Ph.D. in Culture-Independent Metagenomics for Rapid Diagnosis of Bacterial Infections and Antimicro
Deadline: 21.04.2025
Publisert
University of Inland Norway is home to around 15,000 students and 1,450 employees. We have campuses in Lillehammer, Hamar, Elverum, Rena, Evenstad and Blæstad, and offer some courses at Kongsvinger, Tynset and in Oslo.
INN University is known for strong and enduring academic and research environments that will spearhead regionally, nationally and internationally.
Our vision is "Stronger together - we build the university in an interdisciplinary community, together with the communities and the industries"
PhD Research Fellowship
About the position
The Department of Biotechnology within the Faculty of Applied Ecology, Agricultural Sciences, and Biotechnology (ALB) at the University of Inland Norway (INN) invites applications from exceptional candidates for a Ph.D. fellowship. The position will last for three years, commencing in August 2025. The selected candidate will enroll in INN’s Ph.D. program in Applied Ecology and Biotechnology, with a workplace in Hamar.
The selected candidate will thrive in a dynamic scientific community with dedicated academic staff, talented Ph.D. and postdoctoral fellows, and enthusiastic students. The appointed candidate will work in a vibrant scientific environment that includes expertise from experimental methods such as genomics, molecular biology, clinical microbiology, microscopy, and spectroscopy, as well as theoretical methods like machine learning and bioinformatics.
The candidate's primary supervisor will be Professor Rafi Ahmad. In addition, a team of experienced researchers and clinicians from the OH-AMR-Diag and UTI-Diag projects will provide supervision.The Ahmad group (https://www.inn.no/english/find-an-employee/rafi-ahmad.html) 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.
The Ph.D. candidate might spend up to three months on short-term visits at our partner labs, including the All India Institute of Medical Sciences in New Delhi and the University of Tromsø.
About the project
The WHO regards bacterial infections caused by antimicrobial resistance (AMR) as a significant global threat to contemporary healthcare and societal health. It has been over 34 years since a new class of antibiotics was launched. Coupled with the excessive and improper use of current medications, we are moving toward a reality where antibiotics may cease to be effective. Notably, many antibiotic prescriptions and administrations occur without knowledge of the infectious pathogens and their resistance patterns.
The selected candidate will work within the UTI-Diag and OH-AMR-Diag projects funded by the Research Council of Norway. Please find the project details here:
Alongside INN University, we’re excited to have a fantastic group of partners in the project consortium! From Norway - University of Tromsø and Norwegian Institute of Public Health. From India - Indian Institute of Technology, Delhi and All India Institute of Medical Sciences, Delhi. Plus, we’re thrilled to collaborate with the World Health Organization and the European Section of Infections Urology.
The key objectives of this Ph.D. project include: a) optimizing a newly developed in-house method for culture-independent sample preparation from body fluids, such as urine, milk, and blood; b) conducting metagenomic sequencing on these samples; c) analyzing the resulting data; and d) performing a pilot study to assess the method’s effectiveness in clinical and on-site environments.
Kindly check our most recent publications that showcase our work;
For further details about the project, please contact Prof. Rafi Ahmad, Ph.D., rafi.ahmad@inn.no
Qualifications
It is a requirement that the PhD research fellow qualifies for admission to the University's PhD programme in Applied Ecology and 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 biotechnology, 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 HK-dir for approval of your education, alternatively a similar assessment will be made in connection with the application process.
The following qualifications is also required for the position:
Prior experience with methods development for rapid diagnosis of bacterial infection and antimicrobial resistance.
Proficient in metagenomic sequencing technologies from Oxford Nanopore, with hands-on expertise using both MinION and Flongle flow cells.
Proven expertise in the entire sequencing workflow, from sample preparation to bioinformatics analysis, as evidenced by published research article(s).
Extensive hands-on experience handling clinical samples, including urine and milk.
Skilled in analyzing large-scale biological datasets, including whole-genome sequencing and metagenomic nanopore sequencing.
It is also desired that you also have experience working with urinary tract infections and mastitis, and fluency in scripting in Python and R. Documented scientific publications or other writing experience will be emphasized.
Furthermore, emphasis is placed on the following attributes:
Professional and personal prerequisites for completing the doctoral degree program within the employment period.
The ability to work independently as well as strong teamwork and communication skills.
The ability to work in a structured manner and having a large work capacity.
Applicants who cannot document skills in Norwegian, Swedish or Danish at level A2 upon employment must complete training corresponding to at least 15 credits during the scholarship period.
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: documented independent research and development work or experience relevant to the project.
The position and associated tasks must be carried out in accordance with the applicable laws and regulations for government employees, including also the Act on Control of the Export of Strategic Goods, Services and Technology, etc. Candidates who, after assessment of the application and attachments, come into conflict with the criteria in the latter act, will not be able to take up the position at University of Inland Norway. Necessary approvals must be maintained throughout the employment relationship.
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
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
Collaborating within a multidisciplinary team comprising microbiologists, ML/AI specialists, bioinformaticians, medical professionals, and physicists.
Access to cutting-edge computational infrastructure.
Involvement in a stimulating and impactful project that contributes positively to society, offering opportunities for both personal and scientific growth.
An intellectually stimulating work environment with dynamic colleagues focused on a critical and rapidly growing research field.
A flexible and independent work setting where candidates have significant autonomy. Daily interaction with talented and motivated colleagues.
Position is paid and placed in position code 1017, PhD candidate in the Government Salary Scale
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
INN 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.
