PhD Fellowship in Palaeoproteomics at the Globe Institute Faculty of Health and Medical Sciences University of Copenhagen

The Evolutionary Palaeoproteomics research group, led by Associate Professor Enrico Cappellini, is looking for a highly competent, motivated, and dynamic PhD Fellow for a 3-year full-time position starting on the 1 February 2024, or immediately thereafter.

Our group and research
The position is funded partially (80%) by the ERC Advanced Grant “BACKWARD - Overcoming the Frontiers of Biomolecular Studies on Human History and Adaptation Using Palaeoproteomics” awarded to Enrico Cappellini and partially (20%) by other funds already available to Enrico Cappellini. BACKWARD aims to advancing knowledge about the evolution and variation of hominin and other mammalian species that went extinct millions of years ago, by retrieving and sequencing proteins from palaeoanthropological remains, beyond the limits of ancient DNA preservation.

The Evolutionary Palaeoproteomics research group is based at the Globe Institute, a department in the Faculty of Health and Medical Sciences at the University of Copenhagen. The Globe Institute main purpose is to address basic scientific questions through interdisciplinary approaches. The Institute conducts research into, among other topics, the origin, evolution and diversity of the universe, the Earth and life. Within the Globe Institute, the Cappellini Group is part of the Section for GeoGenetics. The GeoGenetics section uses genomics, metagenomics and proteomics to study, among other topics, evolution and human-environment interaction. The section uses state-of-the-art technologies to break scientific boundaries to pursue cross-disciplinary research.

Information on the Globe Institute can be found here
 

Project description
In Africa, the Plio-Pleistocene hominin fossil record is represented by a diversity of species within the genera Australopithecus, Paranthropus, and Homo. In some cases, these species overlapped in time and space. This project will involve extraction of ancient protein remains from Plio-Pleistocene hominin dental enamel specimens from Africa. This will be followed by reconstruction of the hominin dental enamel protein sequences and comparison to the homologous sequences from modern and extinct hominin species to infer their phylogenetic position in the hominin tree. Such an achievement will represent a breakthrough in biomolecular-based hominin phylogeny as both ancient DNA and ancient skeletal proteins are generally considered challenging to retrieve from the Early Pleistocene African hominin fossil record. Finally, ancient protein analysis can also be used to determine the sex of fossil mammalian teeth and consequently to distinguish whether their morphological variation derives from either sexual dimorphism or taxonomic diversity.

The principal supervisor is Associate Professor, Enrico Cappellini, Globe Institute, ecappellini@sund.ku.dk, Direct Phone: +45 35 32 13 38.
 

Job description
Your key tasks as a PhD student at SUND are:

• Carry through an independent research project under supervision.

• Comple PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participate in active research environments including a stay at another research team.
• Obtain experience with teaching or other types of dissemination related to your PhD project
• Teach and disseminate your knowledge.
• Write a PhD thesis on the grounds of your project
• Communicate your scientific activity to a broad audience, for example through outreach activities, public lectures, podcasts, and social media
   

Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. biochemistry, proteomics, molecular biology, evolutionary biology, paleoanthropology, paleontology, or similar discipline. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

• A curious mind-set with a strong interest in human evolution, proteomics and ancient biomolecules,
• Proficient communication skills in written and spoken English,
• Evidence for excellent prior academic performance
• Very good knowledge of protein biochemistry and/or ancient biomolecules degradation processes,
• Very good knowledge of human evolution studies,
• Demonstrated experience in designing, implementing, and optimizing analytical methods for: sample preparation, genomic and/or tandem mass spectrometry (MS)-based proteomics data generation, and data interpretation in high-throughput ancient DNA and/or ancient protein experimental workflows,
• Experience in protein identification and/or amino acid/DNA sequence reconstruction from on MS/MS-based (palaeo)proteomics and/or (palaeo)genomic data,
• Demonstrated experience in statistical validation of (palaeo)proteomics and/or (palaeo)genomic data and results,
• Ability to write, with a high level of independence, scientific manuscripts, reporting the original results generated, for publication in high-impact, peer-reviewed journals.
• Ability to work both independently and as a team member in a highly interdisciplinary environment with colleagues with different scientific backgrounds.

Desirable criteria for the assessment include:

• You have demonstrated hands-on experience in operating LC-MS instruments for proteomic or peptidomic analysis,
• You have demonstrated experience in computationally processing and interpreting data generated by LC-MS-based proteomic or peptidomic analysis,
• You have demonstrated experience in preparing samples for MS-based palaeoproteomic analysis,
• You have demonstrated experience in working with low amounts of highly degraded protein/compound traces,
• You have demonstrated experience in computationally processing LC-MS data by writing and executing command line scripts,
• You have demonstrated experience using, and writing scripts for, software for statistical data analysis, such as “R”,
• You have demonstrated experience in acquiring and processing morphometric data from hominin fossils.
   

Place of employment
The place of employment is at the Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. The Globe molecular biology labs are a core lab facility for the research groups at the institute. The facility is divided into a dedicated clean lab, exclusively designated for ancient biomolecules such as DNA and proteins, and a general molecular biology lab at separate locations. The clean labs are subdivided into human and non-human sections. The labs have positive pressure of filtered air, air-locks, UV-light etc., and all work is conducted in full-body suits protecting the lab products. The Mass Spectrometry analysis of ancient proteins takes place at the Novo Nordisk Foundation Center for Protein Research (CPR), also part of the University of Copenhagen. The proteomic research platform at CPR is equipped with world-leading technology, to provide technical support and maintenance to provide analytical proteomics support for CPR research groups.
 

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 start date is the 1 February 2024 or immediately thereafter.

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. This requires submission and acceptance of an application for the specific project formulated by the applicant.

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 qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your
pension fund.

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 without a picture, 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: 30 November 2023 23.59pm CET

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: https://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.