3 PhD Fellowships in Ancient Genomics and Proteomics at the GLOBE Institute (# of pos: 3)

Updated: 3 months ago
Job Type: FullTime
Deadline: 28 Feb 2021

We are accepting applications for three PhD Fellowships in Ancient Genomics and Proteomics at the GLOBE Institute starting 1 September 2021 or as soon as possible thereafter.

The Fellowships are part of the Marie Skłodowska-Curie Innovative Training Network “ChemArch: The Organic Chemistry and Molecular Biology of Archaeological Artefacts”, funded by the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 956351.

About ChemArch

Archaeology is typically associated with excavation, studies of structures and dating of finds. However, numerous fields have developed advanced techniques and novel chemical and biological tools that are opening the door to detailed information invaluable to our understanding of ancient peoples and cultures. Multidisciplinary training is required to exploit the tremendous potential. The EU-funded ChemArch project is developing a global network of labs, manufacturers and suppliers of analytical equipment, museums and archaeologists to support a doctoral program that bridges the gap between analytical scientific approaches and archaeology. Over the course of the project, ChemArch will provide excellent training opportunities for 15 Early Stage Researchers (ESRs) who will be based at different Universities in Denmark, France, Spain, and the UK. Together, the team of ESRs will also develop best practices and tools for this exciting new field that will help us all better understand and preserve Europe's unique prehistoric artefact record. For more information, please visit the ChemArch website .

About the Fellowships

The Fellowships are 36-month fully funded PhD positions that will enable you to study for a double doctorate at the Universities of Copenhagen and York. Although you will be primarily hired at the University of Copenhagen, as part of the role you will be expected to spend a minimum of 12 months at the University of York, as well as a possible additional short period of time on secondment at a further partner organisation where specified, to advance the research objectives. We are offering three Fellowships as part of the ChemArch project and they are:

ESR3: Ancient DNA analysis of tars and resins associated with artefacts (Copenhagen/York)

ESR5: Blood from Stone: Utilizing novel extraction techniques for the removal of tightly bound molecules from mineral surfaces (Copenhagen/York)

ESR10: Genetic evidence for artefacts associated with prehistoric wine (Copenhagen/York)

For more information about each Fellowship project see below or visit the ChemArch website .

Key responsibilities

Your key responsibilities as a PhD Fellow at the Faculty of Health and Medical Sciences (SUND) of the University of Copenhagen will be to:

  • Carry out one or several independent research projects under supervision
  • Write a PhD thesis consisting of several peer-reviewed scientific articles based on the research carried out during the PhD
  • Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points
  • Gather international research experience, for example through a research visit to another research group in a different country
  • Gather important teaching experience teaching graduate and undergraduate students
  • Disseminate the scientific research results to a broader public through conference presentation and public talks
  • As an ESR within the ChemArch network, you will also be expected to:

  • Attend and actively participate in all the mandatory network wide ChemArch activities
  • Spend a minimum of 12 months at the collaborating institution (University of York)
  • Contribute to overall project aims and deliverables by actively participating and collaborating with other ESR fellows in the network
  • Communicate your scientific activity to a broad audience, for example through outreach activities, public lectures, podcasts, and social media
  • Comply with the highest standards of research integrity, as set out in the European Code of Conduct for Research Integrity
  • Eligibility criteria

    Applicants must have qualifications corresponding to a Master’s degree related to the subject area, e.g. a MSc degree in archaeology, archaeological science, biochemistry, bioinformatics, molecular biology, genetics or a related discipline.

    Further, applicants must fulfil the MSCA Eligibility and Mobility Requirements:

  • Applicants must not have resided or carried out your main activity (work, studies, etc.) in Denmark for more than 12 months in the 3 years immediately prior to their recruitment on 1 September 2021. Compulsory national service, short stays such as holidays, and time spent as part of a procedure for obtaining refugee status under the Geneva Convention are not taken into account
  • Applicants must be in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree. Full-time equivalent research experience is measured from the date when you obtained the first degree entitling you to embark on a doctorate (either in the country in which the degree was obtained or in the country in which you are recruited), even if a doctorate was never started or envisaged.
  • Key criteria for the assessment of applicants

  • The grade point average in undergraduate and graduate studies
  • Relevant work experience
  • Previous publications
  • A proven ability to work independently
  • Demonstrated proficiency in both written and spoken English
  • Detailed information about each Fellowship

    Fellowship 1 (ESR3): Ancient DNA analysis of tars and resins associated with artefacts (Copenhagen/York).

    Project description

    Birch pitch has been used as adhesive as far back as the Middle Pleistocene and recent studies have demonstrated that it is possible to recover human and non-human (microbial and faunal) ancient DNA from chewed pieces of birch pitch found on archaeological sites in Scandinavia, offering a rare snapshot of people's lives and the composition of our ancestral oral microbiome. This project will focus on the scientific analysis of ancient birch pitch from archaeological sites in Scandinavia and beyond. You will primarily be based in Dr Hannes Schroeder's research group at the GLOBE Institute in Copenhagen to carry out ancient DNA analyses of ancient birch pitch samples. Your training will focus on the recovery of ancient DNA as well as the bioinformatics analysis of the DNA sequencing data you generate. For part of the project, you will be based at the University of York to carry out experimental work at the YEAR Centre under the supervision of Dr Aimee Little. To further your understanding of ancient technologies, you will get the opportunity to spend time in the research group of Dr. Geeske Langejans at Delft University of Technology to learn in situ microscopic methods of identifying, recording and sampling hafting adhesives.

    Research group

    For the most part, you will be based in Hannes Schroeder’s research group in the Section for Evolutionary Genomics at the GLOBE Institute, University of Copenhagen. The group in Copenhagen focuses primarily on the use of ancient genomics to tackle unresolved questions relating to the human past and the history of infectious diseases and offers a dynamic and international research environment with access to state-of-the-art laboratory facilities and computing clusters.

