Instructor (Research), Department of Paediatrics and Child Health

Entity Aga Khan University

Location Karachi, Pakistan

Employment Type: (Contractual based)

Introduction

The Outreach and Research Program of the Department of Paediatrics and Child Health have ten community-based field sites across Pakistan (including four in Karachi) and focuses on research for the betterment of women and child health. The Department has a Nutritional Research Laboratory as well as an Infectious Disease Research Laboratory that cater to the needs of its research projects. It has well-acclaimed work to its credit both at the national and international level.

As an equal opportunity employer, AKU believes in promoting a diverse and inclusive culture and is committed to adopt appropriate standards for safeguarding and promoting a respectful relationship with and between diverse workforce of its faculty, staff, trainees, volunteers, beneficiaries, wider communities, and other stakeholders with whom it works, including children and vulnerable adults and expects all employees/trainees and partners to share this commitment.

About the Role:

We are looking for a detail-oriented and analytical Bioinformatician to join our genomics and precision medicine team. The ideal candidate will analyze next-generation sequencing (NGS) data, develop and optimize bioinformatics pipelines, conduct genomic analyses, and support clinical diagnostics and research initiatives.

This role is ideal for professionals passionate about genomics, molecular biology, and translating complex genetic data into meaningful scientific and clinical insights.

The Aga Khan University invites applications for the position of Instructor (Research) in the Department of Paediatrics and Child Health.

Job Role / Responsibilities:

• Develop, implement, maintain, and optimize reproducible bioinformatics pipelines for human genomic data analysis, including whole-exome sequencing (WES), whole-genome sequencing (WGS), targeted gene panels, and long-read sequencing data.

• Perform sequence quality assessment, read preprocessing, alignment, variant calling, normalization, annotation, filtration, and downstream analysis using established bioinformatics tools and workflows.

• Design, automate, validate, and optimize end-to-end genomic analysis platforms and computational workflows to improve efficiency, reproducibility, and scalability.

• Analyse, interpret, classify, and prioritize genetic variants according to ACMG/AMP guidelines and current Clin-Gen recommendations by integrating sequencing quality metrics, inheritance patterns, segregation analysis, phenotype correlation, population frequency, and published clinical evidence.

• Review scientific literature and genomic databases, including Clin-Var, OMIM, gnom-AD, DECIPHER, HGMD, dbNSFP, Franklin, Gene-Be, Exomizer, and related resources, to support accurate variant interpretation.

• Support faculty and researchers in planning, designing, and executing genomics research projects by recommending appropriate bioinformatics methodologies and analytical approaches.

• Prepare high-quality clinical, scientific, and technical reports, quality-control summaries, data visualizations, and documentation for manuscripts, grant applications, and research publications.

• Coordinate the secure transfer, storage, retrieval, and management of genomic datasets while maintaining reproducible workflows, reference databases, software environments, and analytical documentation.

• Collaborate with clinicians, clinical geneticists/genetic counselors, molecular pathologists, laboratory scientists, bioinformaticians, IT teams, researchers, and external collaborators to support clinical diagnostics and genomics research.

• Contribute to validation studies, software development, workflow improvement, scientific publications, conference presentations, and institutional knowledge resources.

• Participate in training sessions, workshops, and mentoring activities to strengthen institutional capacity in genomics and bioinformatics.

• Stay current with advances in genomics, molecular diagnostics, bioinformatics, artificial intelligence, and precision medicine, and evaluate emerging technologies for potential implementation.

• Perform any other duties assigned by the supervisor.

Requirements

• Master's or PhD in Bioinformatics, Computational Biology, and Biotechnology, or a related discipline.

• Demonstrated experience in genomic data analysis, variant interpretation, and bioinformatics pipeline development using Linux.

• Strong understanding of NGS workflows, including quality control, alignment, variant calling, annotation, filtering, and interpretation.

• Experience interpreting genetic variants according to ACMG/AMP guidelines and current Clin-Gen recommendations.

• Familiarity with genomic databases such as Clin-Var, OMIM, gnom-AD, DECIPHER, HGMD, dbNSFP, and related resources.

• Experience using bioinformatics software including BWA, GATK, FastQC, fastp, SnpEff, SnpSift, VEP, ANNOVAR, InterVar, Exomizer, Franklin, and related tools.

• Experience with Linux/Unix environments, workflow management, Conda, Mamba, Docker, and version control systems.

• Strong analytical, problem-solving, scientific writing, documentation, and communication skills.

• Experience working in clinical genomics, molecular diagnostics, or translational research is preferred.

  Preferred Skills

• Programming experience in Python, R, Bash, or other scripting languages.

• Experience developing automated bioinformatics pipelines, computational tools, or genomic analysis platforms.

• Knowledge of software development, workflow automation, and database integration.

• Experience with cloud computing and high-performance computing (HPC) environments.

• Familiarity with artificial intelligence and machine learning applications in genomics.

• Experience in clinical molecular diagnostic laboratories.

• Certification in Clinical Genomics, Molecular Diagnostics, or Bioinformatics is an advantage.

• Ability to work independently while collaborating effectively within multidisciplinary teams.

• Strong organizational, project management, and attention-to-detail skills.

• Commitment to continuous learning and professional development.

Comprehensive employment reference checks will be conducted.