Ranked k-medoids: A fast and accurate rank-based partitioning algorithm for clustering large datasets. - Seyed Mohammad Razavi Zadegan; Mehdi Mirzaie; Farahnaz Sadoughi (Knowl. Based Syst., 2013)

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. - Mohieddin Jafari; Mehdi Mirzaie; Mehdi Sadeghi (BMC Bioinform., 2015)

Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database. - Farnaz Barneh; Mohieddin Jafari; Mehdi Mirzaie (Briefings Bioinform., 2016)

A systematic survey of centrality measures for protein-protein interaction networks. - Minoo Ashtiani; Ali Salehzadeh-Yazdi; Zahra Razaghi-Moghadam; Holger Hennig; Olaf Wolkenhauer; Mehdi Mirzaie; Mohieddin Jafari (BMC Syst. Biol., 2018)

Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer. - Farnaz Barneh; Mehdi Mirzaie; Payman Nickchi; Tuan Zea Tan; Jean-Paul Thiery; Mehran Piran; Mona Salimi; Fatemeh Goshadrou; Amir R. Aref; Mohieddin Jafari (Briefings Bioinform., 2019)

CINNA: an R/CRAN package to decipher Central Informative Nodes in Network Analysis. - Minoo Ashtiani; Mehdi Mirzaie; Mohieddin Jafari (Bioinform., 2019)

IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis. - Minoo Ashtiani; Payman Nickchi; Soheil Jahangiri-Tazehkand; Abdollah Safari; Mehdi Mirzaie; Mohieddin Jafari (BMC Bioinform., 2019)

Identification of native protein structures captured by principal interactions. - Mehdi Mirzaie (BMC Bioinform., 2019)

IrGO: Iranian traditional medicine General Ontology and knowledge base. - Ayeh Naghizadeh; Mahdi Salamat; Donya Hamzeian; Shaghayegh Akbari; Hossein Rezaeizadeh; Mahdi Alizadeh Vaghasloo; Reza Karbalaei; Mehdi Mirzaie; Mehrdad Karimi; Mohieddin Jafari (J. Biomed. Semant., 2021)

The impact of vaccination and social distancing on COVID-19: A compartmental model and an evolutionary game theory approach. - Mohammadali Dashtbali; Mehdi Mirzaie (J. Frankl. Inst., 2024)