PhD Research Fellow in Bioinformatics and Computational Biology

Twoja Norwegia; Lørenskog; Remote; NOK 551,000 - 600,000; Full time

Job summary

University of Oslo, Ahus campus, invites applications for a PhD Research Fellow in bioinformatics and computational biology within EpiGen. The role combines molecular biology, bioinformatics, physics and pathology to build ML models that integrate TF–DNA interactions, epigenetic features and 3D genome data to uncover functional regulatory interactions in cancer.

The successful candidate will work with UiO, Ahus, Oslo University Hospital and international collaborators, aiming for a PhD thesis

Qualifications

• Good written and oral English proficiency.
• Master's degree in bioinformatics or computational biology.
• Documented knowledge of statistical theory and methods; data mining and machine learning methods.
• Programming skills in shell script, R, Python, and C.
• Experience with big data analysis and high-throughput sequencing data analysis.

Responsibilities

• Develop a biophysically interpretable machine learning model integrating TF–DNA interactions, epigenetic features, and 3D genome organization to identify functional long-range regulatory interactions in cancer.
• Focus on data mining methods such as network analysis in 3D genome regulation to identify functional non-coding mutations and their targets.
• Validate predictions in cancer using in vivo and in vitro data.
• Potential 3–6 month research visit to international collaborators for advanced training in single-cell 3D genome regulation.

Skills

English proficiency

Data mining

Machine learning

Programming (shell, R, Python, C)

Big data analysis

Hi-C data analysis

Education

Master's degree in bioinformatics or computational biology

Job description

About the position

We invite applications for a position as PhD Research Fellow in bioinformatics and computational biology available at the Department of Clinical Molecular Biology (EpiGen), Campus Ahus, University of Oslo.

The preferred starting date is as soon as possible.

The fellowship period is three years and is free of any teaching obligations. No one can be appointed for more than one PhD Research Fellowship period at the University of Oslo.

The position is based at the Department of Clinical Molecular Biology (EpiGen; https://epigenahuscom.wordpress.com/) at the University of Oslo, Ahus Campus, Lørenskog. EpiGen is a joint research unit established by the University of Oslo (UiO) and Akershus University Hospital (Ahus). It is actively involved in several major national research initiatives and provides an outstanding research environment with state-of-the-art laboratories and dedicated research facilities. The position is funded by the Research Council of Norway.

The successful candidate will join an interdisciplinary team of molecular biologists, bioinformaticians, physicists, and pathologists to develop a biophysically interpretable machine learning model that integrates diverse biological data—including transcription factor (TF)–DNA interactions, epigenetic features, and three-dimensional (3D) genome organization—to identify functional long-range gene regulatory interactions in cancer. The candidate will work with researchers at UiO, Ahus, and Oslo University Hospital (OUS), as well as by international collaborators in the United States. The research conducted during the appointment is expected to culminate in a PhD thesis submitted to the University of Oslo.

We seek a highly motivated candidate with a strong background in molecular biology, human genetics/genomics, data mining, machine learning, and computational programming. The ideal candidate will hold a Master's degree in bioinformatics or computational biology. Applicants with an MSc in physics, computer science, applied mathematics, or statistics are also encouraged to apply, provided they can demonstrate a strong interest and aptitude for learning molecular biology and human genetics.

More about the position

The project aims to develop novel computational methods and tools for predicting functional non-coding mutations in the cancer genome. These methods will integrate diverse sources of information, including the biophysical principles of protein–DNA interactions, the genetic and epigenetic features of DNA sequences, and the three-dimensional (3D) organization of the genome and its regulatory landscape. A particular focus will be on integrating multi-omics data generated from single-cell experiments to improve both predictive accuracy and biological interpretability.

The PhD research fellow will primarily focus on developing data mining methods such as network analysis in 3D genome regulation that integrate diverse biological information, including transcription factor (TF)–DNA interactions, epigenetic features, and 3D genome organization, to identify functional non-coding mutations and their targets in long-distance regions. Subsequently, the predictions will be validated in cancer by using both in vivo and in vitro experimental data.

Depending on the candidate's qualifications and the progress of the project, there may be an opportunity to undertake a 3–6-month research visit to the laboratory of one of our international collaborators in the United States. This visit will provide advanced training in computational approaches for studying single-cell 3D genome regulation and further strengthen the international collaboration.

What skills are important in this role?

Candidates for the PhD fellowships will be expected to be in the upper segment of their class with respect to academic credentials.

Required qualifications:

• Tobe admitted tothePhDprogramme at theUniversityofOslo, anapplicantmusthave afive-year master'sdegree orequivalent studiesthat thefaculty have recognisedas formingasufficient basisforadmission.
• The facultiesmaystipulateadditionaladmissionrequirements.
• Tobe employed asaPhD ResearchFellow,admissiontoadoctoralprogramis required,orabinding agreementfor admission must be inplace.Normally, one mustapplyforadmission to aPh.D. program within3monthsafter thestartof the researchprojectleadingtothe Ph.D.degree.
• Good written andoralEnglishproficiency.
• Master's degree in bioinformatics or computational biology. Applicants with an MSc in physics, computer science, applied mathematics, or statistics are also encouraged to apply, provided they can demonstrate a strong interest and aptitude for learning molecular biology and the human genome.
• Documented knowledge of statistical theory and methods, data mining, and machine learning methods.
• Documented shell script, R, Python, and C programming skills.
• Documented experience in big dataanalysis.
• Documented experience in high-throughput sequencing data analysis.

