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PhD fellow in Prenatal programming of disease

PhD fellow in Prenatal programming of disease
Department of Biology
Faculty of Science
University of Copenhagen


Department of Biology, Faculty of Science at University of Copenhagen is offering a PhD scholarship in of prenatal programming of disease, specifically focused on how stress transfers between mother and fetus through pregnancy, commencing 1.09.2018 or as soon as possible thereafter.


Description of the scientific environment
The project is a collaboration between the Sandelin group at Bioinformatics Centre, Department of Biology and BRIC, and the Sørig Hougaard group at National Research Centre for the Working Environment (NFA).

The Sandelin group is a high-profile joint computational/experimental group focusing on gene regulation and transcriptomics. The Bioinformatics Centre employs around 50 researchers, and has many international connections to high-profile groups. The groups are housed in the Biocenter in central Copenhagen, Denmark.
The Sørig Hougaard group at NFA group is focused on toxicology, working environment and in particular effects of particles and stress on reproduction and development. NFA is located within biking distance of the Biocenter.

Project description
This project will characterize how acute stress induced in pregnant mothers transfers from mother to fetus and the molecular signalling molecules and regulators that underlie this process. This will be done through a time series analysis in pregnant mice using on RNA and protein levels, coupled to state of the art computational analysis, and parallel investigations of signalling molecules in blood. The project will employ one experimental PhD student and one computational postdoc, working as a team together with dedicated technicians. The successful candidate will work both at the Biocenter, University of Copenhagen and at NFA, and is also expected to make at least one longer stay at proteomics collaborators abroad.

Previous papers by Sandelin and Sørig Hougard groups:

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Boyd et al., Nature Communications 2018 2018; 9: 1661.
Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. Bornholdt et al, ACS Nano. 2017;11(4):3597-3613
Chronic maternal inflammation or high fat feeding programs offspring obesity in a sex-dependent manner. Int J Obesity 2017 41(9):1420-1426.
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Chen et al. Nat Genet. 2016 48(9):984-94.
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner et al, Science. 2015 347(6225):1010-4.
A perspective on the developmental toxicity of nanoparticles. Hougaard et al. Reproductive Toxicology 2015 56:118-40.
An atlas of active enhancers across human cell types and tissues. Andersson et al. Nature. 2014 507(7493):455-461

Principal supervisor is Professor Albin Sandelin, Department of Biology and BRIC, albin@binf.ku.dk, Direct Phone: +45 35 32 12 85. Secondary supervisor is Associate prof. Karin Sørig Hougaard at NFA: KSH@nfa.dk, +45 3916 5217


Job description
The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • To stay at an external research institution for a few months, abroad
  • Work for the department

Formal requirements
Applicants must hold an MSc degree in a life science field (e.g. biology, molecular biomedicine, etc) with excellent results. Although the work focus will be experimental, the candidate will be working closely together with computational scientists, and will be expected to contribute to data analysis and interpretation. Therefore, key skills we seek are:

  • Experience with animal work (mice), ideally with certification
  • Experience with protein-based methods in tissue (eg protein extraction, mass-spec etc)
  • Experience in RNA-based methods in tissue (RNA extraction, RNA-seq, etc)
  • Full fluency and working proficiency in spoken and written English
  • Very high motivation and independence

The following skills or experiences are considered very advantageous:
  • Background/coursework in toxicology and/or inflammatory response
  • Experience with reproduction and developmental programming of disease
  • Bioinformatics experience, in particular R and unix command line tools.
  • Experience in analysis of RNA-seq and/or proteomics data is highly beneficial.

Emphasis will also be laid on previous publications (if any) and relevant work experience.

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 317.459 including annual supplement (+ pension up to DKK 43.852). Negotiation for salary supplement is possible.

Application Procedure
The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include
  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project.
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Acceptance Letter for the relevant MSc Programme at SCIENCE, if any
  • Other information for consideration, e.g. list of publications (if any),
  • Full contact details (Name, address, telephone & email) of 1-3 professional referees
  • Two letters of recommendation.

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 1 July 2018 (year), 23:59 GMT +2.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.
The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Questions
For specific information about the PhD scholarship, please contact the principal supervisor, Professor Albin Sandelin, Department of Biology and BRIC, albin@binf.ku.dk, Direct phone: +45 35 32 12 85 or Associate prof. Karin Sørig Hougaard: KSH@nfa.dk, Direct phone: +45 3916 5217


General information about PhD programmes at SCIENCE is available at http://www.science.ku.dk/phd.



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