PhD fellowship in Computational Biology at the Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen
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PhD fellowship in Computational Biology at the Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen
We are offering a PhD fellowship in Computational Biology commencing September 1st 2025 or as soon as possible hereafter.
Our group and research
The applicant will be an integral part of the recently established Centre for Ancient Environmental Genomics and will be working on a project within the Ancient Environmental Genomics Initiative for Sustainability (AEGIS) within the Centre. These are interdisciplinary research centers committed to unlocking the vast yet largely untapped research potential of ancient environmental genomics by enhancing key experimental and computational capabilities. The goal is to study community-wide and population-level processes on an unprecedented temporal and spatial scale to help resolve fundamental questions about the history of life on Earth. The centers bring together a diverse team of researchers with backgrounds in geology, genetics, ecology, evolutionary biology, computer science, statistics, and more.
Importantly, the centers also host the cutting-edge Sequencing Centre, which is deeply devoted to novel approaches and methodologies for optimizing the output of ancient and possibly very degraded material.
Project description
Hybridization capture has emerged as a central method for targeted sequencing, enabling the enrichment of specific genomic regions from complex samples. This is particularly advantageous in scenarios where DNA is highly degraded or available only in limited quantities, such as ancient environmental DNA (aeDNA). Despite its widespread use, the downstream analysis of hybridization capture data presents several computational and methodological challenges that remain unresolved. These include issues related to probe design, PCR-induced biases, and the limitations of traditional alignment methods. This PhD thesis seeks to address these challenges through the development of novel bioinformatic tools and frameworks, thereby enhancing the utility and accuracy of hybridization capture sequencing.
Core objectives and deliverables of the PhD project include:
Development of a custom probe set) The probes/baits used for hybridization capture are essential for successful hybridization of DNA fragments and further robust downstream bioinformatic analysis. This project will aim to develop a custom probe set focusing on functional plant genes associated with stress response to climatic conditions and apply them to a selected ecological system for thorough evaluation.
Mitigating duplication bias) With hybridization capture follows several polymerase chain reaction (PCR) steps which introduces potential bias in the form of duplicated reads. Due to the nature of PCR, errors have a chance to occur in each cycle and due to the number of cycles needed errors will be present throughout capture sequencing data. The project will aim to evaluate the severity of these errors and develop a workflow/pipeline or standalone software to deal with them in a sufficient and well-informed manner.
Pan-genome graph alignment) Sequencing data has traditionally been aligned to a single or several linear reference genomes. This comes with clear limitations when looking at variation between many species or across taxon levels. A possible solution to this is pan-genome graphs which can catch all the variation in a single alignment. This project will examine the potential use of pan-genome graphs as an alignment tool for hybridization capture data, utilizing the smaller regions of interest associated with capture.
This research is expected to result in a suite of bioinformatic tools and methodological frameworks that will enhance the analysis of hybridization capture data. The outcomes will have broad applicability in fields such as ancient DNA research, ecological genomics, and evolutionary biology, and will contribute to improving the resolution and interpretability of genomic data recovered from complex and degraded samples. The project is focused on drylab methods and will not contain any wetlab experimentation, but a strong knowledge and hands-on experience with existing wetlab protocols is assumed necessary for the phd project.
Secondly, the hosting centre, the CAEG Center of Excellence, is devoted to the generation of ancient environmental genomes as part of a diverse suite of projects spanning million-year-old material from extreme arctic environments to DNA sequencing data from lost civilizations in southeast Asia. The Ph.D. candidate will have the opportunity to develop programs to facilitate and possibly drive the data analyses of one or more of these large projects.
Principal supervisor is Thorfinn Sand Korneliussen, Globe Institute, tskorneliussen@sund.ku.dk, +4550433250.
Start: September 1st 2025 or as soon as possible hereafter
Duration: 3 years as a PhD fellow
Job description
Your key tasks as a PhD fellow at SUND are:
Applicants must have qualifications corresponding to a master’s degree related to genomics, computer science, or mathematics degree with good results and good English skills. Previous publications (if any) and relevant work experience will also be considered criteria for assessing your qualifications.
Requirements for the applicants are:
Place of employment
The place of employment is at the Section for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K.
About Globe Institute
The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: http://www.globe.ku.dk/.
The Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See website for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. The university offers a variety of services for international researchers and accompanying families.
Terms of employment
The average weekly working hours are 37 hours per week.
The position is a fixed-term position limited to a period of 3 years. The starting date is September 1st 2025 or as soon as possible hereafter.
The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen.
The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.
Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at 30,800 DKK/approximately 4,100 EUR (April 2025 level) plus pension.
Questions
For specific information about the PhD fellowship, please contact the principal supervisor.
General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/
Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:
1. Motivated letter of application (max. one page)
2. CV incl. education, experience, language skills and other skills relevant for the position
3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science
4. Publication list (if possible)
Application deadline: 4 June 2025, 23:59 GMT+2.
We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.
The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.
The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.
Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.
You find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/
The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.
The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.
Our group and research
The applicant will be an integral part of the recently established Centre for Ancient Environmental Genomics and will be working on a project within the Ancient Environmental Genomics Initiative for Sustainability (AEGIS) within the Centre. These are interdisciplinary research centers committed to unlocking the vast yet largely untapped research potential of ancient environmental genomics by enhancing key experimental and computational capabilities. The goal is to study community-wide and population-level processes on an unprecedented temporal and spatial scale to help resolve fundamental questions about the history of life on Earth. The centers bring together a diverse team of researchers with backgrounds in geology, genetics, ecology, evolutionary biology, computer science, statistics, and more.