    Principal supervisor: Associate Professor Hannes Schroeder, University of Copenhagen (hschroeder@sund.ku.dk )

    Co-supervisor: Dr Aimee Little, University of York

    Secondment opportunity: Delft University of Technology

    Start date: 1 September 2021 or as soon as possible thereafter

    Duration: 3 years (36 months)

    Assessment criteria

    • Prior experience with ancient DNA workflows (sample preparation, DNA library preparation etc.)
    • Prior experience analysing large ancient genomic datasets (experience with script programming in the languages such as R or Python is a clear advantage)
    • Ability to work both independently and as a team member in a highly interdisciplinary environment with colleagues with different scientific backgrounds
    • Ability to write scientific manuscripts for publication in peer-reviewed journals
    • Experience in developing and delivering public outreach initiatives

    Fellowship 2 (ESR5): Blood from Stone: utilizing novel extraction techniques for the removal of tightly bound molecules from mineral surfaces (Copenhagen/York)

    Project description

    The interaction between organic matter and mineral surfaces is critical to the preservation of biomolecules associated with artefacts yet this process is poorly understood. This is particularly relevant to more polar compounds such as organic acids and proteins that are notoriously difficult to extract and characterise. Proteins are known to persist when sorbed to archaeological mineral artefacts, but their low concentration (1) and difficulty of removal (2) has meant that they have been largely overlooked. You will optimise methods for the combined extraction of a diverse range of compounds from ceramics and evaluate the potential of other mineral artefacts for binding organic molecules. You will then apply optimized extraction protocol to archaeological artefacts generated across the network.

    Research group

    The fellow will join the Collins research group in the Section for Evolutionary Genomics at the GLOBE Institute, University of Copenhagen. The Collins group focuses on the recovery of protein sequences from ancient samples, in order to explore the production of use of material culture. The group offers well found labs for the analysis of ancient proteins with access to state of the art computing.

    Principal supervisor: Professor Matthew Collins, University of Copenhagen

    Co-supervisors: Associate Professor Karina Sand (University of Copenhagen) and Dr Jessica Hendy (University of York)

    Secondment opportunity: Foundation for Research and Technology Hellas FORTH (Crete)

    Start date: 1 September 2021 or as soon as possible thereafter

    Duration: 3 years (36 months)

    Assessment criteria

    • Prior experience with chemistry / biochemistry / archaeological science
    • Experience in data analysis (experience with script programming in the languages such as R or Python is a clear advantage)
    • Ability to work both independently and as a team member in a highly interdisciplinary environment with colleagues with different scientific backgrounds
    • Ability to write scientific manuscripts for publication in peer-reviewed journals
    • Experience in developing and delivering public outreach initiatives

    Fellowship 3 (ESR10): Genetic evidence for artefacts associated with prehistoric wine (Copenhagen/York)

    Project description

    Since the domestication of the grapevine some 8000 years ago, humans have largely used grapes to produce wine. Understanding the past production, transportation, and consumption of wine provides an exciting way to explore how societies change from prehistory to today. This project will unite the artefactual and biological evidence for prehistoric wine consumption. You will examine DNA present in wine vessels and archaeobotanical remains that have been recovered from archaeological sites and test the assumption that grape domestication is associated with viniculture. Your training will initially focus on the paleogenomic testing of archaeological grape seeds, as these provide the most reliable source of genetic information to explore the history of winemaking. This laboratory phase will include DNA enrichment for genetic markers of interest, a method that can be applied to a range of samples. Later training will focus on recovering DNA from ceramic vessels thought to contain wine in antiquity. Thus, the project combines established protocols as well as the high-risk/high-reward investigation of DNA from artefacts, an approach that could be applicable to other archaeological materials if DNA can be reliably recovered. You will also be trained in the bioinformatics analysis of the DNA sequencing data you generate, including metagenomics population genetics. To further your understanding of wine, you will have the opportunity to visit a wine institute where you will partake in major steps of wine production like berry harvesting, pressing, fermentation and clarification.

    Research group

    The work will be done under the supervision of Ashot Margaryan and Tom Gilbert in Copenhagen, and Nathan Wales in York. The research group in Copenhagen has a wide range of expertise, from metagenomics, conservation genomics, population genetics and much more, thereby supporting you in the laboratory and in bioinformatics analyses. During your year in York, you will be integrated in the ancient DNA group and the larger BioArCh community , where you will learn about many other applications of archaeological science.

    Assessment criteria

    Knowledge and experience of population genomics (experience with script programming in the languages such as R or Python is a clear advantage)

    Knowledge and experience of ancient DNA workflows (sample preparation, DNA library preparation, etc.)

    Knowledge and experience of analysing ancient genomic datasets

    Ability to work both independently and as a team member in a highly interdisciplinary environment with colleagues with different scientific backgrounds

    Ability to write scientific manuscripts for publication in peer-reviewed journals

    Experience in developing and delivering public outreach initiatives

    Principal supervisor: Professor Tom Gilbert, University of Copenhagen

    Co-supervisors: Dr Nathan Wales (University of York) and Dr Ashot Margaryan (University of Copenhagen)

    Secondment opportunity: Institute of Grapevine and Wine Sciences (ICVV) in La Rioja, Spain

    Start date: 1 September 2021 or as soon as possible thereafter

    Duration: 3 years (36 months)

    Application deadline: 28 February 2021 at 23:59 pm CET

    Please, read the full job advert on University of Copenhagen’s Jobportal here https://employment.ku.dk/ .

    Appæy online

    Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.


    View or Apply

    Similar Positions