LEDIG STILLING VED HØGSKOLEN I INNLANDET

Ph.D. position - Department of Biotechnology

Deadline: 04.12.2022

Inland Norway University of Applied Sciences

Inland Norway University of Applied Sciences (INN University) is home to over 14,000 students and 1,000 employees, and has campuses in Lillehammer, Hamar, Elverum, Rena, Evenstad and Blæstad.


INN University aspires to build strong and enduring academic and research environments that will spearhead regionally, nationally and internationally.

We are developing a new and better institution with high academic and pedagogical quality, aiming at achieving university accreditation by 2020.


Our vision is "Stronger Together".

Ph.D. position in Novel Enabling Technological Solutions for Rapid Diagnostics of Infection and Antimicrobial Resistance

About the position

The Position

Department of Biotechnology, Faculty of Applied Ecology, Agriculture Sciences and Biotechnology (ALB), at Inland Norway University of Applied Sciences (INN), invites applications from outstanding candidates for a Ph.D. fellowship. The position will run for 3-years, starting in early 2023. The candidate will be enrolled in INN’s Ph.D. program in Applied Ecology and Biotechnology, with a workplace in Hamar.

The appointed candidate will be working within a proliferating scientific environment, consisting of academic staff members, Ph.D./Postdoctoral fellows, and students with scientific expertise ranging from theoretical methods (machine learning, biostatistics, bioinformatics, and business analytics) to experimental methods (genomics, photonics, spectroscopy, cell biology, and clinical microbiology).

The candidate’s main supervisor will be Associate professor Rafi Ahmad, and the supervisory group will include Professor Robert Wilson (INN), Professor Balpreet Ahluwalia (UiT – The Arctic University of Norway), and potentially a Medical Doctor/Clinical Microbiologist from EAU Section of Infections in Urology (ESIU).

As part of the project, the Ph.D. candidate will potentially be on short terms visits (up to 3 months) at our collaboration partners' labs at All India Institute of Medical Sciences - New Delhi and the University of Southampton.

The Ahmad group is also part of the Norwegian Network for One Health Resistome Surveillance (NORSE) – A national network of 13 Norwegian institutions, and the National Centre of Expertise – Heidner Biocluster.

About the project

The WHO considers bacterial infection due to antimicrobial resistance (AMR) a critical global threat to modern healthcare and societal well-being. It’s been 34+ years since a new class of antibiotics was introduced to the market. This, together with the increased and inappropriate use of existing drugs, means that we are heading towards a world where antibiotics are no longer effective. Remarkably, most prescriptions and administration of antibiotics are still carried out in the absence of any information about the causative pathogens and their resistance profiles.

The selected candidate will work within the project “OH-AMR-Diag: Novel technological solutions for rapid detection and screening of AMR from a One-Health perspective, " funded by the Research Council of Norway’s program Collaborative and Knowledge-building for Society and Industry. Please find the project details here.

In addition to INN University, the OH-AMR-Diag consortium has the following partners: academic institutions (University of Tromsø and Harvard University), hospitals (All India Inst. of Medical Sciences -Delhi), Industry partners (TINE, Animalia & Klosser Innovasjon), NGOs (Health Information Systems Programs (HISP) India & HISP Sri Lanka), National Cluster of Expertise (Heidner Biocluster) and Professional Organization (European Section of Infections in Urology).

The main objective of OH-AMR-Diag is to develop a proof of concept (PoC) decision-making diagnostic system for rapid, accurate, sensitive, and on-site detection of bacterial infection, pathogen ID, characterization of its resistance profile, and prediction of antibiotic susceptibility from an OH perspective. The project's long-term objective is to translate the OH-AMR-Diag system from the lab to tertiary care hospitals and farms for detection, screening, and therapeutic intervention.

The main tasks of this Ph.D. project are to (a) Develop a novel method for culture-independent sample preparation; (b) perform experimental genomics and Raman spectroscopy analysis on clinical samples: (c) data analysis of the generated data: (d) pilot study to evaluate the performance of the development method in clinical and on-site settings.

The Ph.D. candidates' competence development and implementation ability are ensured by the research groups' interdisciplinary and complementary experience.

Please refer to our latest publications, which highlight our work.

https://doi.org/10.1038/s41598-020-64616-x

https://doi.org/10.3389/fmicb.2022.822402

https://doi.org/10.1101/2022.02.08.479540

https://doi.org/10.1101/2022.07.07.499154

https://doi.org/10.1016/j.csbj.2021.03.027

Qualifications

It is a requirement that the PhD research fellow qualifies for admission to the University's PhD in Biotechnology. Applicants who already hold a PhD will not be considered.

