Corresponding authorQ2 JournalResearch ArticlePublished2026
From Association to Mechanism: Regulatory Annotation and Pathway Mapping of Genes Surrounding Breast Cancer Risk Variants
Sultana Jannat, Trina Mitra, Nafisa Nawar Fariha, Tasmia Tabassum, Kulsuma Bahar Bethi, Synchita Majumder Kaya, Md. Arif Hossen, Md. Saad Hossain, Jobaier Ibne Deen, Mohammed Emon, Laila Khaleda, Md. Hridoy Ahmed
Computational and Systems Oncology, 6, e70024 · Wiley
How this connects. Regulatory annotation of risk variants - the same interpretive step applied to the ADPKD and PCOS cohorts, here on breast cancer loci.
- Corresponding-author study published open access in Computational and Systems Oncology (Wiley), 2026.
- Examined 175 breast cancer risk variants confirmed by genome-wide association studies and the genes flanking each locus.
- Mapped the risk genes onto androgen receptor, Wnt/β-catenin, and Hedgehog signaling pathways central to mammary biology.
- Annotated correlated variants with HaploReg, finding a 4.8-fold excess of DNase I hypersensitivity and a 15.7-fold excess of enhancer motifs.
First & corresponding authorQ2 JournalReview ArticleIn press2026
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
How this connects. A review of recombinant protein production in plants, written out of the molecular biology and expression work behind the bench programme.
- First-author, corresponding-author review accepted in Engineering in Life Sciences (Wiley), February 2026; article page and DOI to follow on final publication.
- 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.
First authorQ1 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
How this connects. Where the structural modelling and molecular dynamics methods were built - now applied to asking what disease variants do to protein structure.
- 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.
First authorQ1 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
How this connects. Proteome-wide screening and epitope prediction - the computational annotation skills that variant interpretation draws on.
- 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.