How can genomic surveillance detect viral threats earlier?
Integrating molecular assays, metagenomic discovery, targeted sequencing, and clinical and environmental sampling to identify credible signals before outbreaks become obvious.
Genomics since 2015
Pathogen genomics for public-health action.
Research Scientist in the Department of Virology, National Institute of Health, Islamabad, Pakistan. I connect molecular biology, laboratory sequencing, reproducible bioinformatics, and genomic surveillance across emerging, re-emerging, and other priority viral pathogens—including poliovirus—to produce evidence that public-health teams can use.
Maintaining Pakistan SARS-CoV-2 Nextstrain Community Build ↗
M.Phil. Biotechnology & Genetic Engineering
2015– Clinical & public-health genomics
Open Versioned, DOI-backed workflows
New · Practical beginner series
Bioinformatics on a Windows PC
From FASTQ to Phylogeny. Small, practical exercises for wet-lab scientists and first-time bioinformatics learners.
Explore the series →Compare three practice datasets and interpret quality, adapter, and library-pattern warnings before deciding what to do next.
Open Part 5 →Research interests & selected directions
From pathogen detection to public-health action.
I am interested in how integrated molecular and computational approaches can detect viral threats earlier,
explain how they spread and evolve, and turn genomic evidence into practical surveillance systems.
These themes define a core direction while remaining adaptable to adjacent questions in pathogen genomics,
bioinformatics, molecular surveillance, and public-health implementation.
Read the full research agenda ↗
What can viral genomes reveal about transmission and evolution?
Phylogenetics, phylodynamics, variant and antigenic-site interpretation, and epidemiological context to distinguish introductions, sustained transmission, and meaningful change.
How can advanced genomic methods become routine public-health practice?
Reproducible workflows, public-safe data, traceable reporting, SOPs, and training that make sequencing useful and sustainable in resource-limited settings.
How do pathogen evolution, immunity and ecology shape infection patterns?
Combining genomic and epidemiological evidence with statistical modelling to understand why infection patterns change across populations and over time.
Research, collaboration & training
Current work · Islamabad, PakistanDepartment of Virology · National Institute of Health ↗
DDNS project collaborationImperial College London ↗
Training providerWellcome Connecting Science ↗
Training providerDuke-NUS Medical School ↗
Training providerUK Health Security Agency ↗
Training providerNIH Fogarty International Center ↗
Experience & education
A decade across clinical and public-health genomics.
The trajectory moves from clinical sequencing and variant interpretation to genomic surveillance, outbreak response, and deployable workflows for emerging, re-emerging, and priority viral pathogens—including poliovirus.
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Research ScientistDepartment of Virology · National Institute of Health · Islamabad, Pakistan
Work spans molecular biology, clinical and environmental sample processing, Illumina/ONT sequencing, reproducible bioinformatics, phylogenetic and phylodynamic interpretation, and public-health reporting for emerging, re-emerging, and priority viral pathogens—including poliovirus.
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Molecular Biologist & BioinformaticianDepartment of Virology · National Institute of Health · Islamabad, Pakistan
Contributed to national viral genomic surveillance, outbreak response, pathogen pipelines, phylogenetics, dashboards, and staff mentoring.
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Scientific OfficerCenter for Genomic Sciences · Rehman Medical Institute
Clinical whole-exome sequencing, targeted panels, variant interpretation, clinician-facing reporting, QC, and laboratory operations.
Selected publications
Contribution, method, and evidence.
Author position, study question, method, and primary evidence help reviewers understand the contribution—not just count papers. Explore selected publications and findings →
Genomic characterization of the Coxsackievirus A24 variant in an acute hemorrhagic conjunctivitis outbreak
Journal of Virological Methods 338, 115213
A first-author study using metagenomic next-generation sequencing and whole-genome analysis to characterize CV-A24v during the 2023 outbreak in Islamabad.
2024 · First author · Respiratory genomics
Whole-genome characterization of respiratory syncytial virus circulating in Islamabad
RSV whole-genome analysis with outbreak and mutation context.
↗ 2024 · Co-first author · Dengue Serotype and genomic diversity of dengue virus during the 2023 outbreak in PakistanDENV-1 and DENV-2 genomic diversity and phylogenetic interpretation.
↗ 2024 · Co-first author · SARS-CoV-2 Genomic epidemiology and phylogeography during and after Pakistan’s sixth waveVariant dynamics placed in temporal and geographic context.
↗ 2026 · Collaborative output · Respiratory surveillance Influenza, SARS-CoV-2, and RSV surveillance in Islamabad and RawalpindiA recent multi-pathogen genomics contribution.
↗Selected workflows & maintained public resources
Methods that can be inspected, tested, and reused.
Pathogen Discovery & Confirmatory Mapping Pipeline
A conservative, panel-driven metagenomic workflow for host subtraction, candidate screening, competitive confirmatory mapping, coverage assessment, and evidence-based follow-up.
