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PhD scholarship at the Bioinformatics Centre

The Sandelin group is looking to recruit a talented PhD student to our highly dynamic research group working in the interface of computational biology and genomics. The position will be funded by a grant from the Lundbeck Foundation.

Our research
The group is both computational and experimental, and we work with both fundamental gene regulation and medical transcriptomics. In particular, we specialize in tag-based sequencing analysis to find alternative promoters and enhancers, and gene regulation bioinformatics. Highlights include:

  • The definition of promoter and enhancer atlases over human tissues and cells (Forrest, Nature 2014; Andersson, Nature 2014; Arner, Science 2015)
  • The discovery of degradation mechanisms of enhancer RNAs (Andersson, Nature Comm 2014)
  • Inflammation-specific enhancers and promoters (Boyd et al, DNA Res 2013, Bornholdt et al, ACS Nano 2017)
  • Molecular characterization of bidirectional transcription initiation (Chen, Nature Genetics 2016; Andersson, Nature Comm 2014; Ntini, Nature Struct Mol Biol 2013)
  • The widely used JASPAR database (Mathilier, Nucleic Acids Res 2016)

Specific project
Mammalian long non-coding (lnc) RNAs are outnumbering their mRNA counterparts. Yet, the functional relevance of lncRNAs at large remains only poorly understood, not the least because of their frequently low abundance. Together with the Heick-Jensen group at Aarhus University, we have previously devised an approach to profile the susceptibility of lncRNA to rapid decay and in this way identify new functional candidates from the “sea” of pervasive transcripts that our genomes constantly produce. We will now engage disease-relevant model systems coupled to high throughput biochemical and computational methods to further the identification and functional validation of new lncRNA. Collectively, we will reveal new physiologically meaningful RNAs and gain a mechanistic understanding of their regulation and function. In doing so, we will also uncover new regulatory concepts created by the pervasive transcription of mammalian genomes. This will be done as a tight collaboration between experimental and computational biologists. The successful candidate will also be part of the international FANTOM6 project (http://fantom.gsc.riken.jp/6/), where lncRNAs are systematically knocked down followed by phenotypic screening.

Place of employment
The employment is at the Department of Biology and BRIC (Biotech Research and Innovation Centre), University of Copenhagen. Both are located in the Biocenter, close to the centre of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. The candidate will collaborate intensively with the Heick-Jensen group at Aarhus University, which may involve shorter stays in that laboratory.

Please read more about the Sandelin and Jensen research groups at http://people.binf.ku.dk/albin and http://mrnp.au.dk/

Qualifications
We are seeking a highly motivated individual with an MSc of Science or equivalent in bioinformatics or a mathematical discipline with a strong biological interest.

Applicants must have:

  • Strong documented experience in analyzing high-throughput sequencing data, such as RNA-seq, ATAC-seq and ChIP-seq data. DNA methylation data experience is a plus.
  • Documented experience in statistic analyses of such data, including expression analysis, as well as quality control and visualization.
  • Strong programming skills in Python and R, or equivalents, in a linux environment.
  • Excellent English skills

The following is considered strong advantages:

  • Experience in and common molecular biology techniques
  • International experience
  • Publications in peer-reviewed journals
  • Experience in bioinformatics teaching, including programming

Candidates expecting to finish their master thesis before this date are also eligible to apply.

Application
The application must include the following documents/attachments – all in PDF format:

  1. Motivated letter of application (max. one page)
  2. CV incl. education, work/research experience, language skills and other skills relevant for the position
  3. A certified/signed copy of MSc certificate
  4. List of publications if applicable
  5. List of references

Shortlisting procedures
After the expiry of the deadline for application, the authorized recruitment manager selects applicants for assessment on the advice of the interview 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 himself/herself.

The final selection of successful candidates will be made by the Head of Department, based on the recommendations of the assessment committee. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of the Faculty of Science, University of Copenhagen. For more information see: http://www.science.ku.dk/english/research/phd

Terms of employment
Terms of appointment and payment are in accordance with the agreement between the Danish Ministry of Finance and the Danish Federation of Professional Associations (AC). The starting annual salary for candidates with an MSc degree will be a minimum of DKK 309,109 (April 2016 level) plus pension contribution, with the possibility of salary negotiation.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is May 31, 2017

Applications received after the deadline, or with insufficient documentation or otherwise not complying with the above requirements, may not be considered.

It is expected that the successful candidate will be enrolled at the PhD School of the Faculty of Science during late summer or autumn 2017.

Further information
Contact person: albin@binf.ku.dk

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Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

Contact

Albin Sandelin

Info

Application deadline: 31-05-2017
Employment type: Limited period
Employment start: 01-09-2017
Department/Location: Department of Biology

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