Journal Paper

1. "SynergyGraph: predicting cell line specific drug combination synergy scores using knowledge graph representation and hypergraph modeling"
   Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani, Mahdieh Salimi, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad
   Scientific Reports, Vol. 16, 2025
2. "SynergyImage: image-based model for drug combinations synergy score prediction"
   Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani, Ali Masoudi-Nejad
   BMC BIOINFORMATICS, Vol. 26, 2025
3. "Bridging traditional and deep learning methods in H&E histological image normalization: a comprehensive review and introducing a novel framework for comparative analyses"
   Behnaz Haji Molla Hoseyni, Sevda Imany, Ahmadreza Iranpour, Maryam Mehrabani, sina seifori, Maryam Rafieipour-Jobaneh, Sina Firouzbakht, Ali Masoudi-Nejad
   JOURNAL OF ADVANCED RESEARCH, Vol. 85, 2025
4. "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
   COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 192, No 110284, 2025
5. "Heterogeneity and molecular landscape of melanoma: implications for targeted therapy"
   Yasaman Zohrab Beigi, Hossein Lanjanian, Reyhane Fayazi, Mahdieh Salimi, Behnaz Haji Molla Hoseyni, Mohammad Hafez Noroozizadeh, Ali Masoudi-Nejad
   molecular biomedicine, Vol. 5, No 1, 2025
6. "Interplay of lung microbiome and epigenetics in former smokers: A machine learning and fuzzy logic approach on COPD progression"
   Hamidreza Taherkhani, Azadeh KavianFar, Hossein Lenjanian, نازنین حسین خان, Mahdieh Salimi, Sajjad Nematzadeh, Mohammad Mehdi Naghizadeh, صادق عظیم زاده جمالکندی, Ali Masoudi-Nejad
   Heliyon, Vol. 11, No 5, 2025
7. "Keystone bacteria dynamics in chronic obstructive pulmonary disease (COPD): Towards differential diagnosis and probiotic candidates"
   Azadeh KavianFar, Hamidreza Taherkhani, Hossein Lenjanian, Sargol AminNezhad, علی احمدی, صادق عظیم زاده جمالکندی, Ali Masoudi-Nejad
   Heliyon, Vol. 11, No 4, 2025
8. "HLAPepBinder: An Ensemble Model for The Prediction Of HLA-Peptide Binding"
   مهسا سعادتی, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad, Mohammad Farahanchi Baradaran, نازنین حسین خان
   Iranian Journal of Biotechnology, Vol. 22, No 4, 2024
9. "CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction"
   Fatemeh Rafiei, حجت زراعتی, Karim Abasi, Parvin Razzaghi, Jahan Bakhsh Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad
   Journal of Chemical Information and Modeling, Vol. 64, No 7, pp.2577-2585, 2024
10. "Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome"
    Hamidreza Taherkhani, Azadeh KavianFar, Sargol AminNezhad, Hossein Lanjanian, علی احمدی, صادق عظیم زاده جمالکندی, Ali Masoudi-Nejad
    Heliyon, Vol. 10, No 4, 2024
11. "Restoring the epigenetic landscape of lung microbiome: potential therapeutic approach for chronic respiratory diseases"
    Hamidreza Taherkhani, Azadeh KavianFar, علی احمدی, Mahdieh Salimi, Hossein Lenjanian, Ali Masoudi-Nejad
    BMC Pulmonary Medicine, Vol. 24, No 1, 2024
12. "Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation"
    AliReza ShariatMadar Taleghani, Yasaman Zohrab Beigi, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad
    Scientific Reports, Vol. 13, No 1, 2023
13. "Food co-consumption network as a new approach to dietary pattern in non-alcoholic fatty liver diseas"
    Mohammad Mehdi Naghizadeh, Saeed Osati, Reza Homayounfar, Ali Masoudi-Nejad
    Scientific Reports, Vol. 13, No 1, 2023
14. "Identifying common signatures and potential therapeutic biomarkers in COPD and lung cancer using miRNA-mRNA co-expression networks"
    Amirhossein Fathinavid, Zeinabsadat Mousavianhor, Ali Najafi, Sajjad Nematzadeh, Mahdieh Salimi, Ali Masoudi-Nejad
    Informatics in Medicine Unlocked, Vol. 34, No 1, 2023
15. "DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing"
    Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Najmeh Salehi, Ali Masoudi-Nejad
    BMC BIOINFORMATICS, Vol. 24, No 1, 2023
16. "Computational-based strategies to deal with liver injuries induced by the repurposed drugs against SARS-CoV-2"
    Nasim Bakhtiyari, Sepideh Parvizpour, Yosef Masoudi sobhanzadeh, Ali Masoudi-Nejad
    Informatics in Medicine Unlocked, Vol. 41, No 1, 2023
17. "DeepTraSynergy: drug combinations using multimodal deep learning with transformers"
    Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Jahan Bakhsh Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad
    BIOINFORMATICS, Vol. 39, No 8, 2023
18. "A deep learning-based framework for predicting survival-associated groups in colon cancer by integrating multi-omics and clinical data"
    Siamak Salimy, Hossein Lanjanian, Karim Abbasi, Mahdieh Salimi, Ali Najafi, Leili Tapak, Ali Masoudi-Nejad
    Heliyon, Vol. 9, No 7, 2023
19. "DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs"
    Zahra GhorbanAli, Fatemeh Zare-Mirakabad, محمد اکبری, Najmeh Salehi, Ali Masoudi-Nejad
    Journal of Chemical Information and Modeling, Vol. 63, No 8, pp.2532-2545, 2023
20. "Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players"
    Mohammad Mehdi Naghizadeh, Behnaz Bakhshandeh, Farshid Noorbakhsh, Marjan Yaghmaie, Ali Masoudi-Nejad
    Systems Biology in Reproductive Medicine, Vol. ND, pp.1-12, 2023
21. "Parallel molecular alteration between Alzheimer’s disease and major depressive disorder in the human brain dorsolateral prefrontal cortex: an insight from gene expression and methylation profile analyses"
    Saber Rastad, Nadia Barjaste, Hossein Lanjanian, Ali Moeini, Farzad Kiani, Ali Masoudi-Nejad
    GENES & GENETIC SYSTEMS, Vol. 97, No 6, pp.311-324, 2022
22. "Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers"
    Sayyed Sajjad Moravveji, Samane Khoshbakht, Majid Mokhtari, Mahdieh Salimi, Hossein Lanjanian, sajad Nematzadeh, Mahsa Torkamanianafshar, Ali Masoudi-Nejad
    BMC Genomic Data, Vol. 23, No 1, 2022
23. "Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug–gene interaction networks analysis"
    Habib Motieghader, Parinaz Tabrizi Nezhadi, Mahshid Deldar Abad Paskeh, بهزاد برادران, Ahad Mokhtarzadeh, Mehrdad Hashemi, Hossein Lanjanian, seyed Mehdi Jazayeri, Masoud Maleki, Ehsan Khodadadi, Sajjad Nematzadeh, Farzad Kiani, Mazaher Maghsoudloo, Ali Masoudi-Nejad
    Scientific Reports, Vol. 12, No 1, 2022
24. "mRNA–miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis"
    Zahra Abedi, Habib Mottighader, Seyedh Sahar Hosseini, Mohammad Ali Sheikh Beig Goharrizi, Ali Masoudi-Nejad
    Scientific Reports, Vol. 12, No 1, 2022
25. "Re-wiring and gene expression changes of AC025034.1 and ATP2B1 play complex roles in early-to-late breast cancer progression"
    Samane Khoshbakht, Majid Mokhtari, Sayyed Sajjad Moravveji, Sadegh Azimzadeh-Jamalkandi, Ali Masoudi-Nejad
    BMC Genomic Data, Vol. 23, No 1, 2022
26. "Pan-cancer analysis of biological events on cell cycle instability in gastrointestinal cancers with integrative scoring method"
    Sayyed Sajjad Moravveji, Samane Khoshbakht, Majid Mokhtari, Mahdieh Salimi, Ali Masoudi-Nejad
    GENOMICS, Vol. 114, No 1, pp.253-265, 2022
27. "Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer"
    Samane Khoshbakht, Sadegh Azimzadeh-Jamalkandi, Ali Masoudi-Nejad
    BMC MEDICAL GENOMICS, Vol. 14, No 1, 2021
28. "Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis"
    Amirhossein Fathinavid, Mohadeseh Zarei Ghobadi, Ali Najafi, Ali Masoudi-Nejad
    BMC Genomic Data, Vol. 22, No 1, 2021
29. "A fuzzy logic-based computational method for the repurposing of drugs against COVID-19"
    Yosef Masoudi-Sobhanzadeh, Hosein Esmaeili, Ali Masoudi-Nejad
    BioImpacts, Vol. 11, No 5, 2021
30. "A propagation-based seed-centric local community detection for multilayer environment: The case study of colon adenocarcinoma"