MetagenomicsHost subtractionCompetitive mapping
signal_to_evidence.run
- 01Host subtractionRetain non-host read pairsFILTER
- 02Candidate panelCurated references + close relativesSCREEN
- 03Competitive mappingPreferential alignment evidenceMAP
- 04Evidence reviewBreadth, depth + confirmatory follow-upREVIEW
Pakistan SARS-CoV-2 Nextstrain Community Build
I maintain the reproducible analysis and publishing workflow behind the NIH Bioinformatics Group of Virology’s Pakistan-focused SARS-CoV-2 Nextstrain Community build. It combines quality control, time-resolved phylogenetic analysis, and an interactive public view for transparent genomic-surveillance communication.
- 5,104
- sequences in final public tree
- 4,942
- from Pakistan
- 162
- context sequences
NextstrainSARS-CoV-2PhylogeneticsData governance
Direct-Detection Nanopore Sequencing for Poliovirus
An auditable VP1 analysis and reporting pipeline for Oxford Nanopore MinION data, spanning barcode-folder review, reference screening, coverage assessment, consensus attempts, and structured HTML reporting.
PolioVP1MinIONONT
sample_to_report.run
- 01Barcode reviewFASTQ folders + sample mapREADY
- 02Reference screenVP1 mapping + benchmarkingSCREEN
- 03Coverage evidenceDepth, breadth + controlsREVIEW
- 04Consensus & reportFASTA + tables + HTMLREPORT
Integrated case · direct-detection nanopore sequencing
One workflow across bench, sequence, code, and reporting.
Within the NIH–Imperial direct-detection nanopore sequencing (DDNS) collaboration, I work across laboratory processing, Oxford Nanopore sequencing, analysis review, and evidence-based reporting for stool and wastewater surveillance samples.
- 01Prepare & amplifySample processing, extraction, RT-PCR, nested amplification, and controls
- 02Build & sequenceONT library preparation, barcode and sample-map review, and MinION run monitoring
- 03Review evidenceRead triage, VP1 reference screening, coverage, consensus, and run QC
- 04Interpret & reportVP1 and capsid interpretation, auditable HTML outputs, SOPs, and implementation notes
Role: Collaborative method development with Imperial College London; the public repository documents the analysis and reporting component.
GLIDE Falcon Award Project
Contributed Illumina MiSeq workflow development and automated analysis for culture-positive sewage surveillance samples within this NIH-led deep-sequencing initiative.
PoliovirusIllumina MiSeqGenomic surveillance
Whole-Capsid Genomic Analysis for Poliovirus Surveillance
A reproducible Illumina and Snakemake workflow for consensus generation, coverage assessment, antigenic-site interpretation, and phylogenetic analysis of post-culture data.
SnakemakeIlluminaPhylogeny
Phylodynamics and Phylogeography for Viral Surveillance
A reproducible R workflow demonstrated with wild poliovirus type 1 using public-safe synthetic data.
WPV1RGIS
Training & scientific engagement
From specialist training to practical capacity building.
Selected specialist training, scientific exchange, facilitation, and hands-on teaching across Pakistan, the United Kingdom, Malaysia, and Singapore.
2026 Training delivered · National Institute of Health, Islamabad
2025 Polio Sequencing Consortium · London
2024 NGS Bioinformatics · Malaysia
2023 Viral genome & metagenomic sequencing · Duke-NUS, Singapore
2016– Facilitation, speaking, and staff mentoring
Explore training & photographs →
The work, end to end
From sample to defensible evidence.
One connected workflow across laboratory practice, computation, quality review, and communication.
- 01SampleClinical & environmental surveillance
- 02SequenceNanopore, Illumina & Ion Torrent
- 03QualityControls, depth & traceability
- 04InterpretConsensus, variants & phylogeny
- 05CommunicateReports, repositories & training
Research notes
Practical reasoning behind the workflow.
Peer review & professional service
Contributing to rigorous and reusable research.
I contribute through open peer review, invited journal review, and professional communities focused on pathogen genomics and infectious diseases.
10 public PREreviews
Published reviews across pathogen genomics, wastewater surveillance, phylodynamics, and infectious-disease epidemiology.
View public PREreview profile ↗ Public profile count · August 2026BMC Infectious Diseases
Currently providing confidential manuscript peer review for the journal.
Visit the journal ↗ Manuscript details remain confidentialPHA4GE
Member of the Public Health Alliance for Genomic Epidemiology Bioinformatics Pipelines and Visualization Working Group.
View the working group ↗ Public-health bioinformatics community
Memberships & study groups
American Society for Microbiology
Global Outreach – Contributing Member · 2026 · Certificate ↗
European Society of Clinical Microbiology and Infectious Diseases
LMIC member · May 2026–May 2027
Study groups: Respiratory Viruses (ESGREV) · Public Health Microbiology (ESGPHM) · Genomic and Molecular Diagnostics (ESGMD)
What I bring
Bench-to-report practice. Reproducible analysis. Public-health purpose.
My work spans molecular and virology workflows, Illumina and Oxford Nanopore sequencing, reproducible bioinformatics, quality systems, public-database submission, technical reporting, and staff development.
01Bench & sequencingDNA/RNA workflows, amplicon and metagenomic libraries, Illumina, Ion Torrent, and MinION
02BioinformaticsPython, R, Bash, Snakemake, Nextflow, metagenomics, variants, and phylogenetics
03Quality & implementationAcceptance criteria, run review, SOPs, traceability, reports, and public submissions
04Capacity buildingPractical training, mentoring, runbooks, and reusable teaching material
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