PhD fellowship in bioinformatic analysis of host - pathogen interactions in the context of anti-microbial resistance in pigs

A PhD fellowship is available in the Computational Biology and Bioinformatics research group (https://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. Anti-microbial resistance (AMR) is a fast-increasing challenge for human health. The project is a part of the large PIG-PARADIGM consortium (https://pig-paradigm.net/), funded by the Novo Nordic Foundation, has the overall goal to prevent spreading of AMR by reducing antibiotic use in pig-production. Several strategies will be taken including microbial therapies that can diminish the need for antibiotics by production of more resilient pigs. Within this PhD project the goal is to explore and establish the molecular interactions between host and commensal as well as pathogenic microbes in various sections of the pig's intestine. The research aims to identify and associate these interactions in pigs with and without diarrhea. By gaining a deeper understanding of these interactions, the project will offer valuable insights into the characterization of resilience against pathogens. The PhD project will take place in collaboration with the research groups of Prof Merete Fredholm and Prof Mani Arumagam at University of Copenhagen.

Start date is May 1st, 2024 or as soon as possible thereafter.

The Bioinformatics group and research
The Computational Biology and Bioinformatics research group holds a long-standing interest in Computational RNA biology and transcriptomics but works in general on many different topics covering computational, algorithmic and biological aspects. The group holds a long interest in RNA structure, RNA interactions and transcriptome analysis, which over the years have evolved in different directions from gene network analysis and CRISPR. On the computational side the group both apply existing computational frameworks for data analysis, while developing algorithms as well. The group is located on Frederiksberg Campus. Our research environment is highly international and stimulating. We are involved in organizing seminars, workshops, summer schools with international speakers and have retreats with our international collaborators.

Project description

The PhD project concerns how commensal and pathogenic microbiota modulate host signaling in the intestine and aims to elucidate fundamental aspects of disease progression. Within the gut microbiome component, the project will identify microbial species, microbial gene functions, and gene clusters through DNA sequencing by PIG-PARADIGM consortium partners. Combined with tissue/fecal metabolomics, this will lead to microbial species/gene interaction networks and pathways. Conversely, on the host side gene networks and pathways will be identified through total and small RNA-seq data likewise established by PIG-PARADIGM consortium partners. The PhD project will make use of these established sets of host and microbiome gene networks etc and the abundance of genes within them to associate genes between host and microbe. To support the associations RNA-RNA interactions (host – microbe RNA) and RNA – protein interactions will be predicted. Within the analysis (long and short) non-coding RNAs and RNA structure on both host and bacteria will be included alongside the protein coding genes.

Principal supervisor is Professor, Jan Gorodkin, Department of Veterinary and Animal Sciences, Phone: +45 23375667, Email: gorodkin@sund.ku.dk

Start: May 1, 2024 or as soon as possible thereafter.

Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

  • Carrying through an independent research project under supervision, with content as outlined above in the project description.
  • Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
  • Participating in active research environments including a stay at another research team.
  • Obtaining experience with teaching or other types of dissemination related to your PhD project
  • Teaching and disseminating your knowledge.
  • Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants                         
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project such as Bioinformatics, Systems Biology, Computer Science or similar areas. Most importantly that you meet the technical requirements in bullet #2 below. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

  • The grade point average achieved
  • Professional qualifications relevant to the PhD project. This include (but not limited to):
    For the following criteria the level has to be at level where you are able to work independently:
    • A solid knowledge of network biology
    • Knowledge of Machine and Deep learning algorithms
    • Python and knowledge of C/C++, shell scripting and Unix/Linux operating system
  • Relevant biological understanding
  • Previous publications
  • Relevant work experience
  • Demonstrate that you can work independently while keeping the team up to date
  • Pro-active in the project and its planning
  • Other professional activities
  • Language skills

Additional knowledge of RNA structures and interactions is considered as an advantage. Applicants are encouraged to explain in their motivation letter how they match the specific requirements listed in bullet #2 and other relevant qualifications. Motivation letters of general nature that are not specific for the requirements listed above are very often not informative and do not support the application.

Place of employment

The place of employment is at the Computational Biology and Bioinformatics group, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen. The work environment in the lab is highly dynamic and international with good synergy among the different research projects. The group has access to all the necessary computational infrastructure and high-performance computing needed for the project.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years. The start date is May 1, 2024 or as soon as possible thereafter.

The employment is conditioned upon the applicant’s success­ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant during an initial three-month employment as a research assistant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 28,400 DKK/Roughly 3,800 EUR (October 2022 level) plus pension.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.
For specific questions regarding the HR process of recruitment, you can contact sund-hr-ivh@sund.ku.dk.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format: 

1. Motivation letter of application

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

4. Publication list (if possible)

Application deadline:  February 26, 2024, 23.59pm CET (extended from February 12 2024)

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You find information about the recruitment process at: https://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held from February 26 and the following week.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background. 

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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

Jan Gorodkin

Info

Application deadline: 26-02-2024
Employment start: 01-05-2024
Working hours: Full time
Department/Location: Department of Veterinary and Animal Sciences
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