    Ehsan Pournoor, Zeinabsadat Mousavianhor, Abbas Nouzari Dalini, Ali Masoudi-Nejad
    PLoS One, Vol. 16, No 8, 2021
31. "High-throughput analysis of the interactions between viral proteins and host cell RNAs"
    Hossein Lanjanian, sajad Nematzadeh, Shadi Hosseini, Mahsa Torkamanianafshar, Farzad Kiani, مریم معظم جزی , Aydin Nizamettin, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 135, No 1, 2021
32. "Nodes with the highest control power play an important role at the final level of cooperation in directed networks"
    Ali Ebrahimi, Marzieh Yousefi, Farhad Shahbazi, Mohammad Ali Sheikh Beig Goharrizi, Ali Masoudi-Nejad
    Scientific Reports, Vol. 11, No 1, 2021
33. "DNA methylation association with stage progression of head and neck squamous cell carcinoma"
    Vahid Ghafarpour, Mohammad Khansari, Ali Mohammad Banaei Moghaddam, Ali Najafi, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 134, No 1, 2021
34. "Revealing transcriptional and post-transcriptional regulatory mechanisms of γ-glutamyl transferase and keratin isoforms as novel cooperative biomarkers in low-grade glioma and glioblastoma multiforme"
    Faezeh Mottaghitalab, Hossein Lanjanian, Ali Masoudi-Nejad
    GENOMICS, Vol. 113, No 4, pp.2623-2633, 2021
35. "Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries"
    Yosef Masoudi-Sobhanzadeh, Aysan Salemi, Mohammad Pourseifi, Behzad Jafari, Yadollah Omidi, Ali Masoudi-Nejad
    BRIEFINGS IN BIOINFORMATICS, Vol. 1, No 1, 2021
36. "A machine learning method based on the genetic and world competitive contests algorithms for selecting genes or features in biological applications"
    Yosef Masoudi-Sobhanzadeh, Habib Mottighader, Yadolah Omidi, Ali Masoudi-Nejad
    Scientific Reports, Vol. 11, No 1, 2021
37. "In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm"
    Mahsa Torkamanianafshar, sajad Nematzadeh, Maryam Tabarzad, ALI NAJAFI, Ali Masoudi-Nejad
    MOLECULAR DIVERSITY, Vol. 1, No 1, 2021
38. "Identification of new genes and quantitative trait locis associated with growth curve parameters in F2 chicken population using genome‐wide association study"
    Reihane Seifi Moroudi, Saeid Ansari Mahyari, سیدرسول واعظ ترشیزی , Hossein Lanjanian, Ali Masoudi-Nejad
    ANIMAL GENETICS, Vol. 52, No 2, pp.171-184, 2021
39. "Automated Plant Species Identification Using Leaf Shape-Based Classification Techniques: A Case Study on Iranian Maples"
    Mojgan Sadat Mohtashamian, Mahmood Karimian, Faisal Moola, Kaveh Kavousi, Ali Masoudi-Nejad
    Iranian Journal of Science and Technology-Transactions of Electrical Engineering, Vol. 10, No 1, 2021
40. "Appropriate time to apply control input to complex dynamical systems"
    Ali Ebrahimi, Abbas Nouzari Dalini, Mahdi Jalili, Ali Masoudi-Nejad
    Scientific Reports, Vol. 10, No 1, pp.1-7, 2020
41. "A multimodal deep learning-based drug repurposing approach for treatment of COVID-19"
    Seyed Aghil Hooshmand, Mohadeseh Zarei Ghobadi, Seyyed Emad Hooshmand, Sadegh Azimzadeh-Jamalkandi, Seyed Mehdi Alavi, Ali Masoudi-Nejad
    MOLECULAR DIVERSITY, Vol. 1, No 1, 2020
42. "Deep Learning in Drug Target Interaction Prediction: Current and Future Perspective"
    Karim Abasi, Parvin Razzaghi, Anti Poso, Ali Masoudi-Nejad
    Current Medicinal Chemistry, Vol. 27, No 1, 2020
43. "Target controllability with minimal mediators in complex biological networks"
    Ali Ebrahimi, Abbas Nouzari Dalini, Mahdi Jalili, Ali Masoudi-Nejad
    GENOMICS, Vol. 112, No 1, pp.4938-4944, 2020
44. "An efficient hybrid feature selection method to identify potential biomarkers in common chronic lung inflammatory diseases"
    Mazaher Maghsoudloo, Sadegh Azimzadeh-Jamalkandi, Ali Najafi, Ali Masoudi-Nejad
    GENOMICS, Vol. 112, No 5, pp.3284-3293, 2020
45. "mRNA and microRNA selection for breast cancer molecular subtype stratification using meta-heuristic based algorithms"
