduate studies, totally for a maximum of 4 years.




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