University of Bergen

The University of Bergen (UiB) is an internationally recognised research university with more than 14,000 students and close to 3,500 employees at six faculties. The university is located in the heart of Bergen. Our main contribution to society is excellent basic research and education across a wide range of disciplines.

At the Faculty of Medicine, Department of Clinical Science, a full-time (100 %) position as Postdoctoral Fellow is available for a period of 3 years, with the possibility for an extension of the period up to four years if a research-related stay abroad shall be included in the employment period.The position is to work on the project entitled Inferring gene regulatory networks from single cell expression data, financed by the Bergen Research Foundation.

About the Project

Multi-cellularity is achieved by precise control of gene expression during development and differentiation and aberrations of this process leads to disease. A key regulatory process in gene regulation is at the transcriptional level where transcriptional activators and repressors regulate the spatial and temporal expression of the target genes in response to environmental, developmental, and physiological cues obtained from a signaling cascade. The rapid advances in sequencing technology has now made it feasible to study this process at a single cell level. Single cell RNA sequencing (scRNAseq) is used to explore the transcriptomes of cell populations and tissues to understand cellular differentiation processes, tissue heterogeneity in normal and disease states.

Single cell technologies are highly important, particularly in cancer where the genetic diversity within a tumor allows it to evolve leading to poor survival. Despite huge clinical relevance and potential, analysis of single cell RNA-seq data is challenging, partly due to the limited mRNA (low starting material) in a single cell, scRNAseq experiments are more prone to technical variability than bulk RNAseq. This phenomenon predominately affects lowly expressed transcripts, as highly expressed are more likely to be captured during library preparation (Arzalluz-Luque 2017). This provides barriers for using traditional methods for network inference in the context of single-cell data. In this project, we will develop multiple strategies (or methods) to impute missing values in the single cell data to render it suitable for network inference. The imputed datasets will then be used to infer gene regulatory networks using module-based network inference approaches (Bonnet 2015). The developed methods will be primarily tested on the single cell datasets in the context of cancer available publicly as well as through collaborations. The inferred networks will then be validated using other datasets including ChIP-seq as well as by performing perturbation experiments through collaborations.

Postdoctoral Fellow

The main opportunities and responsibilities for the position are

• the fellow will benefit from the dual work environment at the Department of Clinical Medicine and the Department of Informatics to strengthen the research profile in both computational and medical fields
• the fellow will develop and use computational methods to analyze single cell gene expression data mainly in the context of cancer
• the fellow will integrate data from multiple platforms and sources
• the fellow will also dedicate a part of his/her time for collaborative projects with other research teams within the faculty of medicine
• the fellow will participate in teaching of students and relevant administrative tasks

For further information please contact:

• Dr. Anagha Joshi, e-mail: Anagha.Joshi@uib.no, phone: +47 55584200.

Qualifications and qualities

• the applicant must hold a PhD-degree within the field of Bioinformatics, Informatics, Systems Biology and other related topics or have submitted their PhD´s thesis for assessment prior to the application deadline. It is a condition of employment that the PhD degree has been awarded before the period of employment starts
• the candidate must have experience in programming languages and preferentially analyzing sequencing data
• the candidate should have some prior experience in applying computational and statistical techniques to genomic data
• the candidate must be open to working on collaborative projects
• the candidate should be proficient in spoken and written English. This can be demonstrated through first author publications
• personal skills will be emphasized. The candidate should be able to work independently and interactively in a team setting, be motivated and responsible, and also have a great work capacity and enthusiasm for research

We can offer

• a good and challenging work environment in research environment at both the department of clinical medicine and the computational biology unit (CBU) within the Department of Informatics.
• salary level 59 (code 1352/pay framework 24.3) at present NOK 515 200 gross p.a., with a degree in Medicine or Dentistry level 59 (code 1352/pay framework 24.3) at present NOK 515 200 gross p.a., with a medical specialization level 61 (code 1352/pay framework 24.5) at present NOK 534 100 gross p.a. on the government salary scale. Further promotion will be after service seniority in the position. A pension contribute of 2 % will be deducted and deposited to the state pension scheme. In the case of highly qualified applicant, a higher salary may be considered. Salary is under adjustment.
• a good pension scheme in the Norwegian Public Service Pension Fund
• inclusive workplace (IW)
• good welfare benefits

For more information regarding what the University of Bergen can offer its employees please visit:

http://www.uib.no/en/poa/74243/what-can-university-bergen-offer-its-employees

About postdoctoral fellowships

In general, the purpose of postdoctoral positions at the University of Bergen is the building of competence by means of further development of research work to a higher level than what is possible within an ordinary PhD program. The main goals of the positions are to qualify the successful candidate for professional top positions.

It is a goal that the employment period is carried out as a continuous research program. Hence, leaves of absence for other purposes than those laid down by law are normally not granted.

Applicants must present proposals for projects for the qualifying work. The project description must also include a work plan. It is a condition that the successful candidate completes the project during the employment period.

The employee may be assigned up to 25 % required duties in the form of teaching and similar work at the department.

Postdoctoral fellowships are fixed term positions. You can not be employed as a postdoctoral fellow for more than one fixed term period at the same institution. Also, you cannot be employed in a postdoctoral position if you have previously held this type of position at a different institution in the region.

The fixed term period for the position is three years, with the possibility for an extension of the period up to one years if a research-related stay abroad shall be included in the employment period.

Recruitment to state employment

State employment shall reflect the multiplicity of the population at large to the highest possible degree. The University of Bergen has therefore adopted a personnel policy objective to ensure that we achieve a balanced age and sex composition and the recruitment of persons of various ethnic backgrounds and persons with disabilities. Persons of different ethnic backgrounds and persons with disabilities are therefore encouraged to apply for the position.

The successful applicant must comply with the guidelines that apply to the position at any time.

The University of Bergen applies the principles of public openness when recruiting staff to scientific positions. Information about the applicant may be made public even though the applicant has requested not to be named in the list of applicants. The applicant will be notified if their request is not respected.

How to apply

Send your CV and application with attachments electronically via “Jobbnorge” by clicking on the button marked “Apply for this job”.

The application must contain:

• a brief letter of application stating your motivation for the position and why you are applying
• witnessed copies of diplomas and relevant certificates (applicants with education from other countries than Norway must enclose witnessed diplomas in both the original language and authorized translations)
• complete list of publications
• publications (pdf) it is important that each of the scholarly works on which the committee should place special emphasis, is attached in its entirety
• two referees (name and contact information)

The applications will be sent electronically to the assessment committee.

Please notice that the applications will be assessed only with the information available in “Jobbnorge” when the deadline expires.

For further information about the recruitment process, click here.

Apply for this job