Skip to content
About

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.

Portrait of Md. Hridoy Ahmed

Md. Hridoy Ahmed

Molecular Geneticist · Disease Variant Genomics

hridoy.geb.cu@gmail.com Chattogram, Bangladesh ORCID 0000-0003-2077-4401
Download CV (PDF)

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 – 2025

    University 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 – 2023

    University 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 – Present

    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.
  • Thesis Researcher, Functional Genomics & Proteomics Laboratory

    2024 – 2025

    Variant 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

    2023

    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.
  • Research Intern, National Institute of Biotechnology

    2023

    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.

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.
Visit BioPC

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