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Exploring the genome through computational and translational biology

I am Md. Hridoy Ahmed, a molecular genetics and computational biology researcher working where genomic variant interpretation, wet-lab molecular biology, and computer-aided drug and vaccine discovery meet.

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Md. Hridoy Ahmed

Researcher · Molecular & Computational Biology

About

A researcher between the bench and the algorithm

I am a Molecular and Computational Biology researcher with training in Genetic Engineering & Biotechnology from the University of Chittagong. My work integrates laboratory genetics, bioinformatics, structure-based drug discovery, immunoinformatics, and microbiome research to uncover the genetic drivers of complex diseases and accelerate therapeutic development. As a first-author researcher and founder of BioPC, I am committed to advancing both scientific discovery and accessible research education. My current focus is precision genomics, disease-associated variants, and computational approaches to molecular medicine

BioinformaticsDrug DiscoveryMicrobiomeComputational BiologyAI in Life SciencesResearch Communication
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First-author publications

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Research projects

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Learners mentored

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Training programmes led

Education

  • 2023 – 2025

    M.Sc. (Thesis) — Genetic Engineering & Biotechnology

    University of Chittagong

    First Class, · CGPA 3.94 / 4.00

  • 2019 – 2023

    B.Sc. (Honours) — Genetic Engineering & Biotechnology

    University of Chittagong

    First Class, · CGPA 3.89 / 4.00

Research positions

  • Research Associate

    FGPL, University of Chittagong · 2025 – Present

  • Thesis Researcher

    FGPL, University of Chittagong · 2024 – 2025

  • Summer Research Intern

    Alternative Medicine & Natural Product Research Lab · 2023

  • Research Intern

    NIB, Bangladesh · 2023

Research Interests

Where my curiosity concentrates

Eight connected areas, from the wet bench to the simulation, that together shape how I read disease and design responses to it.

Genomics & Variant Analysis

Interpreting disease-associated variants from PCR, Sanger sequencing, and whole-exome data.

Computational Drug Discovery

Virtual screening, molecular docking, and dynamics simulation for lead identification.

Immunoinformatics & Vaccine Design

Epitope prediction and multi-epitope vaccine construction against viral targets.

Structural & Systems Biology

Protein modelling, binding-free-energy analysis, and network-level interpretation.

Molecular Biology (Wet Lab)

DNA and RNA work, qPCR, electrophoresis, and sequencing from bench to chromatogram.

Cancer Biology

GWAS-based annotation and target screening for cancer-associated loci and proteins.

Bioinformatics Pipelines

Reproducible NGS workflows for quality control, alignment, and variant calling.

Precision Medicine

Linking population-level genetic variation to individual disease risk and therapy.

Scientific Expertise

Skills measured across the research lifecycle

From sample preparation at the bench to molecular dynamics on the cluster, and from analysis to writing and teaching.

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Wet-Lab Skills

PCR/qPCR, Sanger sequencing, electrophoresis, extraction, assays.

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Computational Biology

Docking, MD simulation, virtual screening, ADMET, DFT.

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Data Analysis

R, Python, NGS variant analysis, statistics, visualisation.

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Scientific Writing

Two first-author Q1 papers and ongoing manuscripts.

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Teaching & Mentorship

3,000+ learners trained through BioPC across 25 programmes.

Publication Highlights

Peer-reviewed, first-author research

Three first-author articles, including two in Q1 journals and a Wiley review, each validated across rigorous methods.

All publications
Q2 JournalReview Article2026

Molecular Pharming: Advances, Applications, and Future Prospects in Biotechnology and Medicine

Md. Hridoy Ahmed, Md. Mustak Khan, Shishir Dutta, Md. Foyzur Rahman, Mohammad Shariful Islam, Md. Najmul Hosen, Md. Saad Hossain, Md. Aftabur Rahman, Md. Sadman Hasan Sahil, Tanjuma Tasnim Hira, Ifthesum Ashikur Rahaman, Md. Afser Rabbi, Laila Khaleda

Engineering in Life Sciences · Wiley

  • First-author, corresponding-author review accepted in Engineering in Life Sciences (Wiley), February 2026.
  • Traces the evolution of molecular pharming and plant-based production of recombinant proteins, vaccines, and industrial enzymes.
  • Surveys host organisms, genetic-engineering methods (including CRISPR/Cas9), and protein extraction and purification strategies.
  • Weighs advantages against challenges of public perception, regulation, and economic sustainability, and maps future directions.
View article PDF
Q1 JournalResearch Article2024

A structure-based drug design approach for the identification of antiviral compounds targeting the Chikungunya virus RdRp protein

Md. Hridoy Ahmed, Gagandeep Singh, Melvin Castrosanto, Alomgir Hossain, Md. Morshedul Islam Rifat, Sadia Hosna Rima, Vandana Gupta, Rajesh K. Kesharwani, Mariusz Jaremko, Abdul-Hamid Emwas, et al.

