About & Academic CV
I am Md. Hridoy Ahmed, a molecular geneticist working on the genetic basis of complex disease. I generate my own data - DNA extraction, PCR, Sanger sequencing, targeted panels and exomes on patient cohorts - and interpret it computationally. My question is which inherited variants carry disease risk, and what those variants actually do.

Md. Hridoy Ahmed
Molecular Geneticist · Disease Variant Genomics
Academic Profile
I am a molecular geneticist working on the genetic basis of complex disease. My research begins at the bench: extracting DNA from patient samples, optimising PCR, running gels, and calling variants from Sanger chromatograms - then carrying those calls through targeted panel and whole-exome sequencing to an annotated, interpretable result. The computational half of my training exists to serve that question, not to replace it.
I completed both my B.Sc. and M.Sc. in Genetic Engineering and Biotechnology at the University of Chittagong, finishing among the top ranks of my cohort. My M.Sc. thesis profiled MMP-1, MMP-3 and MMP-9 variants in apical periodontitis influenced by diabetes - a study I ran end to end, from sample handling through to variant interpretation. That work set the pattern for everything since.
At the Functional Genomics & Proteomics Laboratory I now work across three bench-led cohort studies with manuscripts in preparation: the first ADPKD variant spectrum reported from Bangladesh, across a nine-gene cystic kidney disease panel in 37 patients; a combined Sanger and whole-exome study of polycystic ovary syndrome in 300 patients and 300 matched controls; and a genomic-epidemiology survey of 38 ESBL-producing Escherichia coli isolates across three regions of the country.
My published record reflects how I built the interpretive half of that toolkit. I have three first-author articles - two in Q1 journals - covering structure-based antiviral design against the Chikungunya RdRp, immunoinformatics-driven vaccine design for the Mpox virus, and a Wiley review on molecular pharming. A fourth paper, on which I am corresponding author, maps the regulatory landscape around breast cancer risk variants: the same annotation step I apply to the clinical cohorts above.
Beyond my own projects, I founded BioPC, a research and training community that has supported more than three thousand learners across several countries. Through it I have mentored students, led collaborative research, and run hands-on bioinformatics workshops and national olympiads.
Mission
To establish the genetic basis of complex disease in populations that genomics has largely overlooked - generating the data at the bench, interpreting it rigorously, and making the training that requires reach students who would otherwise go without it.
Philosophy
Good science is patient and honest. I prefer results that survive validation across methods over findings that merely look striking. I also believe knowledge grows when it is shared, which is why teaching and open mentorship sit at the centre of my work.
Goals
I am pursuing doctoral study in human molecular genetics, working on disease-associated variation in patient cohorts. My aim is an independent, laboratory-based research line on the functional consequences of inherited variants in complex disease.
Education
M.Sc. (Thesis) - Genetic Engineering & Biotechnology
2023 – 2025University of Chittagong · First Class, 2nd Position · CGPA 3.94 / 4.00
- Thesis: Molecular Mechanisms of Apical Periodontitis Influenced by Diabetes via MMP-1, MMP-3 and MMP-9 Variant Analysis.
- Techniques: DNA extraction and quantification, PCR/qPCR, Sanger sequencing, whole-exome sequencing QC, and variant annotation.
B.Sc. (Honours) - Genetic Engineering & Biotechnology
2019 – 2023University of Chittagong · First Class, 4th Position · CGPA 3.89 / 4.00
- Maintained first class standing across every academic year.
- Key coursework: Molecular Biology, Genetics, Genomics, Microbiology, Immunology, Recombinant DNA Technology, Cell Signalling, Bioinformatics, and Clinical Biotechnology.
Research Experience
Research Associate, Functional Genomics & Proteomics Laboratory
2025 – PresentVariant 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.
Thesis Researcher, Functional Genomics & Proteomics Laboratory
2024 – 2025Variant analysis across diabetes and periodontitis.
- PCR and qPCR, Sanger sequencing, and gel electrophoresis.
- NGS data analysis with GATK, Hisat2, BWA, VCFtools, and SAMtools.
Summer Research Intern, Alternative Medicine & Natural Product Research Lab
2023Isolation 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.
Research Intern, National Institute of Biotechnology
2023Hands-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.
