Research Associate, Department of Pathology at Aga Khan University Hospital

Job Summary

• The Department of Pathology is seeking a Research Assistant to support laboratory and bioinformatics workflows in a retrospective study investigating the prevalence, genomic diversity and antimicrobial resistance of animal -adapted Mycobacterium tuberculosis complex (aMTBC) strains. The role contributes to understanding zoonotic transmission and multidrug resistance within a One Health framework.

Responsibilities

• Retrieve and culture archived TB isolates.
• Perform PCR screening for RD9 gene extract  
• Coordinate procurement and management of study supplies and maintain inventory; to ensure availability of materials.
• Conduct flow-cell QC, sequencing runs, variant calling, phylogenetic analysis
• Maintain lab records and isolate metadata.
• Assist in preparation of figures, tables, and manuscript outputs.
• Participate in stakeholder liaison meetings. 
• Support manuscript development and contribute to dissemination activities 
• Ensuring the confidentiality and security of the collected data.

Requirements

• Master of Science in Molecular Biology, Microbiology, Genomics, Bioinformatics, or any other relevant qualification.
• A minimum of two years’ experience working with clinical teams is an added advantage.
• Measurable hands on wet lab experience working with Mycobacterium tuberculosis (MTB), including TB culturing, sample processing, biosafety level workflows, and handling of clinical isolates.
• Proven proficiency in molecular diagnostics techniques such as DNA extraction, PCR, qPCR, gel electrophoresis, and preparation of libraries for Oxford Nanopore Technologies (ONT) sequencing.
• Experience performing quality control of DNA/RNA samples, optimization of extraction protocols, and troubleshooting of lab assays in high containment environments.
• Familiar with foundational bioinformatics approaches, including FASTQ data handling, basic command line workflows, sequence quality assessment, and introductory analysis pipelines for pathogen genomics.
• Ability to integrate wet lab and genomics workflows by coordinating sample preparation with downstream sequencing and preliminary data interpretation.
• Strong documentation and adherence to biosafety protocols when working with high risk pathogens.