EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. - Ali Masoudi-Nejad; Koichiro Tonomura; Shuichi Kawashima; Yuki Moriya; Masanori Suzuki; Masumi Itoh; Minoru Kanehisa; Takashi Endo; Susumu Goto (Nucleic Acids Res., 2006)

A New Approach for Touching Cells Segmentation. - Shirin Nasr-Isfahani; Atefeh Mirsafian; Ali Masoudi-Nejad (BMEI (1), 2008)

Kavosh: a new algorithm for finding network motifs. - Zahra Razaghi Moghadam Kashani; Hayedeh Ahrabian; Elahe Elahi; Abbas Nowzari-Dalini; Elnaz Saberi Ansari; Sahar Asadi; Shahin Mohammadi; Falk Schreiber; Ali Masoudi-Nejad (BMC Bioinform., 2009)

Support Vector Clustering: From Local Constraint to Global Stability. - Bahman Yari Saeed Khanloo; Daryanaz Dargahi; Nima Aghaeepour; Ali Masoudi-Nejad (Foundations of Computational Intelligence (6), 2009)

Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network. - Hamid Ravaee; Ali Masoudi-Nejad; Saeed Omidi; Ali Moeini (BIBE, 2010)

Network Evolution: Theory and Mechanisms. - Saeed Omidi; Ali Masoudi-Nejad (Computational Social Network Analysis, 2010)

Hubs and Non-hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation. - Ali Salehzadeh-Yazdi; Ali Masoudi-Nejad; Ali Akbar Saboury; Shiva Akbari-Birgani (DEXA Workshops, 2012)

Modeling and analysis of abnormality detection in biomolecular nano-networks. - Siavash Ghavami; Farshad Lahouti; Ali Masoudi-Nejad (Nano Commun. Networks, 2012)

Protein-Protein Interaction Network Clustering Using Particle Swarm Optimization. - Iman Sharafuddin; Mehrdad Mirzaei; Masoud Rahgozar; Ali Masoudi-Nejad (IWBBIO, 2013)

Computational structure analysis of biomacromolecule complexes by interface geometry. - Sedigheh Mahdavi; Ali Salehzadeh-Yazdi; Ali Mohades; Ali Masoudi-Nejad (Comput. Biol. Chem., 2013)

Normalized Similarity Index: An adjusted index to prioritize article citations. - Isar Nassiri; Ali Masoudi-Nejad; Mahdi Jalili; Ali Moeini (J. Informetrics, 2013)

Extracting a cancer model by enhanced ant colony optimisation algorithm. - Reza Shamsaee; Mahmood Fathy; Ali Masoudi-Nejad (Int. J. Data Min. Bioinform., 2014)

CeFunMO: A centrality based method for discovering functional motifs with application in biological networks. - Morteza Kouhsar; Zahra Razaghi-Moghadam; Zaynab Mousavian; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2016)

Task modulates functional connectivity networks in free viewing behavior. - Hossein Seidkhani; Andrey R. Nikolaev; Radha Nila Meghanathan; Hamid Pezeshk; Ali Masoudi-Nejad; Cees van Leeuwen (NeuroImage, 2017)

Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer. - Fariba Dehghanian; Zohreh Hojati; Nazanin Hosseinkhan; Zaynab Mousavian; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2018)

Link prediction potentials for biological networks. - Sadegh Sulaimany; Mohammad Khansari 002; Ali Masoudi-Nejad (Int. J. Data Min. Bioinform., 2018)

FeatureSelect: a software for feature selection based on machine learning approaches. - Yosef Masoudi-Sobhanzadeh; Habib Motieghader; Ali Masoudi-Nejad (BMC Bioinform., 2019)

Systematic analysis of genes and diseases using PheWAS-Associated networks. - Ali Khosravi; Morteza Kouhsar; Bahram Goliaei; B. Jayaram 001; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2019)

DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy. - Yosef Masoudi-Sobhanzadeh; Yadollah Omidi; Massoud Amanlou; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2019)

Deep Transferable Compound Representation across Domains and Tasks for Low Data Drug Discovery. - Karim Abbasi; Antti Poso; Jahan B. Ghasemi; Massoud Amanlou; Ali Masoudi-Nejad (J. Chem. Inf. Model., 2019)

DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks. - Karim Abbasi; Parvin Razzaghi; Antti Poso; Massoud Amanlou; Jahan B. Ghasemi; Ali Masoudi-Nejad (Bioinform., 2020)

Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm. - Yosef Masoudi-Sobhanzadeh; Ali Masoudi-Nejad (BMC Bioinform., 2020)

Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. - Yosef Masoudi-Sobhanzadeh; Aysan Salemi; Mohammad M. Pourseif; Behzad Jafari; Yadollah Omidi; Ali Masoudi-Nejad (Briefings Bioinform., 2021)

DNA methylation association with stage progression of head and neck squamous cell carcinoma. - Vahid Ghafarpour; Mohammad Khansari 002; Ali Mohammad Banaei-Moghaddam; Ali Najafi; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2021)

High-throughput analysis of the interactions between viral proteins and host cell RNAs. - Hossein Lanjanian; Sajjad Nematzadeh; Shadi Hosseini; Mahsa Torkamanian-Afshar; Farzad Kiani; Maryam Moazzam-Jazi; Nizamettin Aydin; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2021)

DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs. - Zahra Ghorbanali; Fatemeh Zare-Mirakabad; Mohammad Akbari; Najmeh Salehi; Ali Masoudi-Nejad (J. Chem. Inf. Model., 2023)

DeepTraSynergy: drug combinations using multimodal deep learning with transformers. - Fatemeh Rafiei; Hojjat Zeraati; Karim Abbasi; Jahan B. Ghasemi; Mahboubeh Parsaeian; Ali Masoudi-Nejad (Bioinform., 2023)

DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing. - Zahra Ghorbanali; Fatemeh Zare-Mirakabad; Najmeh Salehi; Mohammad Akbari; Ali Masoudi-Nejad (BMC Bioinform., 2023)

CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction. - Fatemeh Rafiei; Hojjat Zeraati; Karim Abbasi; Parvin Razzaghi; Jahan B. Ghasemi; Mahboubeh Parsaeian; Ali Masoudi-Nejad (J. Chem. Inf. Model., 2024)

Molecular landscape of endometrioid Cancer: Integrating multiomics and deep learning for personalized survival prediction. - Behnaz Haji Molla Hoseyni; Hossein Lanjanian; Yasaman Zohrab Beigi; Mahdieh Salimi; Fatemeh Zare-Mirakabad; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2025)