Projects

Research Projects

One question runs through this work: which inherited variants drive complex disease, and what do they actually do. I answer it at the bench first - extraction, PCR, Sanger sequencing, targeted panels and exomes on patient cohorts - then interpret the calls computationally. The structural and immunoinformatics work below is the method I bring to that interpretation, and the record of how I learned it.

3Bench-led cohort studies

700+Samples and isolates processed

15+Research projects

BenchOngoing

MMP1, MMP3 & MMP9 Variant Profiling in Periodontitis and Diabetes

M.Sc. thesis cohort

Identify disease-associated matrix metalloproteinase variants in patients with apical periodontitis influenced by diabetes.

Methods

Genomic DNA extraction, quantification, and quality assessment
PCR amplification, optimisation, and gel electrophoresis
Sanger sequencing and chromatogram-level variant calling
Functional annotation with GATK, VEP, and ClinVar

Outcome. Novel variants identified across a Bangladeshi study population; the basis of my M.Sc. thesis.

BenchIn preparation

Common and Rare Coding Variants in Polycystic Ovary Syndrome

300 patients · 300 matched controls

Test whether common polymorphisms and rare coding variants implicate the same reproductive and metabolic pathways in Bangladeshi women with PCOS.

Methods

PCR and Sanger genotyping of five FSHR, INSR and SHBG polymorphisms in 300 patients and 300 matched controls
Whole-exome sequencing with GRCh38 alignment and GATK Best Practices variant calling
Rare-variant prioritisation, protein stability prediction, and pathway enrichment analysis

Outcome. All five polymorphisms associated with PCOS, and rare damaging variants converged on gonadotropin, insulin, and androgen signalling.

BenchIn preparation

Targeted Panel Sequencing of Cystic Kidney Disease Genes in ADPKD

37 patients · 9 controls · 9-gene panel

Describe the first ADPKD variant spectrum reported from a Bangladeshi cohort across a nine-gene cystic kidney disease panel.

Methods

Targeted sequencing of PKD1, PKD2, PKHD1 and six further cystic kidney genes in 37 patients and nine controls
Variant calling with GATK HaplotypeCaller, annotated against ClinVar and gnomAD v4
Call-set quality control by transition/transversion ratio, mapping quality, and reference-allele verification

Outcome. Fourteen pathogenic or likely pathogenic variants across PKD1, PKD2 and PKHD1, with a candidate variant in 41% of patients; one ClinVar-listed variant shown to be a mapping artefact.

BenchIn preparation

Clone- and Plasmid-Structured Resistance in ESBL-Producing E. coli

38 isolates · 3 regions

Determine whether antimicrobial resistance in Bangladeshi ESBL E. coli is structured by geography or by clone and plasmid.

Methods

Isolate characterisation, DNA extraction, and sequencing library preparation
Whole-genome analysis of 38 ESBL-producing isolates from Barishal, Chattogram and Dhaka
In silico MLST with a Prokka-Panaroo-IQ-TREE core-genome phylogeny and pan-genome modelling
MOB-suite plasmid reconstruction, mobile-element profiling, and Mash comparison against global genomes

Outcome. Seventeen sequence types resolved: a homogeneous CTX-M-15/ST131 background countrywide, with a focal, Dhaka-centred carbapenemase signal on international high-risk clones.

BenchCompleted

P53 Nanophytocompound Screening & MD Validation

Investigate natural compounds targeting P53, with computational predictions tested experimentally.

Methods

Ligand screening and in-silico toxicity prediction
100 ns molecular dynamics for stability analysis
RMSD/RMSF and free-energy profiling with animal-model bioactivity testing

Outcome. Two lead compounds validated for binding affinity and bioactivity, with laboratory results matching the computational predictions.

BenchCompleted

Sanger Sequencing & NGS Training - NIB

Gain hands-on command of Sanger workflows and next-generation sequencing instrumentation.

Methods

DNA extraction and quantification
PCR optimisation
Gel electrophoresis and sequence analysis

Outcome. Practical command of core sequencing instrumentation.

BenchCompleted

Nanophytocompound Extraction & Animal Testing

Experimentally validate two lead compounds with high binding affinity to P53.

Methods

Plant extract preparation and column chromatography
Animal-model toxicity and bioactivity testing
Correlation with computational predictions

Outcome. Laboratory results consistent with the computational binding predictions.

Published

Breast Cancer GWAS-Based Regulatory Variant Annotation

175 GWAS-confirmed risk variants

Move from statistical association to mechanism by annotating the regulatory landscape around confirmed breast cancer risk loci.

Methods

GWAS dataset curation and flanking-gene mapping
Regulatory annotation with HaploReg
Pathway mapping and functional prioritisation

Outcome. Published in Computational and Systems Oncology (Wiley) as corresponding author: a 4.8-fold excess of DNase I hypersensitivity and 15.7-fold excess of enhancer motifs among correlated variants.

Completed

Whole-Exome Sequencing: Variant Discovery Pipeline

Build a reproducible high-throughput WES workflow for disease-associated SNPs and indels, used by the cohort studies above.

Methods

Quality control with FastQC and Trimmomatic
Alignment with Hisat2 and BWA
Variant calling with GATK, downstream analysis with VCFtools and SnpEff

Outcome. A reproducible pipeline from raw reads to annotated, filtered variants.

Ongoing

Lead Optimisation for Viral Targets

Identify small molecules targeting viral membrane and polymerase proteins.

Methods

Molecular docking and energy minimisation
Binding hotspot analysis
Drug-likeness scoring

Outcome. A shortlist of optimised candidates for further evaluation.

Published

Structure-Based Drug Design Against Chikungunya RdRp

Identify lead compounds targeting the CHIKV RNA-dependent RNA polymerase.

Methods

Protein preparation and active-site mapping
Virtual screening and docking with AutoDock and PyRx
Molecular dynamics with GROMACS, plus ADMET and DFT validation

Outcome. First-author Q1 publication identifying multi-target RdRp inhibitor candidates.

Submitted

Reverse Vaccinology for C. trachomatis

Computational antigen discovery and epitope prioritisation for C. trachomatis.

Methods

Proteome mining
Subcellular localisation prediction
B/T-cell epitope mapping and population coverage analysis

Outcome. A prioritised antigen set proposed for vaccine development.

Published

Mpox Multi-Epitope Vaccine Design

Generate epitope-based vaccine candidates through a complete immunoinformatics pipeline.

Methods

CTL, HTL, and B-cell epitope screening
Molecular docking with immune receptors
Allergenicity and antigenicity profiling with in-silico cloning

Outcome. First-author Q1 publication presenting a validated vaccine construct.

Completed

Vaccine Candidate Selection for S. pyogenes

Identify conserved epitopes for rational vaccine design.

Methods

Antigenic region mapping and conservancy analysis
Adjuvant design
3D modelling and immunological simulation

Outcome. A conserved multi-epitope construct with simulated immune response.

Completed

Undergraduate Research: CHIKV RdRp Targeting

Run a complete bioinformatics pipeline for antiviral drug discovery.

Methods

Research design and protein modelling
Docking and molecular dynamics simulation
HOMO-LUMO and DFT studies

Outcome. Foundational work that led to the first-author CHIKV publication.