Research

Human molecular genetics of complex disease

Molecular biology first: DNA extraction, PCR and qPCR, Sanger sequencing, targeted panels and whole-exome sequencing - interpreted with computational genomics.

Research themes

Three themes, all bench-led. Each states the question it asks, the laboratory work that answers it, and the studies it covers.

Genetic Basis of Complex Disease

Bench-led

Finding the variants that carry risk in diabetes, kidney disease, PCOS, and periodontitis - genotyped in my own hands.

The question

Which inherited variants shape risk in common, multifactorial disease, and which of them actually change protein function?

Laboratory work

DNA extraction, PCR and qPCR, gel electrophoresis, and Sanger genotyping across patient and control cohorts.

Studies in this theme

OngoingM.Sc. thesis cohort
MMP1, MMP3 & MMP9 Variant Profiling in Periodontitis and Diabetes
In preparation300 patients · 300 matched controls
Common and Rare Coding Variants in Polycystic Ovary Syndrome
In preparation37 patients · 9 controls · 9-gene panel
Targeted Panel Sequencing of Cystic Kidney Disease Genes in ADPKD

Clinical Variant Discovery & Interpretation

Bench-led

Taking a patient sample from extraction through sequencing to an annotated, clinically interpretable variant call.

The question

How do we move reliably from a clinical sample to a variant call that a clinician could act on - and how do we catch the artefacts on the way?

Laboratory work

Sample preparation, targeted panel and exome library workflows, Sanger confirmation of called variants.

Studies in this theme

In preparation37 patients · 9 controls · 9-gene panel
Targeted Panel Sequencing of Cystic Kidney Disease Genes in ADPKD
Completed
Whole-Exome Sequencing: Variant Discovery Pipeline
Published175 GWAS-confirmed risk variants
Breast Cancer GWAS-Based Regulatory Variant Annotation

Genomic Epidemiology of Antimicrobial Resistance

Bench-led

Tracking resistance through bacterial isolates - whether it travels by clone, by plasmid, or by region.

The question

Is resistance in Bangladeshi clinical isolates structured by geography, or by the clones and plasmids that carry it?

Laboratory work

Isolate culture and characterisation, DNA extraction, and sequencing library preparation ahead of whole-genome analysis.

Studies in this theme

In preparation38 isolates · 3 regions
Clone- and Plasmid-Structured Resistance in ESBL-Producing E. coli

Methods

Computational biology is how the variants get interpreted, not a separate research line. Each capability below carries published work behind it - the Chikungunya and Mpox studies are where most of it was built.

Structural Modelling & Docking

Protein modelling, binding-site mapping, and binding-free-energy analysis to ask what a variant does to a structure.

Molecular Dynamics Simulation

GROMACS trajectories with RMSD/RMSF and stability profiling, used to test whether a predicted effect holds up.

Computer-Aided Drug Discovery

Virtual screening, docking, ADMET and DFT - the method behind the Chikungunya RdRp work.

Immunoinformatics & Vaccine Design

Epitope prediction and multi-epitope construct design - the method behind the Mpox vaccine study.

NGS Pipelines & Variant Calling

Reproducible workflows from raw reads to filtered, annotated variants using GATK Best Practices.

Statistical & Network Analysis

Association testing, pathway enrichment, and interaction-network interpretation in R and Python.

Full technique inventory

Laboratory & research experience

2025 – Present

Research Associate

Functional Genomics & Proteomics Laboratory

Variant analysis across diabetes, cardiovascular disease, chronic kidney disease, PCOS, and periodontitis.

Disease-associated variant discovery and interpretation.
Targeted panel and whole-exome sequencing for inherited kidney disease and PCOS cohorts.
Bacterial whole-genome surveillance: MLST, core-genome phylogenomics, and plasmid mobility typing.
PCR and qPCR, Sanger sequencing, and gel electrophoresis.
NGS data analysis with GATK, Hisat2, BWA, VCFtools, and SAMtools.

2024 – 2025

Thesis Researcher

Functional Genomics & Proteomics Laboratory

Variant analysis across diabetes and periodontitis.

PCR and qPCR, Sanger sequencing, and gel electrophoresis.
NGS data analysis with GATK, Hisat2, BWA, VCFtools, and SAMtools.

2023

Summer Research Intern

Alternative Medicine & Natural Product Research Lab

Isolation and screening of nanophytocompounds with computational and laboratory validation.

Nanophytocompound isolation and purification.
Antioxidant and antimicrobial assays in animal models.
Molecular docking and dynamics simulation for compound screening.

2023

Research Intern

National Institute of Biotechnology

Hands-on exposure to Sanger sequencing and next-generation sequencing workflows.

Sanger sequencing and NGS workflow exposure.
DNA extraction, PCR amplification, and gel visualisation.
Training on molecular instrumentation.