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PhD Fellowship in computational biology of the human microbiome

Novo Nordisk Foundation Center for Basic Metabolic Research  
Faculty of Health and Medical Sciences, University of Copenhagen  
 
PhD Fellowship in computational biology of the human microbiome  
 
Position: PhD Fellow  
 
Tenure: 3 years  
 
Background  
The Novo Nordisk Foundation Center for Basic Metabolic Research was established at the Faculty of Health and Medical Sciences, University of Copenhagen, to conduct fundamental research on metabolism. The Microbiome Systems Biology group of Associate Professor Arumugam at Section for Metabolic Genetics is recruiting PhD fellows to perform bioinformatic analysis of human microbiome datasets.  
 
You can read more about Novo Nordisk Foundation Center for Basic Metabolic Research at http://metabol.ku.dk
 
 
Project Description  
The human gut microbiota, the collection of trillions of microbes inhabiting the human body, has a strong influence on human health and diseases. Microbiome Systems Biology group has a vision to achieve therapeutic modulation of human microbiome to improve human health. Towards that long-term goal, we have two research directions: (1) Understanding molecular mechanisms of host-microbial crosstalk in metabolic diseases through a systems approach that integrates gut microbial multi-omics data together with environmental, host genetic, transcriptomic and metabolomic data, and (2) Developing novel approaches for therapeutic manipulation of gut microbiota using in silico and in vitro approaches.  
 
We are seeking up to two highly motivated PhD fellows to join us in these research directions. The successful applicants will process and model high-dimensional human gut microbiome data, using graph theory, machine learning and probabilistic methods. The group has access to a high-performance computing cluster with more than 500 CPUs to support this and other computational projects.  
 
Candidates with additional background in microbiology, molecular biology, or genetics would be highly regarded.  
 
Selection Criteria
Essential criteria  
  • Master’s degree in computer science, mathematics, informatics or bioinformatics  
  • Academic preparation as well as experience in implementing graph theory, machine learning or probabilistic methods
  • Ability to formulate real world problems as well-defined theoretical problems (please highlight this in cover letter)  
  • Experience in high performance computing environment using any flavour of UNIX  
  • Strong programming skills in C/C++, Java, Perl, Python, or R  
  • Experience with next generation sequencing data analysis  
  • Demonstrated capacity for effective team work  
  • Excellent written and oral communication skills  
 
Desirable criteria
  • Basic knowledge of microbiology and molecular biology  
  • Experience in distributed and cloud computing technologies  
  • Experience in collecting and processing large-scale metagenomics data  
  • Experience with applying statistical and mathematical methods to biological problems  
 
Relationships 
  • The holder of the position will report to the Leader of the Microbiome Systems Biology group (Associate Professor Manimozhiyan Arumugam)
  • The holder of the position must be able to interact with staff at all levels, both internally and externally, regarding relevant research topics.       
 
Employment Conditions  
The Novo Nordisk Foundation Center for Basic Metabolic Research is seeking up to two PhD fellows in the field of bioinformatics of the human microbiome. The position is offered for a period of three years and employment is governed by the Protocol on PhD Research Fellows signed by the Danish Ministry of Finance and AC (the Danish Confederation of Professional Associations).  
The successful candidate must apply for enrolment as a PhD student at the SUND Graduate School. Employment as a PhD fellow will be conditional on successful enrolment in the PhD program.  
The starting salary for candidates with an MSc degree will be a minimum of DKK 312,800 (April 2017 level) plus pension contribution, with the possibility of salary negotiation.  
 
Starting date is 1 October 2017 or as soon as possible hereafter.  
 
Questions  
For further information, please contact Associate Professor Manimozhiyan Arumugam arumugam@sund.ku.dk or SUND HR at sund-hr-cbmr@sund.ku.dk  
 
How to apply?  
The application must be submitted in English by clicking “apply online” below and must include the following:  
  • Letter of motivation (max 1 page)  
  • CV with contact details of two references, without list of publications (max 2 pages)  Complete list of publications (only published or accepted publications in peer reviewed journals).  
The deadline for applications is 15 September 2017 at 23:59 CET  
 
Any applications received after this time will not be considered.  
 
We only accept online applications.  
 
Recruitment Process  
In addition to the above material, the Assessment Committee may include further material in their assessment of the applicants. In such circumstances, it is the responsibility of the applicant, on request, to send the material to the Committee. Receipt of the applications will be acknowledged. The applicant will be assessed according to the Ministry of Science Technology and Innovation Executive Order no. 284 of April 25th 2008.  
 
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.  
 
Highly motivated and ambitious candidates are encouraged to apply. Solid experience and an excellent track record gained in leading laboratories in the research field will be considered a distinct advantage. In all cases, ability to perform the job will be the primary consideration, and thus we encourage all - regardless of their personal background and status - to apply.  
 
For more information on working and living in Denmark: http://ism.ku.dk/ and http://www.workingconditions.ku.dk  
 
 

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Kontakt

Manimozhiyan Arumugam

Info

Ansøgningsfrist: 15-09-2017
Ansættelsesdato: 01-10-2017
Arbejdstid: Fuldtid
Afdeling/Sted: Microbiome Systems Biology

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