Research Fellow – Ancient Pathogen DNA and Medium Throughput Genomics of Modern Salmonella (78443-086)

Fixed term contract for 5 years.

This five year fellowship is associated with a £2.2M Wellcome Trust Investigator award to Professor Mark Achtman to determine How old are bacterial pathogens, and what evolutionary steps have they undergone?. The research fellow will play a key role in the sequencing and analysis of modern bacterial genomes and metagenomes from ancient DNA, with a focus on Salmonella enterica. Ancient DNA has huge potential to shed light on the evolution of pathogens.

We have already demonstrated that an ancient S. enterica genome can be reconstructed from a thousand year old human tooth, providing unique insights into evolutionary history of these bacteria. During the course of the project we will be generating hundreds of ancient DNA metagenomes from ancient human and human associated remains and sequencing ten thousand modern pathogen genomes. This unique data set will allow us to paint a historical picture of the evolution of this important vertebrate pathogen.

Generating this data will be the responsibility of the Ancient Metagenomics Fellow (AMF). The AMF will be responsible for manual extraction of DNA from 100s of archaeological samples in a dedicated aDNA laboratory, and their sequencing (Illumina NextSeq).

Secondly, the AMF will be responsible for supervising a dedicated technical assistant, and running a medium throughput, robotically assisted pipeline for isolating bacterial DNA from 10,000 bacterial isolates, and normalizing their concentrations, prior to external sequencing. Finally, the AMF will be responsible for processing sequence reads through existing software pipelines, ensuring that the data are uploaded to existing databases, and collaborating with experienced bioinformaticians in the population genetic and evolutionary analyses of these data.

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The ideal candidate will have a background in ancient DNA analyses with an interest in bioinformatics and/or population genetics. The candidate should have a first degree in natural sciences or engineering, and hold a PhD in a relevant field. Expertise in the evaluation of genomic sequences is desired, as evidenced by high quality publications in this area. The ideal candidate will also integrate tightly into an existing group of bioinformaticians and population geneticists.

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