Language requirement:

• Good written and oral English proficiency.
• English requirements for applicants from outside of EU/ EEA countries and exemptions from the requirements:
• https://www.mn.uio.no/english/research/phd/regulations/regulations.html#toc8

Grade requirements:

• The average grade point for the course in the Bachelor's degree must be C or better (Norwegian educational system)
• The average grade point for the course in the Master's degree must be B or better in the Norwegian educational system
• The Master's thesis must have the grade B or better in the Norwegian educational system

Personal qualities

• Academic and personal ability to finish tasks on time
• Ability to work either independently or collaboratively in an interdisciplinary team
• Self-motivated to learn, easily adapted to new tasks, and interested in solving challenging scientific problems.
• Good communication skills and openness to new perspectives

Desired qualifications

• Experience with ChIP-seq, ATAC-seq/scATAC-seq, RNA-seq/scRNA-seq, WGS, WGBS, or Hi-C data analysis.
• Experience in computational genome studies (e.g., TF-DNA interactions, gene networks, DNA mutations, and histone modifications).
• Experience with integrated multi-omics data analysis.aaa

Employmentin thepositionis basedona comprehensiveassessmentofallqualification requirements applicabletotheposition,including

personal qualifications.

We need different perspectives in our work

UiO is an open and internationally oriented comprehensive university that strives to be an inclusive and diverse workplace and academic environment. You can read more about UiO’s work on equality, inclusion, and diversity at uio.no.

We fulfill our mission most effectively when we draw upon our variety of experiences, backgrounds, and perspectives. We are looking for great colleagues—could you be the next one?

We will provide appropriate accommodations should you need them. Relevant adjustments may include modifications to working hours, task adaptations, digital, technical, or physical adjustments, or other practical measures.

If you have an immigrant background, a disability, or CV gaps, we encourage you to indicate this in the job application portal. We always invite at least one qualified candidate from each group for an interview. In this context, disability is defined as an applicant who identifies as having a disability that requires workplace or employment-related accommodations. For more details about the requirements, please refer to the Employer portal (Norwegian).

The selections made in the job application portal are used for anonymized statistics that all state employers include in their annual reports. More information about gender equality initiatives at UiO can be found here.

We hope you will apply for the position with us.

We offer

• Exciting and meaningfultasksinan organization with animportantsocietalmission,contributingtoknowledge development,education, andenlightenment that promote sustainable, fair,andknowledge-basedsocietaldevelopment.
• Committedcolleaguesin agoodworking environment.Apleasantand stimulatingworkenvironment.
• Goodwelfare schemes.
• Opportunityof upto 1.5hoursa week ofexercise duringworkinghours. Aworkplace withgooddevelopmentandcareeropportunities.
• Membershipin theStatens Pensjonskasse, whichis one ofNorway'sbestpension schemes,with beneficialmortgages andgood insuranceschemes.
• Salary in thepositionas DoctoralResearch Fellow, position code1017in the salary range of NOK 550 800 -600 000,dependingoncompetenceand experience.From the salary, 2percentisdeducted instatutorycontributionstotheState PensionFund.
• Read more aboutthebenefitsof workinginthepublic sectoratEmployerPortal.

Application

Your application should include:

• Application coverletter (statement of motivation and research interests)
• CV (summarizing education, positions and academic work - scientific publications)
• A copy of the Master's thesis, alistof publications and academic works (maximum 5) that you wish to be considered by the committee
• Certified copies of the original Bachelor and Master's degree diploma and the transcripts of records
• Documentation of English proficiency if applicable
• Contact information for at least3references (name, relation to the candidate, institutional email address and telephone number)

Contact information

For further information, please contact:

• Junbai Wang, [e-mail]

For questions regarding Jobbnorge, please

• Maren Retterstøl Olaisen, HR advisor, [e-mail]

Placeofservice:

Department of Clinical Molecular Biology (EpiGen)

University of Oslo, Ahus campus

1748 Lørenskog

General information

The best qualified candidates will invited for interviews.

Applicant lists can be published in accordance with Norwegian Freedom of Information Act § 25. When you apply for a position with us, your name will appear on the public applicant list. It is possible to request to be excluded from this list. You must justify why you want an exemption from publication and we will then decide whether we can grant your request. If we cannot, you will hear from us. Please refer to Regulations for the Act on universities and colleges chapter 3 (Norwegian), Guidelines concerning appointment to recruitment positions at UiO and Regulations for the degree of Philosophiae Doctor (PhD) at the University of Oslo.

The University of Oslo has a transfer agreement with all employees to secure the rights to all research results and related intellectual property.