Chemical Physics Impact, 8, 100450 · Elsevier

  • Designed antiviral candidates through pharmacophore-based virtual screening and molecular docking.
  • Carried out structural analysis, binding free-energy evaluation, and molecular dynamics simulation.
  • Identified multi-target compounds with strong RdRp inhibitory potential.
  • Published in a Q1 Elsevier journal as first author.
View articleDOI PDF
Q1 JournalResearch Article2023

An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine design against the Mpox virus

Md. Hridoy Ahmed, Gagandeep Singh, Melvin Castrosanto, Prawez Alam, Faizul Azam, et al.

Journal of Biomolecular Structure and Dynamics, 42(10), 5288-5307 · Taylor & Francis

  • Identified antigenic proteins through proteome-wide immunoinformatics screening.
  • Designed a multi-epitope vaccine construct targeting Mpox viral proteins.
  • Performed molecular docking with immune receptors, including TLR-4 and MHC alleles.
  • Simulated immune responses using computational immunology tools.
View articleDOI PDF
Research Metrics

The record so far

Figures drawn from peer-reviewed work, research projects, and a community of more than a thousand trained learners.

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First-author publications

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Research projects

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Conference presentations

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Awards & honours

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Learners mentored

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Training programmes led

View on ORCIDView on ResearchGateView on Google Scholar
Current Projects

Research in motion

My research spans four connected domains: genomics, computational drug discovery, immunoinformatics, and wet-lab experimental biology. I pair molecular techniques with computational workflows to investigate disease-associated variants, design therapeutic candidates, and build immunoinformatics-driven vaccines.

Explore all projects
12+Research projects
5+Major disease targets
4Interdisciplinary domains
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.

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.

Ongoing

MMP3 & MMP9 Variant Profiling in Periodontitis and Diabetes

Identify disease-associated MMP variants using combined wet-lab and computational workflows.

Methods

  • PCR amplification and Sanger sequencing
  • NGS-based variant calling
  • Functional annotation with GATK, VEP, and ClinVar

Outcome. Novel variants identified across a Bangladeshi study population.

Completed

Whole-Exome Sequencing: Variant Discovery Pipeline

Build a high-throughput WES workflow for disease-associated SNPs and indels.

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.

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.

Completed

P53 Nanophytocompound Screening & MD Validation

Investigate natural compounds targeting P53 for therapeutic potential.

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.

Academic Timeline

A path through study, research, and service

Education, research positions, peer-reviewed publications, awards, and the founding of a national training community.

  1. 2026 · Publication

    First-author review — Molecular Pharming (Wiley)

    Engineering in Life Sciences, Wiley

    A comprehensive review of plant-based biopharmaceutical production, accepted February 2026 as first and corresponding author.

  2. 2024 – Present · Research

    Thesis Researcher

    Functional Genomics & Proteomics Laboratory, University of Chittagong

    Disease-associated variant analysis across diabetes, CVD, CKD, PCOS, and periodontitis using PCR/qPCR, Sanger sequencing, and NGS pipelines.

  3. 2024 · Publication

    First-author Q1 publication — CHIKV RdRp drug design

    Chemical Physics Impact, Elsevier

    Structure-based identification of antiviral candidates targeting the Chikungunya virus RNA-dependent RNA polymerase.

  4. 2023 – 2025 · Education

    M.Sc. in Genetic Engineering & Biotechnology

    University of Chittagong

    First Class, 2nd Position, CGPA 3.94/4.00. Thesis on MMP variant analysis in diabetes-influenced apical periodontitis.

  5. 2023 · Publication

    First-author Q1 publication — Mpox vaccine design

    Journal of Biomolecular Structure and Dynamics, Taylor & Francis

    Immunoinformatics annotation of hypothetical proteins and a multi-epitope vaccine construct against the Mpox virus.

  6. 2023 · Research

    Research Internships — NIB & Natural Product Lab

    National Institute of Biotechnology & Alternative Medicine Lab

    Sanger and NGS workflow training, plus nanophytocompound isolation with docking-guided screening.

  7. 2023 · Award

    Best Research Paper Presenter — Darwin International Conference

    4th Edition

    Recognised for the clarity and rigour of the Mpox multi-epitope vaccine presentation.

