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PhD stipend in computational biology of the human microbiome

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The Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR),

Faculty of Health Sciences, University of Copenhagen

PhD stipend in computational biology of the human microbiome


The Novo Nordisk Foundation Center for Basic Metabolic Research is seeking a candidate for a 3-year PhD-scholarship to develop novel computational methods to better model microbial co-occurrence networks. The PhD position is in the group for bioinformatics led by Associate Professor Manimozhiyan Arumugam. The starting date is 15th of December 2015 or as soon as possible thereafter.

The Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) has been established at the Faculty of Health Sciences, University of Copenhagen to conduct basic research on metabolism ( The Center, which consists of six scientific sections and a number of international research satellites, was established through a DKK 885 million unrestricted grant from the Novo Nordisk Foundation. We are a center of excellence where talented researchers and experienced laboratory technicians is bringing scientific discoveries from the laboratory to the society in an effort to tackle some of today’s biggest challenges – diabetes and obesity. We are proud of the outstanding discoveries made by the Center, and we are committed to the translation of this knowledge into novel approaches to patient care. The available PhD-Scholarship is in the Section of Metabolic Genetics, headed by Scientific Director Professor Oluf Pedersen. You can read more about the Novo Nordisk Foundation Center for Basic Metabolic Research on:

The human microbiome, the collection of trillions of microbes inhabiting the human body, has a strong influence on human health and diseases. Understanding the interactions (both positive and negative) between these microbes is essential to understand their role in human health. Traditionally, interactions in such ecosystems are studied using microbial co-occurrence networks, which are inferred using simple pairwise correlations between relative abundances of microbial groups. Although these methods have provided useful insights into the ecosystems of the human microbiome, they can only identify highly frequent pairwise relationships. There is a need for developing novel methods to better model microbial co-occurrence networks, which this PhD project will address. Microbial co-occurrence patterns identified by this PhD project will improve our understanding of the human microbiome, and better interpret the role of gut microbiome in diseases. The Section has a high-performance computing cluster with more than 500 CPUs to support this and other computational projects.

Job Description
The position is a 3 year PhD scholarship in computational biology under the supervision of Associate Professor Manimozhiyan Arumugam, where the candidate will be responsible for developing novel computational methods based on sound probabilistic and statistical theories of co-occurrence patterns. He/she must be able to understand advanced machine learning, probabilistic and statistical theories as well as implement them. He/she is also expected interact and collaborate with other medical researchers, geneticists, and IT specialists in the Section as well as the Center, to enhance and ensure proper interpretation of experimental results.

Qualification requirements
In connection with the appointment to the post special importance will be attached to the applicant having the professional and personal qualifications stated below:

  • Master’s degree in computer science, mathematical modelling or informatics
  • Academic preparation as well as experience in implementing advanced machine learning and probabilistic methods
  • Ability to formulate real world problems as well-defined theoretical problems
  • Experience in high performance computing environment using any flavour of UNIX
  • Strong programming skills in C/C++, Java, Perl, or Python
  • Strong communication skills in English, both spoken and written, are essential

The following qualifications are preferred, but not required.

  • Candidates who possess these qualifications are encouraged to highlight them in the application.
  • Basic knowledge of microbiology and molecular biology
  • Academic preparation and/or experience in bioinformatics
  • Experience in distributed and cloud computing technologies
  • Experience in handling large scale (meta)genomic and/or genetic data
  • Familiarity with bioinformatics programming environments such as BioPerl/BioPython/BioRuby
  • Understanding of human disease biology and/or microbiology
  • An excellent research record exemplified by strong publications

As an equal opportunities employer, the University welcomes applications from suitable qualified people, regardless of age, race, religion, gender or ethnic background.

Terms of Employment
The position is offered for a period of three years and employment is governed by the Protocol on Ph.D. Research Fellows signed by the Danish Ministry of Finance and AC (the Danish Confederation of Professional Associations). The starting salary for candidates with a M.Sc. degree will be a minimum of DKK 305,291 per year (April 2014 level) plus pension contributions and with the possibility to negotiate a qualification supplement.

For more information on working and living in Denmark: and

For further information, please contact Associate Professor Manimozhiyan Arumugam at or HR officer Ditte Maria Bohn at

Please apply by clicking “Apply Online” at the bottom of the page. Please note that only online applications will be accepted.

Applications - in English - must include:

  • A letter of motivation
  • Curriculum vitae
  • At least two letters of references, maximum four
  • Documentation of experience implementing advanced algorithms

The deadline for applications is 15th of November 2015, 23:59 CET. Any applications received after this time will not be considered. Applicants failing to submit the online application form will not be considered either.

Application procedure
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.

You can read about the recruitment process at