In silico phylogenetic analysis of Vibrio cholerae isolates based on three housekeeping genes. - Tayebeh Farhadi; Navid Nezafat; Younes Ghasemi (Int. J. Comput. Biol. Drug Des., 2015)

Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches. - Navid Nezafat; Zeinab Karimi; Mahboobeh Eslami; Milad Mohkam; Sanam Zandian; Younes Ghasemi (Comput. Biol. Chem., 2016)

Proteome-scale identification of Leishmania infantum for novel vaccine candidates: A hierarchical subtractive approach. - Bahareh Vakili; Navid Nezafat; Gholam Reza Hatam; Bijan Zare; Nasrollah Erfani; Younes Ghasemi (Comput. Biol. Chem., 2018)

Evaluating the effect of BDNF Val66Met polymorphism on complex formation with HAP1 and Sortilin1 via structural modeling. - Mozhdeh Zamani; Mahboobeh Eslami; Navid Nezafat; Seyed Vahid Hosseini; Younes Ghasemi (Comput. Biol. Chem., 2019)

An in silico approach to de novo design of anti-microbial peptide from inspirited Komodo dragon's original VK6 peptide. - Milad Mohkam; Navid Nezafat; Younes Ghasemi (Int. J. Data Min. Bioinform., 2024)

Computational design of a multi-epitope mRNA vaccine against orthopoxviruses: A path toward comprehensive poxvirus protection. - Nafiseh Maghsoodi; Navid Nezafat; Amin Ramezani (Comput. Biol. Medicine, 2025)