Connecting genomes to human health.
Working across clinical and pathogen genomics, with experience in inherited disorders, cancer, infectious diseases and genomic surveillance.
I am a Research Scientist in the Department of Virology, National Institute of Health, Islamabad, Pakistan, with more than ten years of experience connecting laboratory methods, sequencing, bioinformatics and genomic interpretation.
Clinical genomics · Rehman Medical Institute · October 2015–January 2021
As a Scientific Officer at the Center for Genomic Sciences, I worked on whole-exome and targeted-panel sequencing for inherited disorders and cancer. My responsibilities combined laboratory work, bioinformatic analysis, germline and somatic variant review, and clinician-facing reporting supported by reference databases and published literature. I contributed to research on thalassemia, familial deafness and oral cancer.
Clinical experience · Related publications
Pathogen genomics · NIH Islamabad · April 2021–present
My work supports surveillance and outbreak investigations involving emerging, re-emerging and other priority pathogens, using clinical and environmental samples. It spans molecular biology, Illumina and Oxford Nanopore sequencing, metagenomics, comparative genomics, phylogenetics and public-health reporting. I develop documented analysis workflows and maintain Pakistan's public SARS-CoV-2 Nextstrain Community build.
Pathogen genomics experience · Related publications
- Laboratory and sequencing: DNA/RNA workflows, whole-exome and targeted-panel sequencing, amplicon and metagenomic libraries; Illumina, Oxford Nanopore and Ion Torrent.
- Analysis and interpretation: sequence-quality review, mapping, assembly, variant interpretation, consensus generation, comparative genomics and phylogenetics.
- Reproducible workflows: Linux, Python and R; documented pipelines using Nextstrain, Snakemake and Nextflow.
- Reporting and training: evidence-based interpretation, technical reports, standard operating procedures and practical bioinformatics teaching.
These repositories focus on pathogen genomics and reproducible analysis. My clinical genomics experience and related papers are linked above.
| Project | What it covers | Related evidence |
|---|---|---|
| Pathogen Discovery Pipeline | Host subtraction and competitive confirmatory mapping for cautious metagenomic interpretation | Citable release |
| Pakistan SARS-CoV-2 Nextstrain Build | Reproducible analysis and public visualization for genomic surveillance | Live community build |
| Dengue Outbreak Analysis | DENV-1 and DENV-2 genome reconstruction, evolutionary comparisons and mutation analysis | Publication |
| Conjunctivitis Outbreak Analysis | Coxsackievirus A24 variant screening, genome reconstruction and evolutionary comparisons | Publication |
| Respiratory Virus Outbreak Analysis | Respiratory syncytial virus (RSV-A and RSV-B) genomes, evolutionary comparisons and mutations | Publication |
| Viral Genomics Nextflow Demo | A synthetic FASTQ-to-report demonstration with quality checks, mapping, masked consensus and HTML reporting | Citable release |
Explore more projects · Clinical and pathogen genomics publications · Google Scholar
FASTQ to Phylogeny: Bioinformatics on a Windows PC is an ongoing practical series for learners moving from wet-lab work into bioinformatics. The lessons include step-by-step commands, slides and small practice datasets.
Start the series · Training and workshops
- Website: syedadnanhaider.com
- Email: adnan.haider@nih.org.pk
- LinkedIn: Syed Adnan Haider
- ORCID: 0009-0008-7426-6561