Improving computational methods in proteomics of ancient skeletal remains using genomic data

This is a summer student position supervised by Oded Rimon in Pontus Skoglund's lab.

Introduction to the science

The Ancient Genomics Group bridges biochemistry and genetics with archaeology and history. We apply highly sensitive molecular methods in a specialised clean room to extract and analyse highly degraded ancient DNA and proteins from skeletal remains, and use computational tools optimised to deal with genomic and proteomic data from highly damaged biomolecules. While our genomic tools are advanced and mature, our tools for proteomics are in their infancy, and require further development and validation. Robust proteomic data from archaeological skeletal remains will enable us to extend our studies of the genetics of human populations into the deeper past, when Homo sapiens was not yet the dominant hominin species on earth.

About the project

The study of aDNA (ancient DNA from archaeological remains) has significantly exceeded expectations, and led to a wide array of discoveries about human origins and migrations. However, aDNA has limited preservation, especially in hot and humid environments. Sub-Saharan Africa, where much of the human origin story has likely taken place, unfortunately falls into that category. Luckily, proteins bound to the mineral matrix of bones and teeth can outlast DNA by hundreds of millennia, opening the door to molecular insight into the human story substantially deeper in time.

After the death of an organism, their biomolecules degrade due to a complex network of biochemical processes. For DNA, these result in fragmented molecules, as well as modifications that induce sequencing errors. The field of ancient genomics has harnessed these unique characteristics to authenticate sequences as ancient, while finding ways to overcome them for sequencing endeavours. While a growing number of publications in ancient proteomics suggest it could mirror the success of aDNA, the possibility of authenticating and verifying protein sequences is still hotly debated.

We work on a diverse range of tools to address these challenges, including:

1) Parallel analysis of DNA and proteins from the same ancient individual.

2) Databases that dynamically link genomic and proteomic data.

3) Statistical frameworks to authenticate and verify peptide sequences, despite complex combinations of chemical modifications and incomplete references (e.g. extinct species).

The student could get involved in any of these efforts, depending on their background and preferences. They stand to learn the theoretical concepts of ancient biomolecule extraction and analysis, and get hands-on experience with bioinformatic approaches for aDNA and palaeoproteomics.

The Ancient Genomics Group is a multidisciplinary environment, and the student will interact with lab members of different scientific backgrounds (molecular biology, bioinformatics, archaeology, forensics) and a range of career paths (PhD students, postdocs, technicians).

Candidate background