Postdoctoral Researcher in Bioinformatics & Ancient Proteomics

Postdoctoral Researcher in Bioinformatics & Ancient Proteomics

About the CODICUM Project
The CODICUM project, funded by the European Research Council, is an ambitious, multi-disciplinary initiative exploring the rich world of medieval manuscript fragments in Northern Europe (c. 1,000-1,500 AD). This project uses a combination of traditional manuscript studies, cutting-edge scientific analysis, and innovative digital techniques to reconstruct lost books, map knowledge networks, and reveal the hidden histories of this fascinating era. A core element of this work is the application of biomolecular methods to parchment and other manuscript components, including genomics and proteomics.

Job Description
We are seeking a highly motivated and skilled Postdoctoral Researcher to lead the bioinformatics analysis of ancient protein mass spectrometry data generated within the CODICUM project. This position will focus on analyzing ZooMS data from parchment to investigate the patterns and groups within the collection of medieval manuscript fragments in order to explore their origins, manufacturing and relationships within Northern Europe.

The successful candidate will work within an interdisciplinary research team and will be responsible for:

• ZooMS and LC-MS/MS high-throughput processing and analysis:
  • Developing pipelines for processing MALDI-TOF MS data for ZooMS, species identification, estimation of deamidation and identification of taxonomic markers.
  • Analysing LC-MS/MS data for identification of peptides, proteins and PTMs.
  • Establish best practices for open data in ZooMS, applying FAIR principles for sharing data in the wider ZooMS community.
  • Identify samples for further analysis using tandem mass spectrometry (LC-MS/MS) and DNA sequencing.

• Statistical Analysis:
  • Perform unsupervised cluster analysis in order to identify groups from different parchment production centers and networks.
  • Conducting statistical analyses of the ZooMS data to test hypotheses about livestock economy and parchment manufacturing centers.
  • Interpreting results in the context of archaeological, historical, and textual evidence.

• Data Integration & Collaboration:
  • Integrating the data and metadata of results obtained via ancient proteomics, and those obtained by the project partners in genomics, palaeography, history and other disciplines.
  • Aid in the analysis of genomic data obtained from the parchment.
  • Collaborating with other team members (including biologists, archaeologists, historians, and manuscript specialists) to interpret results and disseminate findings.
  • Generating the data sets required for long-term preservation and inclusion in Open Science resources.

• Dissemination & Publication:
  • Presenting research findings at conferences and workshops.
  • Preparing manuscripts for publication in peer-reviewed journals.

• Supervision and teaching:
  • Supervising junior researchers.
  • Teaching and organising workshops for computational tools for ZooMS and palaeoproteomics.

Essential Qualifications

• A PhD in Palaeoproteomics, Bioinformatics, Mass Spectrometry, or a related field.
• Proven experience in proteomics data analysis, including MALDI-TOF MS and LC-MS/MS.
• Proficiency in programming languages Python and/or R to develop scripts, pipelines and tools.
• Strong statistical and analytical skills and experience with specialised statistical packages.
• Familiarity with the challenges of ancient proteins data analysis and biomolecular archaeology.
• Excellent communication and collaboration skills.
• Fluency in English (written and spoken).

Desirable Qualifications

• Experience working with livestock genomic data.
• Experience with genomic and metagenomic analysis.
• Knowledge of the principles of ancient proteins research and handling degraded samples.
• Experience with data management best practices and FAIR principles.
• Familiarity with version control systems (e.g., Git).
• Background in archaeology or history.
• Experience working with HPC systems.

We Offer

• A full-time position with a fixed-term contract for 2 years and an opportunity to make a significant contribution to the field.
• A competitive salary commensurate with qualifications and experience.

Place of employment
The place of employment is at the Section for GeoBiology, Globe Institute, Øster Farimagsgade 5A, 1014 Copenhagen K, Denmark.

We offer a creative, dynamic, and international research environment, opportunities to participate in scientific publications and presentations, continuous professional development and access to state-of-the-art facilities and computing resources.

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 2 years. The starting date is on 1 June 2025 or after agreement.

Application Procedure

Your application should be in English and include:

• Letter of application addressing the requirements (max. one page).
• Curriculum Vitae
• A certified/signed copy of certificate(s) of education. If the PhD is not completed, a written statement from the supervisor.
• Contact information for two references.
  Please submit your application by clicking on “Apply Now” below. Only online applications will be accepted.

Application deadline: 14 April 2025, 23:59 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 University of Copenhagen wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of age, disability, gender, nationality, race, religion, or sexual orientation. Appointment will be based on merit alone.