Importantly, the centers also host the cutting-edge Sequencing Centre, which is deeply devoted to novel approaches and methodologies for optimizing the output of ancient and possibly very degraded material.
Project description
Hybridization capture has emerged as a central method for targeted sequencing, enabling the enrichment of specific genomic regions from complex samples. This is particularly advantageous in scenarios where DNA is highly degraded or available only in limited quantities, such as ancient environmental DNA (aeDNA). Despite its widespread use, the downstream analysis of hybridization capture data presents several computational and methodological challenges that remain unresolved. These include issues related to probe design, PCR-induced biases, and the limitations of traditional alignment methods. This PhD thesis seeks to address these challenges through the development of novel bioinformatic tools and frameworks, thereby enhancing the utility and accuracy of hybridization capture sequencing.
Core objectives and deliverables of the PhD project include:
Development of a custom probe set) The probes/baits used for hybridization capture are essential for successful hybridization of DNA fragments and further robust downstream bioinformatic analysis. This project will aim to develop a custom probe set focusing on functional plant genes associated with stress response to climatic conditions and apply them to a selected ecological system for thorough evaluation.
Mitigating duplication bias) With hybridization capture follows several polymerase chain reaction (PCR) steps which introduces potential bias in the form of duplicated reads. Due to the nature of PCR, errors have a chance to occur in each cycle and due to the number of cycles needed errors will be present throughout capture sequencing data. The project will aim to evaluate the severity of these errors and develop a workflow/pipeline or standalone software to deal with them in a sufficient and well-informed manner.
Pan-genome graph alignment) Sequencing data has traditionally been aligned to a single or several linear reference genomes. This comes with clear limitations when looking at variation between many species or across taxon levels. A possible solution to this is pan-genome graphs which can catch all the variation in a single alignment. This project will examine the potential use of pan-genome graphs as an alignment tool for hybridization capture data, utilizing the smaller regions of interest associated with capture.
This research is expected to result in a suite of bioinformatic tools and methodological frameworks that will enhance the analysis of hybridization capture data. The outcomes will have broad applicability in fields such as ancient DNA research, ecological genomics, and evolutionary biology, and will contribute to improving the resolution and interpretability of genomic data recovered from complex and degraded samples. The project is focused on drylab methods and will not contain any wetlab experimentation, but a strong knowledge and hands-on experience with existing wetlab protocols is assumed necessary for the phd project.
Secondly, the hosting centre, the CAEG Center of Excellence, is devoted to the generation of ancient environmental genomes as part of a diverse suite of projects spanning million-year-old material from extreme arctic environments to DNA sequencing data from lost civilizations in southeast Asia. The Ph.D. candidate will have the opportunity to develop programs to facilitate and possibly drive the data analyses of one or more of these large projects.
Principal supervisor is Thorfinn Sand Korneliussen, Globe Institute, tskorneliussen@sund.ku.dk, +4550433250.
Start: September 1st 2025 or as soon as possible hereafter
Duration: 3 years as a PhD fellow
Job description
Your key tasks as a PhD fellow at SUND are:
- Carrying through an independent research project under supervision.
- Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
- Participating in active research environments including a stay at another research team.
- Obtaining experience with teaching or other types of dissemination related to your PhD project
- Teaching and disseminating your knowledge.
- Writing a PhD thesis on the grounds of your project
Applicants must have qualifications corresponding to a master’s degree related to genomics, computer science, or mathematics degree with good results and good English skills. Previous publications (if any) and relevant work experience will also be considered criteria for assessing your qualifications.
Requirements for the applicants are:
- MSc degree in Ecology, Evolution, Biology, bioinformatics or other relevant field.
- Proficiency in spoken and written English
- Completed formal courses in introductory programming
- Has proven experience with the analyses and interpretation of high-throughput sequencing data
- has experience and a strong interest in population genetics and statistical genetics
- has experience with programming languages such as R and Python.
- has experience working in Linux, using command line interfaces and remote access.
- has experience with slurm cluster environments
- has experience in working with genetic data, including low-depth sequencing data
- The grade point average achieved
- Professional qualifications relevant to the PhD project
- Previous publications and relevant work experience
- Other professional activities
- A curious mindset with a strong interest in computational biology
- Language skills
- Is highly motivated, reliable, and able to work independently in a structured manner
- has good communication skills
- Knowledge of lab protocols for hybridization capture
- Understanding of advantages and challenges of capture protocols and the generated data
- Completed formal courses in the analysis of large genetic data sets including NGS data
Place of employment
The place of employment is at the Section for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K.
About Globe Institute
The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: http://www.globe.ku.dk/.
The Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See website for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. The university offers a variety of services for international researchers and accompanying families.
Terms of employment
The average weekly working hours are 37 hours per week.
The position is a fixed-term position limited to a period of 3 years. The starting date is September 1st 2025 or as soon as possible hereafter.
The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen.
The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.
Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at 30,800 DKK/approximately 4,100 EUR (April 2025 level) plus pension.
Questions
For specific information about the PhD fellowship, please contact the principal supervisor.
General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/
Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:
1. Motivated letter of application (max. one page)
2. CV incl. education, experience, language skills and other skills relevant for the position
3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science
4. Publication list (if possible)
Application deadline: 4 June 2025, 23:59 GMT+2.
We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.
The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.
The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.
Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.
You find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/
The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.
The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.