  8. 2021 – Present · Leadership

    Founder & Chief Trainer, BioPC

    Bioinformatics Lab of Research and Training

    Built one of Bangladesh's largest bioinformatics communities, training 1,000+ learners across 15 programmes and two national olympiads.

  9. 2019 – 2023 · Education

    B.Sc. (Honours) in Genetic Engineering & Biotechnology

    University of Chittagong

    First Class, 4th Position, with consistent first class standing across all academic years.

  10. 2016 – 2017 · Award

    Grameen Bank Scholarship & Most Brilliant Student Award

    Kishoreganj

    Early recognition for academic performance and scientific promise.

Awards & Honours

Recognition for research and leadership

National fellowships, conference honours, and academic distinctions earned across the journey.

All awards & competitions

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.

Teaching & Mentorship

BioPC — training the next cohort of computational biologists

BioPC is one of the largest bioinformatics communities in Bangladesh. I founded it to give students rigorous, hands-on research training that is often hard to find, and to open a path into computational biology for learners who would otherwise go without it.

  • Bioinformatics fundamentals and command-line workflows
  • Computer-aided drug and vaccine design
  • NGS data analysis and variant interpretation
  • Statistical analysis with R, SPSS, and KoboToolbox
  • Scientific writing and research methodology
See teaching & community work

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Learners trained

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Training programmes

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National olympiads

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Bioinformatics workshops

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Research projects with trainees

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Q1 articles from the community

Featured Articles

Writing & science communication

Beyond the journals, I write to make bioinformatics approachable and to guide students into research.

Visit the blog
Tutorials

Bioinformatics, Explained Simply

Walkthroughs of the tools and workflows behind drug discovery, docking, and sequence analysis, written for students starting out.

Guidance

Research Career Guidance

Practical notes on scholarships, manuscript writing, and finding a footing in academic research from a low-resource setting.

Reflections

Notes from the Lab and the Terminal

Reflections on training a thousand learners through BioPC, and on the everyday craft of careful science.

Endorsements

Words from supervisors, collaborators, and mentees

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I have had the pleasure of supervising Hridoy Ahmed during his graduate research in molecular genetics and disease genomics. He consistently demonstrated exceptional intellectual curiosity, technical competence, and scientific integrity. His ability to integrate wet-lab molecular biology techniques with advanced bioinformatics analyses is uncommon among early-career researchers. Hridoy approaches research problems with maturity and independence, whether working on genetic variant interpretation, computational drug discovery, or translational genomics. He is meticulous in data analysis, rigorous in scientific reasoning, and highly committed to producing research of publishable quality. His achievements, including first-author publications in reputable international journals, reflect both his dedication and his potential to become an outstanding scientist. I strongly recommend Hridoy for advanced research opportunities, doctoral training, and collaborative scientific projects.

Prof. Dr. Laila Khaleda

Principal Investigator, FGPL, University of Chittagong

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Working with Hridoy Ahmed has been an exceptionally rewarding experience. As a collaborator, he brings a rare combination of biological insight, computational expertise, and strong project management skills. During our research collaborations, he consistently contributed innovative ideas, performed rigorous analyses, and ensured that every stage of the project met high scientific standards. What distinguishes Hridoy is his ability to bridge disciplines. He can move seamlessly from molecular biology concepts to bioinformatics workflows, making him a valuable contributor in interdisciplinary research teams. Beyond his technical strengths, he is highly professional, dependable, and always willing to support colleagues. I would gladly collaborate with him again and confidently recommend him to any research group seeking a motivated and capable scientist.

Gagandeep Singh Khurana

Co-author / Collaborator, India

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I had the opportunity to learn under Hridoy Ahmed through BioPC, and his mentorship played a significant role in shaping my research journey. He has a remarkable ability to explain complex concepts in genetics, bioinformatics, and computational biology in a way that is both accessible and inspiring. Beyond teaching technical skills, Hridoy encourages critical thinking, scientific curiosity, and confidence in independent research. His mentorship extends far beyond the classroom; he genuinely invests in the growth and success of his students. Through his guidance, I gained practical research experience and developed the skills necessary to pursue advanced studies in life sciences. Hridoy is not only an accomplished researcher but also an outstanding mentor who empowers the next generation of scientists.

Mustak Khandokar

BioPC Trainee

Contact

Let's discuss research, study, and collaboration

I welcome enquiries about doctoral positions, fellowships, co-authorship, and bioinformatics training. The fastest way to reach me is by email.

Emailhridoy.geb.cu@gmail.com
Based inChattogram, Bangladesh
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