Research Fellow (Postdoctoral) – School of Biosciences – 107071 – Grade 7 Full-time

Post-Doctoral Position in Metagenomic Sequencing

The ARTIC network and the NIHR Health Protection Research Unit (HPRU) in Public Health Genomics are seeking a post-doctoral position to develop 'broadband' metagenomic sequencing capabilities for rapid detection and characterization of emerging and unknown pathogens. This role will advance cost-effective, rapidly-deployable metagenomic sequencing across diverse sample types and pathogen classes.

Key focus areas include dramatically reducing sequencing costs through optimized workflows and open-source reagents, simplifying complex clinical metagenomic protocols, improving sensitivity through novel amplification and extraction methods, and developing long-read metagenomics approaches for reference-quality genome assembly. This work will enhance preparedness for future outbreaks by enabling metagenomic surveillance that maintains both targeted sensitivity for known pathogens and untargeted capability for novel pathogen discovery.

Role Summary

• Develop cost-effective metagenomic sequencing workflows compatible with ARTIC field-deployable approaches and applicable across RNA viruses, bacteria, fungi, and parasites
• Design and validate hybrid strategies such for SMART-Seq or multiplex PCR methods to improve sensitivity for low-biomass samples
• Optimise host-depletion and pathogen-enrichment strategies for diverse sample types including blood, respiratory samples, urine, milk, water, and air
• Develop and validate extraction methods optimized for long-read metagenomics, including lysis approaches for difficult-to-lyse organisms
• Contribute to the development of standardized controls and mock communities for robust cross-site comparison of metagenomic methods
• Contribute to the development bioinformatic pipelines for long-read metagenomics, clinical metagenomics and assembly and taxonomic classification of metagenome-assembled genomes (MAGs).

Main Duties

• Design, execute, and analyze experiments to develop and validate metagenomic sequencing protocols for DNA/RNA and combined workflows
• Optimise library preparation workflows incorporating SMART-9N and related template-switching methods to increase complexity and sensitivity and reduce costs
• Develop and test hybrid enrichment strategies balancing targeted pathogen detection with untargeted discovery capabilities using combinations of gene-specific and random primers
• Apply knowledge in a way which develops new intellectual understanding
• Contribute to developing new models, techniques and methods
• Disseminate research findings for publication, research seminars etc
• Optimise host-depletion methods (e.g. Saponin/DNase) across diverse sample types and evaluate performance using standardized controls
• Develop application-specific protocols for challenging sample types including blood samples, clinical swabs, water/air samples, stool, and sludge
• Create and validate extraction formulations optimized for Gram-positive bacteria and fungi, including evaluation of novel fungal lysis compounds for key pathogens (Cryptococcus neoformans, Candida auris)
• Establish extraction methods that preserve DNA integrity for long-read sequencing and evaluate current methods against novel approaches
• Design and produce modular mock community controls that are sample-realistic, consistent, safe, and stable for shipping between sites to enable standardized method validation
• Develop host and vector species identification methods from residual mRNA or mitochondrial DNA data for zoonotic and vector-borne disease investigations
• Contribute to the development of analysis pipelines for assembly and polishing of large long-read metagenomic datasets (e.g. PromethION scale) to generate reference-quality metagenome-assembled genomes (MAGs)
• Document all methods as clear, reproducible standard operating procedures
• Collaborate with international partners in Africa (INRB, WACCBIP, KWTRP) and with UKHSA/HPRUs to validate protocols and perform cross-site comparisons
• Contribute to training materials, virtual workshops, and open-source community engagement to facilitate global adoption of developed methods
• Prepare scientific manuscripts for peer-reviewed publication and present findings at national and international conferences
• Work collaboratively within multidisciplinary teams across both projects and communicate effectively with stakeholders in genomics, bioinformatics, microbiology, and public health

Person Specification

• First degree in area of specialism and normally, a higher degree relevant to research area or equivalent qualifications
• High level analytical capability
• Ability to communicate complex information clearly
• Fluency in relevant models, techniques or methods and ability to contribute to developing new ones
• Ability to assess resource requirements and use resources effectively
• Understanding of and ability to contribute to broader management/administration processes
• Contribute to the planning and organizing of the research programme and/or specific research project
• Co-ordinate own work with others to avoid conflict or duplication of effort
• Knowledge of the protected characteristics of the Equality Act 2010, and how to actively ensure in day to day activity in own area that those with protected characteristics are treated equally and fairly

Informal enquiries to Joshua Quick, email: j.quick@bham.ac.uk