Skills
Wet-Lab Skills
Sanger sequencing (preparation to chromatogram analysis) · DNA & protein isolation · Gel electrophoresis (agarose & PAGE) · PCR, qPCR & RT-PCR · Centrifugation & sample fractionation · Karyotyping · Plant extract preparation · Organic compound isolation & fractionation · Phytochemical screening · Anti-inflammatory assays (protein denaturation, membrane stabilisation) · Determination of blood components · ELISA & SDS-PAGE
Computational Biology & Bioinformatics
AutoDock, PyRx, Schrödinger Suite · GROMACS (MD simulation) · LigandScout, Discovery Studio · SwissADME / SwissModel · MarvinJS, GaussView, Gaussian, Gabedit · Cytoscape (network analysis) · STRING (protein interactions) · GEO & ArrayExpress (transcriptomics) · NAMD & VMD · MEGA (phylogenetics) · IPA (pathway analysis), DFT-based analysis · GATK (Best Practices, HaplotypeCaller), Hisat2, BWA · SAMtools, VCFtools, SnpEff · FastQC, Trimmomatic · ClinVar & gnomAD annotation, rare-variant prioritisation · Whole-genome assembly, genome annotation, RNA-seq, GWAS · SPAdes assembly with QUAST quality assessment · Prokka annotation, Panaroo pan-genome, IQ-TREE phylogenomics · In silico MLST and Mash genome-distance comparison · ABRicate with ResFinder & CARD, PlasmidFinder, MOB-suite mobility typing · Snippy SNP calling and IntegronFinder mobile-element profiling
Programming, Systems & Visualisation
R (ggplot2, Bioconductor) · Python (Biopython, Pandas, NumPy) · HTML / CSS · SPSS · Linux / Ubuntu (command line, bash scripting) · macOS · Windows · GraphPad Prism, OriginPro · LaTeX · MS Word, Excel, PowerPoint
Awards & Honours
National Science & Technology (NST) Fellowship
Government of Bangladesh. Awarded for outstanding research potential and academic excellence through a competitive national selection.
Best Research Paper Presenter - Darwin International Conference
4th Edition. Recognised for clarity, scientific rigour, and innovative methodology for the Mpox multi-epitope vaccine study.
Most Brilliant Student Award - Kishoreganj (2016)
Science category. District-level recognition for academic performance and scientific excellence.
Best Campus Representative
International Conference on Natural Science & Technology, Asian University for Women, Chittagong. Awarded for leadership and coordination.
Best Poster Presenter - Senior Category
Department of Genetic Engineering & Biotechnology, University of Chittagong. Recognised for scientific visualisation and presentation.
Grameen Bank Scholarship Recipient (2016–2017)
Awarded on the basis of merit and community contribution.
Certifications & Training
Sanger Sequencing Training
FGPL, University of Chittagong
Sample preparation and purification · Cartridge filling and sequence loading · Chromatogram interpretation and troubleshooting
Research Methodology
BRAC University (Red & White)
Research proposal writing · Scientific project design · Basic bioinformatics tools
Diabetes Course
University of Copenhagen (Coursera)
Diabetes pathophysiology · Clinical management and treatment strategies · Epigenetic factors and diet-exercise interactions
Advanced Bioinformatics & Data Analysis
NextGenHelper, India
Network construction with Cytoscape, microbiome data analysis · Python and Biopython pipelines, R and RStudio statistics · Linux workflows and NGS techniques (assembly, annotation, RNA-seq, GWAS, variant analysis)
Linux Training
Bioscience Factory Research Center, Bangladesh
Linux essentials and bash scripting for biologists · File and data handling · Pipeline automation
Professional Activities
Founder, Research Coordinator & Chief Instructor, BioPC
- Instructed 25 training programmes as chief trainer for more than 3,000 students.
- Organised two nationwide virtual bioinformatics olympiads and roughly five workshops.
- Led six research projects involving 40 trainees.
- Mentored contributors toward two Q1 journal publications.
Invited & contributed talks
- “An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine design against the Mpox virus” - Darwin International Conference - 4th Edition, India
- “A structure-based drug design approach for the identification of antiviral compounds targeting the Chikungunya virus RdRp protein” - International Conference on Natural Science & Technology - Asian University for Women
- “Immuno-informatics study targeting 20 membrane glycoproteins for B and T cell epitope prediction and multi-epitope vaccine design against Monkeypox virus” - ICSB–RSG Bioinformatics Symposium
Leadership & innovation competitions
- “Biomass Energy: Turning Organic Matter into Power” - Hult Prize - University of Chittagong
- “Discreet and Private: Sanitary Napkins Delivered to Your Home” - Startup Chattogram - Business Idea Contest