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At the Faculty of Science, research and education is carried out in the fields of mathematics, physics, chemistry, biology, computer science, earth sciences and environmental sciences. The Faculty is home to 9 Departments, gathered in the north of the University campus. Around 1700 undergraduate students, 440 PhD students and 800 employees are active within the Faculty.
Post doctoral position in Bioinformatics applied on targeted metagenomics
Type of employment: Limit of tenure, two years
Extent: 100 %
Location: Department of Biology (Ecology), Lund
First day of employment: as soon as possible
Official Records Number: NPA 2011/371
Extent: 100 %
Location: Department of Biology (Ecology), Lund
First day of employment: as soon as possible
Official Records Number: NPA 2011/371
Subject area
Bioinformatics applied on targeted metagenomicsSpecific subject description
Bioinformatics applied on targeted metagenomicsJob assignments
Our aim with the research project in which this position will be placed is to identify the functional diversity of soil microorganisms on gene level involved in carbon cycling in agricultural soils.
Previously it has not been feasible to study functions by soil microorganisms involved in the carbon cycle at a high resolution due to the complexity of the microbial community in soil (i.e. metagenome). Now we will adopt a novel technique called sequence capture (Albert et al 2007) coupled with next generation sequencing (NGS) to efficiently enrich for genes involved in the degradation of complex carbon sources without the need for culturing of the organisms. The NGS approaches are up to 200 times faster and 100 times cheaper than the conventional technology of gene sequencing. The vast amounts of sequences generated will provide us with new possibilities to examine the structure and functions of genomes of organisms in natural soil communities.
Specific objectives
Develop the sequence capture method as a tool box for working with links between functional diversity of soil microorganisms and carbon cycling
Previously it has not been feasible to study functions by soil microorganisms involved in the carbon cycle at a high resolution due to the complexity of the microbial community in soil (i.e. metagenome). Now we will adopt a novel technique called sequence capture (Albert et al 2007) coupled with next generation sequencing (NGS) to efficiently enrich for genes involved in the degradation of complex carbon sources without the need for culturing of the organisms. The NGS approaches are up to 200 times faster and 100 times cheaper than the conventional technology of gene sequencing. The vast amounts of sequences generated will provide us with new possibilities to examine the structure and functions of genomes of organisms in natural soil communities.
Specific objectives
Develop the sequence capture method as a tool box for working with links between functional diversity of soil microorganisms and carbon cycling
Determine the functional diversity on a gene level that is directly affecting carbon cycling and turnover in agricultural soils with the sequence capture and next generation sequencing technology (NGS).
Analyse metagenomic data from agricultural soils in order to identify the main microbial actors of the carbon cycling.
The candidate will be studying the functional and genetic diversity of genes involved in the carbon cycling in agricultural soils. The main duty for the candidate will be to develop bioinformatics tools and databases for the targeted metagenomics project. The candidate will be responsible for generating probes to target genes involved in carbon sequestration and nitrogen/phosphorus metabolism. These probes will subsequently be used for large scale sequencing of soil samples and the metagenomics data will require substantial bioinformatics analyses.
The post doc will work within the context of two large scale research projects SoilService (http://www.kem.ekol.lu.se/soilservice/index.html) and BECC (http://www.cec.lu.se/o.o.i.s/24960) and be part of a research group that will focus on the metagenomics of soil functional diversity. The Department of Ecology has a next generation sequencing facility (454 pyrosequencing) and bioinformatics resources, which will be essential for the project.
Eligibility/Entry Requirements
To be eligible for an appointment a person must have successfully completed a PhD degree or have corresponding scientific competence in a relevant subject area. A person who holds a foreign degree that is deemed equivalent to a doctorate shall be qualified for appointment. Priority should be given to candidates who have completed their degree no more than three years before the last date for applications. Candidates who have completed their degree earlier than this should receive equal priority if special grounds exist, for example documented leave of absence because of illness or parental leave.Basis of Assessment
The applicant should have a PhD in bioinformatics preferably with competences in microbial ecology. Further skills in metagenomics of natural communities are skills that show experience in use of large data sets are qualifying for the position. The candidate should have experience in sequence analysis preferably from next generation sequencing technologies. Working experience in Perl programming is required while other programming language is a plus. Experience of relational databases (e.g. MySQL) and dissemination of data through web resources is of added value. The successful candidate will work in an interactive group of scientists with expertise in microbiology, ecology and bioinformatics. Good communication skills are essential and fluency both in spoken and written English is required.For further information please contact:
Katarina Hedlund, Professor
+46 (0)46 222 3798
katarina.hedlund@biol.lu.se
Dag Ahrén, postdoctoral research fellow
+46 (0)46-222 39 95
dag.ahren@biol.lu.se
Tina Nilsson, personnel administrator - will only answer questions about the application process
+46 (0)46 222 02 85
tina.nilsson@biol.lu.se
+46 (0)46 222 3798
katarina.hedlund@biol.lu.se
Dag Ahrén, postdoctoral research fellow
+46 (0)46-222 39 95
dag.ahren@biol.lu.se
Tina Nilsson, personnel administrator - will only answer questions about the application process
+46 (0)46 222 02 85
tina.nilsson@biol.lu.se
Labour union
SACO: Anneli Carlsson046 -222 42 52
Anneli.Carlsson@busilaw.lu.se
OFR/S: Lena Thiman
046-222 77 96
Lena.Thiman@med.lu.se
Last Day of Applying 2011-10-13
Appointment Procedure
Complete information about the application process can be found here:http://admin.lu.se/o.o.i.s?id=22598&Dnr=377119&Type=E
Applications for promotion may be made at any time during the year. Applications for advertised positions must be received by the date specified in the announcement.
