Ali Masoudi-Nejad

32 papers C 1Journal 26Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Molecular landscape of endometrioid Cancer: Integrating multiomics and deep learning for personalized survival prediction. Comput. Biol. Medicine Behnaz Haji Molla Hoseyni, Hossein Lanjanian, Yasaman Zohrab Beigi, Mahdieh Salimi, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad
2025	J	`jnl`	SynergyImage: image-based model for drug combinations synergy score prediction. BMC Bioinform. Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani, Ali Masoudi-Nejad
2024	J	`jnl`	CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction. J. Chem. Inf. Model. Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Parvin Razzaghi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad
2023	J	`jnl`	DeepTraSynergy: drug combinations using multimodal deep learning with transformers. Bioinform. Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad
2023	J	`jnl`	DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing. BMC Bioinform. Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Najmeh Salehi, Mohammad Akbari, Ali Masoudi-Nejad
2023	J	`jnl`	DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs. J. Chem. Inf. Model. Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Mohammad Akbari, Najmeh Salehi, Ali Masoudi-Nejad
2021	J	`jnl`	DNA methylation association with stage progression of head and neck squamous cell carcinoma. Comput. Biol. Medicine Vahid Ghafarpour, Mohammad Khansari, Ali Mohammad Banaei-Moghaddam, Ali Najafi, Ali Masoudi-Nejad
2021	J	`jnl`	High-throughput analysis of the interactions between viral proteins and host cell RNAs. Comput. Biol. Medicine Hossein Lanjanian, Sajjad Nematzadeh, Shadi Hosseini, Mahsa Torkamanian-Afshar, Farzad Kiani, Maryam Moazzam-Jazi, Nizamettin Aydin, Ali Masoudi-Nejad
2021	J	`jnl`	Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. Briefings Bioinform. Yosef Masoudi-Sobhanzadeh, Aysan Salemi, Mohammad M. Pourseif, Behzad Jafari, Yadollah Omidi, Ali Masoudi-Nejad
2020	J	`jnl`	DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks. Bioinform. Karim Abbasi, Parvin Razzaghi, Antti Poso, Massoud Amanlou, Jahan B. Ghasemi, Ali Masoudi-Nejad
2020	J	`jnl`	Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm. BMC Bioinform. Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad
2019	J	`jnl`	Deep Transferable Compound Representation across Domains and Tasks for Low Data Drug Discovery. J. Chem. Inf. Model. Karim Abbasi, Antti Poso, Jahan B. Ghasemi, Massoud Amanlou, Ali Masoudi-Nejad
2019	J	`jnl`	DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy. Comput. Biol. Medicine Yosef Masoudi-Sobhanzadeh, Yadollah Omidi, Massoud Amanlou, Ali Masoudi-Nejad
2019	J	`jnl`	FeatureSelect: a software for feature selection based on machine learning approaches. BMC Bioinform. Yosef Masoudi-Sobhanzadeh, Habib Motieghader, Ali Masoudi-Nejad
2019	J	`jnl`	Systematic analysis of genes and diseases using PheWAS-Associated networks. Comput. Biol. Medicine Ali Khosravi, Morteza Kouhsar, Bahram Goliaei, B. Jayaram, Ali Masoudi-Nejad
2018	J	`jnl`	Link prediction potentials for biological networks. Int. J. Data Min. Bioinform. Sadegh Sulaimany, Mohammad Khansari, Ali Masoudi-Nejad
2018	J	`jnl`	Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer. Comput. Biol. Medicine Fariba Dehghanian, Zohreh Hojati, Nazanin Hosseinkhan, Zaynab Mousavian, Ali Masoudi-Nejad
2017	J	`jnl`	Task modulates functional connectivity networks in free viewing behavior. NeuroImage Hossein Seidkhani, Andrey R. Nikolaev, Radha Nila Meghanathan, Hamid Pezeshk, Ali Masoudi-Nejad, Cees van Leeuwen
2016	J	`jnl`	CeFunMO: A centrality based method for discovering functional motifs with application in biological networks. Comput. Biol. Medicine Morteza Kouhsar, Zahra Razaghi-Moghadam, Zaynab Mousavian, Ali Masoudi-Nejad
2014	J	`jnl`	Extracting a cancer model by enhanced ant colony optimisation algorithm. Int. J. Data Min. Bioinform. Reza Shamsaee, Mahmood Fathy, Ali Masoudi-Nejad
2013	J	`jnl`	Computational structure analysis of biomacromolecule complexes by interface geometry. Comput. Biol. Chem. Sedigheh Mahdavi, Ali Salehzadeh-Yazdi, Ali Mohades, Ali Masoudi-Nejad
2013	J	`jnl`	Normalized Similarity Index: An adjusted index to prioritize article citations. J. Informetrics Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini
2013	—	`conf`	Protein-Protein Interaction Network Clustering Using Particle Swarm Optimization. IWBBIO Iman Sharafuddin, Mehrdad Mirzaei, Masoud Rahgozar, Ali Masoudi-Nejad
2012	—	`conf`	Hubs and Non-hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation. DEXA Workshops Ali Salehzadeh-Yazdi, Ali Masoudi-Nejad, Ali Akbar Saboury, Shiva Akbari-Birgani
2012	J	`jnl`	Modeling and Analysis of Abnormality Detection in Biomolecular Nano-Networks CoRR Siavash Ghavami, Farshad Lahouti, Ali Masoudi-Nejad
2012	J	`jnl`	Modeling and analysis of abnormality detection in biomolecular nano-networks. Nano Commun. Networks Siavash Ghavami, Farshad Lahouti, Ali Masoudi-Nejad
2010	C	`conf`	Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network. BIBE Hamid Ravaee, Ali Masoudi-Nejad, Saeed Omidi, Ali Moeini
2010	—	`ch.`	Network Evolution: Theory and Mechanisms. Computational Social Network Analysis Saeed Omidi, Ali Masoudi-Nejad
2009	J	`jnl`	Kavosh: a new algorithm for finding network motifs. BMC Bioinform. Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, Ali Masoudi-Nejad
2009	—	`ch.`	Support Vector Clustering: From Local Constraint to Global Stability. Foundations of Computational Intelligence (6) Bahman Yari Saeed Khanloo, Daryanaz Dargahi, Nima Aghaeepour, Ali Masoudi-Nejad
2008	—	`conf`	A New Approach for Touching Cells Segmentation. BMEI (1) Shirin Nasr-Isfahani, Atefeh Mirsafian, Ali Masoudi-Nejad
2006	J	`jnl`	EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res. Ali Masoudi-Nejad, Koichiro Tonomura, Shuichi Kawashima, Yuki Moriya, Masanori Suzuki, Masumi Itoh, Minoru Kanehisa, Takashi Endo, Susumu Goto