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stillingsbetegnelse: Postdoc in Bioinformatics in the Gorodkin lab

jobbeskrivelse:
A two-year Postdoc position is available in the Gorodkin lab (http://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (http://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. The Postdoc position concerns bioinformatics analyses of transcriptomic data from neurodegenerative diseases. The position is to commence as soon as possible.

You will be a team player working with great excitement, and a key person in the project essential for obtaining successful results. The Postdoc position is part of the Indo-Danish NeuroStem project, which aims to discover RNA mediated regulation in neurodegeneration through stem cell models. The Postdoc will be interacting closely with the Group for Stem Cells and Embryology (https://ivh.ku.dk/english/research/anatomy-biochemistry-physiology/stemcells/). See http://neurostem.dk for details. The Neurostem project is supported by Innovation Fund Denmark. The project holds strong synergy to the BrainStem center: http://brainstem.dk.

Background
The NeuroStem project aims at identifying the underlying neuronal pathology of causative genes and regulatory elements to obtain novel functional insight in Alzheimer’s and Parkinson’s diseases that can enable improved treatment. Transcripts will be extracted from neurons derived from iPSC, previously generated from patient skin fibroblasts. In cases where the patients carry specific disease-causing mutations, the iPSCs are gene corrected using CRISPR/Cas9 (isogenic control) allowing for strict comparisons of diseased and isogenic neuronal cells. In addition neurons from engineered healthy control iPSC, into which the genetic mutation is introduced, will be part of the analyses to circumvent the low numbers of samples due to rare mutations. Finally neurons from sporadic iPSC will be investigated to identify novel disease causative genes and pathways as well as validation of common pathways affected in both sporadic and familial forms of Alzheimer’s disease.

Job abstractJV_description
The project takes outset in differential expression analysis of transcripts between disease and gene edited and healthy control neurons. This involves detection and analysis of coding and noncoding transcripts as well as structured RNA and other regulatory elements. From the differential expression analysis, relevant pathways will further be included to obtain candidates for downstream functional analysis in terms of knock-out and knock-in experiments. In addition to transcriptome analysis and gene network methods in silico methods concerning structured RNA and RNA-RNA interactions will be can be incorporated in the integrated pipelines and relevant method development be included in the project.


Required qualifications and selection criteria
The applicant should hold the professional as well as personal skills and qualifications as stated below:

• A completed PhD degree in bioinformatics, computer science or in a similar area
• General background knowledge of biological areas of genome structure and transcriptomes
• Strong experience with script languages such as Perl or Python (or similar)
• Strong experience with the Linux/Unix environment, command lines and shell scripting
• Solid experience with transcriptome analysis
• Good interpersonal skills
• Excellent in English both in writing and speech

Candidates fulfilling one or more of the following qualifications will be prioritised:

• Strong experiences with transcriptome data analysis
• Algorithmic insight broad and for RNA (2D) structure
• Experience with transcriptomic data from neurodegenerative diseases
• Experience in at least one of the following programming languages: C, C++ or Java

It is recommended that the applicant address the qualification requirements one by one in the cover letter.

Terms of employment
Salary and other terms and conditions of appointment are set in accordance with the Agreement between the Ministry of Finance and AC (Danish Confederation of Professional Associations) or other relevant professional organisations. The position is covered by the “Memorandum on Job Structure for Academic Staff at the Universities” of June 28, 2013.

The gross basic salary range for Postdoctoral Fellows is DKK 33,766 to DKK 35,552 per month (level 6 to 8). To the basic salary a supplement could be negotiated, dependent on the candidate’s experience and qualifications. An additional 17.1 % monthly contribution to pension will be paid by the employer. Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark for the last 10 years.

The position is limited to a two-year period.

Place of employment
RTH is located on Frederiksberg Campus; however, as part of the NeuroStem project research visits to project partners will be a part of the Postdoc employment. Our research environment is highly international and stimulating. We frequently organise seminars, workshops, PhD summer schools with international speakers and have retreats with our international collaborators.

Questions
For further information about the scientific content of the position please contact Professor Jan Gorodkin, email gorodkin (at) sund.ku.dk, phone +45 23375667.

Application procedure
Apply by clicking "Apply online" below. Please note that only online applications will be accepted.

Applications - in English - must include:

• Cover letter detailing your motivation and background for applying for the specific Postdoc project
• CV
• Diploma and detailed transcripts of records
• Other information for consideration, e.g. list of publications, peer reviewed and other
• Personal Recommendations (if any)
• A maximum of 3 relevant scientific works which the applicant wishes to be included in the assessment

The deadline for applications is 27 February 2019. Any applications received after this time or incomplete will not be considered.

Receipts of the applications will be acknowledged, and the applicant will be kept continuously informed of the progress of the application.

The further process
Shortlist: After the expiry of the deadline for applications, the authorised 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 http://employment.ku.dk

Assessment: The selected applications will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities and the University of Copenhagen’s guidelines 2013. The Assessment Committee makes a non-prioritised assessment of the academic qualifications and experience with respect to the mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Please note that the applicant will be contacted if the assessment committee requires further documentation.

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



numberOfPosts: 1

jobCategoriesCodes_0: http://data.europa.eu/esco/isco/C2310

abstractJV_contact_0: Please apply using one of the specified channels

positionTypeCode: directhire

contractTypeCodes_0: fulltime

Arbejdsgiver Navn: KU - SUND - IVS

source: DK-STAR