To be admitted to the doctoral program, the applicant must normally have a minimum master's degree or master's level (120 credits, §3 master's in the Norwegian system) or equivalent education, within molecular biology, microbiology, genomics, or another relevant scientific discipline

Furthermore, you must have a strong academic background from your previous studies, ie. the average grade should normally be B or better from the master's program (120 credits) or equivalent education. Calculation of the average grade is based on the credits for each course and for the master's thesis. Applicants with weaker grades than what is normally required for admission must document that they will be able to complete a doctoral degree. In cases where the education has been approved with the use of the grades passed / failed, the applicant is admitted after an individual assessment. If you have education from abroad, you can contact NOKUT for approval of your education, alternatively a similar assessment will be made in connection with the application process.

Required qualifications

The enabling technologies that will be covered within the scope of the Ph.D. program of the candidate are next-generation sequencing methods, Raman spectroscopy, bioinformatics (data analyses), and possibly advanced optical microscopy methods. The candidate should have exposure to next-generation sequencing and should be open to learning Raman spectroscopy methods during the Ph.D. program.

The required qualifications are:

  • Experience with next-generation sequencing technology, preferably Illumina and Oxford Nanopore.
  • Experience and demonstrated proficiency with the entire sequencing workflow, from sample preparation to bioinformatic analysis.
  • Hands-on experience with working on human clinical samples like blood, urine, feces, etc.
  • Experience with analyzing large-scale next-generation sequence data, especially whole-genome sequencing and metagenomics.

Desired qualifications

  • Previous experience within infection biology and antibiotic resistance.
  • Hand-on experience in working with spectroscopy methods such as Raman or absorption spectroscopy.
  • Fluency in scripting in Python/Perl and R.

Further preference will be given to candidates with good teamwork and communication skills and documented scientific publications or other writing experience.

Language proficiency:

  • Applicants must be proficient in both written and oral English. Applicants from non-English-speaking countries must document English competence through an approved test (TOEFL, IELTS, Cambridge Certificate in Advanced English (CAE) or Cambridge Certificate of Proficiency in English (CPE).

Evaluation of candidates for the position will be based on a total assessment of educational background, experience and personal suitability, as well as motivation and other eligibility requirements, as defined in the advertisement. In addition, the following will be emphasized: quality of the project description, documented independent research and development work or experience relevant to the project.

How to apply

Your application must include:

  • Application letter including a brief account of the applicant's research interests and motivation for applying for the position
  • Proposed project description of the study (max 8 pages, including references), outlining its academic relevance, methods, challenges and possibilities, and containing a tentative progression plan. The project description must be written in English.
  • CV detailing your relevant educational background and experience (registered in Jobbnorge's form).
  • Copies of academic diplomas and transcripts (A certified English translation of all educational documents is required unless the documents are in Norwegian.)
  • A list of publications.
  • The names and contact information for two referees.
  • Any other documentation you would like us to consider.

Attachments must be uploaded as separate files. If the attachments exceed 30 MB, they must be compressed prior to upload. It is the applicant's responsibility to ensure that all attachments are uploaded. Documents submitted after expiry of the deadline will not be considered in the evaluation of your application.

We offer

  • A place in an ambitious and highly international environment.
  • Working in a multidisciplinary team including computer scientists, ML/AI experts, bioinformaticians, medical doctors, biologists, and physicists.
  • Access to state-of-the-art computer infrastructure, including access to a Norwegian supercomputer.
  • A challenging and exciting project having a positive societal impact. Along with opportunities for personal and scientific development.
  • An academically stimulating work environment with engaging colleagues in a critical, expanding, and prioritized research area.
  • An independent and flexible work setting that the successful candidate may, to a large extent, influence themselves. Daily contact with inspiring, skilled colleagues.
  • A campus setting surrounded by forests and mountains with opportunities for outdoor recreation.
  • Position is paid and placed in position code 1017, PhD candidate in the Government Salary Scale, paygrade 54 (NOK 501 200,-)
  • Membership in the Norwegian Public Service Pension, with among other things, good pension and insurance schemes.

For more information about INN University as an employer, please see here.

General information

For further details about the position, please contact the:

HINN believes that there is strength in inclusion and diversity. We desire employees with different competencies, professional combinations, life experiences and perspectives to contribute to an even better way of solving problems. We will facilitate for employees who need assistance to realise their goals. Relevant adaptations can be, for example, technical aids, adapting furniture or adjusting routines, work tasks and working hours.

If there are qualified applicants with disabilities, gaps in the CV or immigrant background, we shall call at least one applicant in each of these categories for an interview. In order to be considered as an applicant in these groups, the applicants must meet certain requirements. You can read more on this here.

We encourage applicants to tick in Jobbnorge if they have a disability, a gap in their CV or immigrant background. The ticks in the jobseeker portal form the basis for anonymised statistics that all state-owned enterprises report in their annual reports

Information about applicants may be made public even if the applicant has asked not to be named on the list of persons who have applied. The applicant must be notified if the request to be omitted is not met.

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