Research scientist in emerging, re-emerging and priority pathogen genomics, connecting molecular biology and sequencing with reproducible bioinformatics for public-health surveillance.
I work in the Department of Virology, National Institute of Health, Islamabad, Pakistan, supporting genomic surveillance of emerging, re-emerging and priority pathogens, including poliovirus. My work connects molecular biology, Illumina and Oxford Nanopore sequencing, reproducible bioinformatics, phylogenetics, dashboards, standard operating procedures and technical reporting for public-health laboratories.
- Molecular and sequencing workflows: molecular biology, Illumina sequencing and Oxford Nanopore sequencing.
- Reproducible analysis: quality control, mapping and assembly, consensus generation, phylogenetics, Nextstrain, Snakemake and Nextflow.
- Public-health translation: dashboards, standard operating procedures, technical reporting and hands-on training.
| Project | What it demonstrates | Evidence |
|---|---|---|
| DDNS MinION VP1 Analysis Pipeline | Oxford Nanopore barcode review, VP1 reference screening, consensus calling and HTML/TSV reporting | CI · Zenodo |
| Pakistan SARS-CoV-2 Nextstrain Build | Reproducible national build workflow, phylogenetic analysis and public visualization; maintained since 2022 | Live build · CI · Zenodo |
| Viral Genomics Nextflow Demo | Synthetic FASTQ-to-report workflow with Nextflow DSL2, containers and an end-to-end automated test | CI · Zenodo |
| Polio Whole-Capsid NGS Workflow | Illumina quality control, mapping, masked consensus, antigenic-site analysis and phylogeny | CI · Zenodo |
| Pathogen Discovery Pipeline | Host subtraction and competitive confirmatory mapping for cautious metagenomic interpretation | CI · Zenodo |
| CV-A24v Outbreak Genomics | Publication-linked outbreak workflow with assembly, mapping, phylogenetics and amino-acid comparison | CI · Paper |
Public, reproducible workflows reflecting methods reported in peer-reviewed studies:
- Coxsackievirus A24 variant outbreak genomics — Journal of Virological Methods (2025), DOI.
- Dengue virus genomic diversity — Journal of Medical Virology (2024), DOI.
- Respiratory syncytial virus outbreak genomics — Archives of Virology (2024), DOI.
View the complete publication record on Google Scholar →
- Genomic surveillance of emerging, re-emerging and priority pathogens, including poliovirus
- Wastewater and environmental surveillance
- Pathogen discovery, metagenomics and confirmatory mapping
- Reproducible sequencing workflows, phylogenetics and hands-on training
- Portfolio: syedadnanhaider.com
- Email: adnan.haider@nih.org.pk
- ORCID: 0009-0008-7426-6561