PhD scholarship within bioinformatics, using data science in microbial metagenomics
Deadline: 15.06.2025
Publisert
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About The Faculty of Chemistry, Biotechnology and Food Science
The Faculty of Chemistry, Biotechnology and Food Science (KBM) has about 180 employees, 80 PhD students and 500 BSc and MSc students. The faculty has 11 research groups within chemistry and biochemistry, microbiology and microbial gene technology, bioinformatics and data analysis, food science and nutrition. The Faculty has a state-of-the-art infrastructure for research and education: A biorefinery lab, proteomics platform, fermentation lab, a murine facility, platform for studies of microbial regulation of GHG release and a small-scale pilot plant for processing of food, incl. a microbrewery. Additionally, KBM has a strong competence in enzymology, fermentation and biorefining. KBM aims at a strong research position and collaborates in networks and research projects both nationally and internationally.
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About the position
The Faculty of Chemistry, Biotechnology and Food Science at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year PhD-position related to the discovery of microbial biomarkers for monitoring the ecological state of seafloor sediments.
The project BIOmdARK aims to improve our abilities to find stable biomarker information about seafloor sediment ecological status from the sequencing of environmental microbial DNA. Seafloor samples contain many new or uncharacterized microbial organisms, typically referred to as Biological Dark Matter (BDM). A main idea of this project is to make use of the pattern matching abilities of the Tsetlin Machine in machine learning to be able to recognize signals in the BDM in addition to performing a taxonomic classification in the classical context.
It will also require a broader array of machine learning methods in performing feature selection, clustering, regression and classification. This is a position in bioinformatics located at the BIAS group of KBM, but with supervisors from data science and microbial ecology as well.
The applicant is made aware that an application for a PhD position at NMBU is at the same time an application for admission to a PhD programme at the institution. The documentation that is necessary to ensure that the admission requirements are met must be uploaded as an attachment.
Main tasks
From other ongoing projects we have available large amounts of metagenome and ecological data, but interaction with public data repositories will be needed. The daily work will be on a High Performance Computing (HPC) cluster involving the use of a range of bioinformatic software tools in addition to coding in python, R and bash.
These are the main tasks:
Implement the Tsetlin Machine for taxonomic classification of metagenome contigs, and compare performance to existing tools
Taxonomy-guided clustering of the Biological Dark Matter. This may extend on the previous bullet point, but alternatives exist
Optimized feature selection for finding the stable biomarkers from metagenome data
The three bullet points may be seen as sketches for three scientific publications, and the main task for any PhD is to produce such manuscripts. This means overviewing literature and scientific writing are also important tasks.
The successful candidate is expected to enter a plan for the progress of the work towards a PhD degree during the first months of the appointment, with a view to completing a doctorate within the PhD scholarship period.
Competence
The successful applicant must meet the conditions defined for admission to a PhD programme at NMBU. The applicant must have an academically relevant education corresponding to a five-year master’s degree or a cand.med.vet. degree, with a learning outcome corresponding to the descriptions in the Norwegian Qualification Framework, second cycle. The applicant must have a documented strong academic background relevant to the position and be able to document proficiency in both written and oral English. For more detailed information on the admission criteria please see the PhD Regulations and the relevant PhD programme description.
The applicant must document expertise and interest in the research subject.
Required Academic qualifications
Master's degree (MSc) in Bioinformatics, Data Science or similar fields with a large overlap with these two.
Excellent skills in coding. We will use both python, R and bash (UNIX shell scripting).
The following experiences and skills will be emphasized:
Experience with metagenome data analysis.
Experience with the use of High Performance Computing facilities.
Insight into a range of machine learning methods and ideas.
You need to:
Write an application where you clearly demonstrate that you have a strong motivation for, and understanding of, the aims of this project. How do you see the use of a Tsetlin machine in this context (max 250 words)?
Demonstrate excellent scientific writing skills and communication abilities.
Demonstrate your ability to do structured and tidy work when handling large data sets and complex analyses.
Be able to make realistic plans and execute them in time.
Remuneration and further information
Salary in position as Doctoral Research Fellow, position code 1017 in salary range NOK from 536 200 - 575 400 depending on competence and experience. From the salary, 2 percent is deducted in statutory contributions to the State Pension Fund.
Employment is conducted according to national guidelines for University and Technical College PhD scholars.
For further information, please contact:
Lars Snipen, professor, E-mail: lars.snipen@nmbu.no
To apply online for this vacancy, please click on the 'Apply for this job' button above. This will route you to the University's Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form.
Application deadline: 15.06.2025
Your CV must be entered in JobbNorge's CV form and not just included as an attachment. This is to be able to comply with the regulations of §15 of the Public Administration Act.
In the application, the candidate must confirm that information and documentation (in the form of attachments) submitted via the job application can also be used by NMBU in a possible admission process.
Applicants invited for an interview are expected to present original diplomas and certificates.
The following documents must be attached to the application:
Motivation letter (maximum 1 page) This must be specific and motivate why you apply for this position.
Complete CV
Certified copies of academic diplomas and certificates. (i.e. Diploma, transcript. Diploma supplement for both bachelor and master). Diplomas, transcripts and diploma supplements that are not in Norwegian or English must be uploaded in the original language. An English translation of these documents must also be attached.
Applicants from universities outside Norway are kindly requested to send a diploma supplement, or a similar document, which describes in detail the study program and grading system.
Additional relevant documentation of professional knowledge (for example, list of scientific works). If it is difficult to judge the applicant’s contribution for publications with multiple authors, a short description of the applicant’s contribution must be included.
