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PhD fellowship in computational modeling of genetic variants and their impact on transcriptional regulation

PhD fellow in Bioinformatics
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 Bioinformatics commencing 01.10.2020[RA1] or as soon as possible thereafter.

Description of the scientific environment

The Andersson lab is looking to recruit a highly motivated and talented PhD student to join our group working on computational biology with a strong focus on enhancers and transcriptional regulation. The successful candidate will join ENHPATHY (https://www.enhpathy.eu/), a multidisciplinary science consortium created in the frame of the Marie Sklodowska-Curie actions (MSCA)-ITN-ETN European Training Networks call and regrouping 12 academic and 3 non-academic European organizations in the continuum of basic, translational and clinical research on enhancers and associated diseases.



The lab of Robin Andersson focuses on genomics and computational/statistical modeling of transcriptional regulation based on large-scale sequencing data, including experimental data generated from within the lab. We aim to characterize and better understand the architectures and complexities of transcriptional regulation (see e.g. Andersson et al. 2014, Nature) and gain insights into the mechanisms of regulation. We further focus on the fundamental properties of enhancers and promoters (see e.g. Andersson and Sandelin 2020, Nat Rev Genet, 2020). For more information, see http://anderssonlab.org.



The Andersson lab is based in a highly collaborative environment at the Bioinformatics Centre in the Section for Computational and RNA Biology, which is currently composed of 11 strong research groups. The Department of Biology is located at the Biocenter in central Copenhagen, Denmark.


Project description
This project aims to explore the impact of regulatory genetic variation. In particular, the major aims are to establish accurate and interpretable machine learning approaches to learn how DNA sequence influences enhancer and promoter activities and to use derived models to interpret the determinants of regulatory function and the impact of regulatory genetic variation on their activities in health and disease. To this end, part of the project will focus on in vivo (CAGE, ATAC-seq, Hi-C) and in vitro (STARR-seq, SURE-seq) data generated in our lab and within the ENHPATHY network across a genotyped panel of lymphoblastoid cell lines, displaying large individual regulatory variation. Inferred models will further our understanding of the determinants of regulatory function and improve genetic variant interpretation, which will be useful for a large scientific and medical community, ultimately leading to insights into why and when regulatory genetic variation may cause phenotypical or pathological changes.

Principal supervisor is Associate Professor Robin Andersson, Department of Biology, robin@bio.ku.dk.

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, preferably abroad
  • Work for the department
Formal requirements
We are seeking a highly motivated individual with a MSc in Bioinformatics, Computational Biology or in a related quantitative discipline. Theoretical understanding and practical experiences with machine learning, statistical modeling, or statistical learning techniques are expected from the applicant. Experiences with deep learning in genomics and the analysis of functional genetic variation are considered a major plus. Importantly, the applicant should have a strong interest in transcription and transcriptional regulation.



In particular, we are looking for candidates with the following background:

  • A MSc in Bioinformatics or Computational Biology
  • Strong programming and data analytical skills
  • Documented expertise in machine learning and/or statistical learning techniques
  • A high proficiency in spoken and written English


In addition, as part of the regulations within Marie Sklodowska-Curie actions, the candidate must

  • Fulfill the mobility rule, i.e. have resided or carried out their main activity (work, studies, etc.) in the country of the host organization for no more than 12 months in the 3 years immediately before the recruitment date
  • Fulfill the Early Stage Researchers (ESRs) rule, i.e. be within their first four years (full-time equivalent research experience) of their research careers at the date of recruitment by the host organization and have not been awarded a doctoral degree.


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 331,125 (approx. €43,750) including annual supplement (+ pension at a minimum DKK 53,811). 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
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Other information for consideration, e.g. list of publications (if any)
  • 1-3 reference letters
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 03.07.2020 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 Associate Professor Robin Andersson, Department of Biology, robin@bio.ku.dk.

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





[RA1]Please make this date as early as possible

[RA2]Please fill in a date as early as possible


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