Projects

✨ Project Summary

My research spans four interconnected domains: Genomics, Computational Drug Discovery, Immunoinformatics, and Wet-Lab Experimental Biology. I integrate molecular techniques with advanced computational workflows to investigate disease-associated variants, design therapeutic candidates, and develop immunoinformatics-driven vaccines.

12+ research projects • 5+ major disease targets • 4 interdisciplinary domains

🧬 1. Genomics & Variant Analysis

MMP3 & MMP9 Variant Profiling in Periodontitis and Diabetes

Identifying disease-associated MMP variants using wet-lab and computational workflows.
Highlights:

PCR amplification, Sanger sequencing
NGS-based variant calling
Functional annotation (GATK, VEP, ClinVar)
Novel variants identified across Bangladeshi population

Whole Exome Sequencing: Variant Discovery Pipeline

High-throughput WES analysis for disease-associated SNPs and INDELs.
Highlights:

QC: FASTQC, Trimmomatic
Alignment: Hisat2 / BWA
Variant calling: GATK
Downstream analysis: VCFtools, SnpEff

Breast Cancer GWAS-Based Variant Annotation (In preparation)

Screening population-level SNPs to identify risk-associated loci.
Highlights:

GWAS dataset curation
Manhattan and QQ plot analysis
Functional annotation & pathogenicity scoring

💻 2. Computational Drug Discovery

Structure-Based Drug Design Against Chikungunya RdRp

First-author Q1 publication on lead compound identification targeting CHIKV RdRp.
Highlights:

Protein preparation & active-site mapping
Virtual screening & docking (AutoDock, PyRx)
MD simulation (GROMACS)
ADMET & DFT validation

P53 Nanophytocompound Screening & MD Validation

Investigating natural compounds targeting P53 for therapeutic potential.
Highlights:

Ligand screening & in silico toxicity prediction
100 ns MD simulation for stability analysis
RMSD/RMSF free energy profiling
Animal model bioactivity testing (wet-lab validation)

Lead Optimization for Viral Targets

Computational identification of small molecules targeting viral membrane and polymerase proteins.
Highlights:

Molecular docking
Energy minimization
Hotspot analysis
Drug-likeness scoring

💉 3. Immunoinformatics & Vaccine Design

Mpox Multi-Epitope Vaccine Design (Q1 publication)

A complete immunoinformatics pipeline to generate epitope-based vaccine candidates.
Highlights:

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

Reverse Vaccinology for C. trachomatis (Submitted)

Computational antigen discovery and epitope prioritization.
Highlights:

Proteome mining
Subcellular localization prediction
B/T-cell epitope mapping
Population coverage analysis

Vaccine Candidate Selection for S. pyogenes

Identifying conserved epitopes for rational vaccine design.
Highlights:

Antigenic region mapping
Conservancy analysis
Adjuvant design
3D modeling & immunological simulation

🧪 4. Wet Lab Research & Internships

Sanger Sequencing & NGS Training — NIB

Hands-on experience with Sanger workflow and next-generation sequencing concepts.
Highlights:

DNA extraction & quantification
PCR optimization
Gel electrophoresis
Sequence analysis

Nanophytocompound Extraction & Animal Testing

Experimental validation of two lead compounds with high binding affinity to P53.
Highlights:

Plant extract preparation
Column chromatography
Animal model toxicity & bioactivity testing
Correlation with computational predictions

Undergraduate Research: CHIKV RdRp Targeting

Complete bioinformatics pipeline for antiviral drug discovery.
Highlights:

Research design
Protein modelling
Docking & MD simulation
HOMO–LUMO, DFT studies