PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis. - Payman Nickchi; Mohieddin Jafari; Shiva Kalantari (Database J. Biol. Databases Curation, 2015)

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)

Network Centrality Analysis of Tehran Urban and Suburban Railway System. - Mohieddin Jafari; Sayed Mohammad Fakhar (CoRR, 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)

DrugComb: an integrative cancer drug combination data portal. - Bulat Zagidullin; Jehad Aldahdooh; Shuyu Zheng; Wenyu Wang; Yinyin Wang; Joseph Saad; Alina Malyutina; Mohieddin Jafari; ZiaurRehman Tanoli; Alberto Pessia; Jing Tang 002 (Nucleic Acids Res., 2019)

Predicting Meridian in Chinese traditional medicine using machine learning approaches. - Yinyin Wang; Mohieddin Jafari; Yun Tang 001; Jing Tang 002 (PLoS Comput. Biol., 2019)

Network-based modeling of herb combinations in traditional Chinese medicine. - Yinyin Wang; Hongbin Yang; Linxiao Chen; Mohieddin Jafari; Jing Tang 002 (Briefings Bioinform., 2021)

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 ENDS of assumptions: an online tool for the epistemic non-parametric drug-response scoring. - Ali Amiryousefi; Bernardo Williams; Mohieddin Jafari; Jing Tang 002 (Bioinform., 2022)