Background information about the job or company (e.g., role context, company overview)

Aga Khan University Hospitals in Karachi, Pakistan and Nairobi, Kenya are private, not-for-profit institutions providing high quality health care. The Main Hospitals serve as the principal sites for clinical training for the University's Medical Colleges and Schools of Nursing and Midwifery in Pakistan and East Africa. Our Vision of Aga Khan University Ho...

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 or duties

• 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.

Qualifications or requirements (e.g., education, skills)

• 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.

• 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.

• 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.
• Familiarity 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.

• 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.