PhD Research Fellow in Bioinformatics and Computational Biology

University of Oslo; Lørenskog; On-site; NOK 551,000 - 600,000; Full time

Benefits offered by this job

State-of-the-art labs

International collaboration

Research visits

Job summary

University of Oslo invites applications for a PhD Research Fellow in bioinformatics and computational biology at the EpiGen unit, Ahus Campus, Lørenskog. The three-year fellowship is teaching-free and aims to produce a PhD thesis for submission to UiO.

You will join molecular biologists, bioinformaticians, physicists and pathologists to develop a biophysically interpretable ML model integrating TF-DNA, epigenetics, and 3D genome data in cancer.

Qualifications

• Master's degree in bioinformatics or computational biology or equivalent.
• Strong background in molecular biology, human genetics/genomics and data mining.
• Experience with machine learning and computational programming.
• Good written and oral English proficiency.

Responsibilities

• Develop data mining methods for integrating multi-omics data.
• Build models linking TF-DNA interactions, epigenetic features and 3D genome data.
• Validate predictions in cancer using in vivo and in vitro data.
• Collaborate with UiO, Ahus, OUS and international partners.

Skills

Molecular biology

Genomics

Data mining

Machine learning

Computational programming

Education

Master's degree in bioinformatics or computational biology

Strong background in genetics/genomics

English proficiency

Tools

R

Python

Java/Scala

Job description

PhD Research Fellow in Bioinformatics and Computational Biology

University of Oslo

Stillingstittel PhD Research Fellow in Bioinformatics and Computational Biology

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 the human genome.

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.

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 the human genome.

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

Employment in the position is based on a comprehensive assessment of all qualification requirements applicable to the position, 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 offer

• Exciting and meaningfultasksinan organization with animportantsocietalmission,contributingtoknowledge development,education, and enlightenment that promote sustainable, fair,andknowledge-basedsocietaldevelopment.
• Committedcolleaguesin a good working environment. Apleasantand stimulating work environment.
• Good welfare schemes.
• Opportunityof upto 1.5hoursa week of exercise during working hours. A workplace with good development and career opportunities.
• Membershipin the Statens Pensjonskasse, whichis one of Norway's best pension schemes,with beneficial mortgages and good insurance schemes.
• Salary in the position as Doctoral Research Fellow, position code1017 in the salary range of NOK 550 800 -600 000, depending on competence and experience. From the salary, 2 percent is deducted in statutory contributions to the State Pension Fund.
• Read more about the benefits of working in the public sector at Employer Portal.

Contact information

For further information, please contact:

• Junbai Wang, [e-mail]

For questions regarding Jobbnorge, please

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

Place of service:

Department of Clinical Molecular Biology (EpiGen)

University of Oslo, Ahus campus

1748 Lørenskog

General information

Please note that we are unable to add documentation after the application deadline. As the deadline applies equally to all applicants, this policy ensures equal treatment throughout the recruitment process. If you experience difficulties uploading documents in Jobbnorge, please contact their customer service: Phone: [phone] or Email: [e-mail]

The primary method of communication throughout the process will be e-mails and messages through the recruitment system Jobbnorge. When you receive a notification of a message in Jobbnorge, please log in to read it, as it may be important.

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.

Om bedriften

The University of Oslo is Norway’s oldest and highest ranked educational and research institution, with 26 500 students and 7 200 employees. With its broad range of academic disciplines and internationally recognised research communities, UiO is an important contributor to society.

The Institute of Clinical Medicine (Klinmed) is one of three institutes under the Faculty. Klinmed is responsible for the Faculty's educational and research activities at Oslo University Hospital and Akershus University Hospital. With about 900 employees spread across approximately 425 man-labour years, Klinmed is the university’s largest institute. Our activities follow the clinical activity at the hospitals and are spread across a number of geographical areas.

Integreat -Norwegian Centre for Knowledge-driven Machine Learning