    Habib Motieghader, Yosef Masoudi-Sobhanzadeh, Saman Ashtiani, Ali Masoudi-Nejad
    GENOMICS, Vol. 112, No 5, pp.3207-3217, 2020
46. "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 BIOINFORMATICS, Vol. 21, No 1, 2020
47. "DeepCDA: Deep Cross-Domain Compound-Protein Affinity Prediction through LSTM and Convolutional Neural Networks"
    Karim Abasi, Parvin Razzaghi, Antti Poso, Massoud Amanlou, Jahan Bakhsh Ghasemi, Ali Masoudi-Nejad
    BIOINFORMATICS, Vol. 5, No 1, 2020
48. "RPINBASE: An online toolbox to extract features for predicting RNA-protein interactions"
    Mahsa Torkamanianafshar, Hossein Lenjanian, sajad Nematzadeh, Maryam Tabarzad, Ali Najafi, Farzad Kianian, Ali Masoudi-Nejad
    GENOMICS, Vol. 112, No 3, pp.2623-2632, 2020
49. "Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1"
    Naghmeh Poorinmohammad, Javad Hamedi, Ali Masoudi-Nejad
    Scientific Reports, Vol. 1, No 1, 2020
50. "Identification of Key Components in Colon Adenocarcinoma Using Transcriptome to Interactome Multilayer Framework"
    Ehsan Pournoor, Zeinabsadat Mousavianhor, Abbas Nouzari Dalini, Ali Masoudi-Nejad
    Scientific Reports, Vol. 10, No 1, 2020
51. "Distinguishing drug/non-drug-like small molecules in drug discovery using deep belief network"
    Seyed Aghil Hooshmand, Sadegh Azimzadeh-Jamalkandi, Seyed Mehdi Alavi, Ali Masoudi-Nejad
    MOLECULAR DIVERSITY, Vol. 10, No 1, 2020
52. "Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis"
    Mazaher Maghsoudloo, Sadegh Azimzadeh-Jamalkandi, Ali Najafi, Ali Masoudi-Nejad
    MOLECULAR MEDICINE, Vol. 26, No 1, 2020
53. "Deep Transferable Compound Representation Across Domains and Tasks for Low Data Drug Discovery"
    Karim Abasi, Anti Poso, Jahan Bakhsh Ghasemi, Massoud Amanlou, Ali Masoudi-Nejad
    Journal of Chemical Information and Modeling, Vol. 2, No 2, 2019
54. "Introducing a panel for early detection of lung adenocarcinoma by integration of genomics, epigenomics, transcriptomics and proteomics"
    Niloofar Haghjoo, Ali Moeini, Ali Masoudi-Nejad
    EXPERIMENTAL AND MOLECULAR PATHOLOGY, Vol. 1, No 1, 2019
55. "Novel Potential Drugs for Therapy of Age-Related Macular Degeneration Using Protein-Protein Interaction Network (PPI) Analysis"
    Zahra Abedi, Habib Mottighader, Mazaher Maghsoudloo, Mohammad Ali Sheikh Beig Goharrizi, Ahmad Shojaei, Ali Masoudi-Nejad
    Journal of Ophthalmic and Optometric Sciences, Vol. 3, No 4, pp.11-13, 2019
56. "Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia"
    Zeinabsadat Mousavianhor, Abbas Nouzari Dalini, Yasir Rahmatallah, Ali Masoudi-Nejad
    MOLECULAR MEDICINE, Vol. 25, No 1, 2019
57. "Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues"
    Nadia Barjaste, maryam shahhoseini, Parvaneh Afsharian, Ali Sharifi-zarchi, Ali Masoudi-Nejad
    JOURNAL OF ASSISTED REPRODUCTION AND GENETICS, Vol. 1, No 1, 2019
58. "Trader as a new optimization algorithm predicts drug-target interactions efficiently"
    Yosef Masoudi-Sobhanzadeh, Yadolah Omidi, Massoud Amanlou, Ali Masoudi-Nejad
    Scientific Reports, Vol. 9, No 1, 2019
59. "Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data"
    Ali Khosravi, B.BB Jayaram, Bahram Golyaei, Ali Masoudi-Nejad
    MOLECULAR MEDICINE, Vol. 25, No 1, 2019
60. "Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis"
    Morteza Kouhsar, Sadegh Azimzadeh-Jamalkandi, Ali Moeini, Ali Masoudi-Nejad
    Scientific Reports, Vol. 9, No 1, 2019
61. "DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy"
    Yosef Masoudi-Sobhanzadeh, Yadolah Omidi, Massoud Amanlou, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 109, No 1, pp.254-262, 2019
62. "Drug databases and their contributions to drug repurposing"
    Yosef Masoudi-Sobhanzadeh, Yadolah Omidi, Massoud Amanlou, Ali Masoudi-Nejad
    GENOMICS, Vol. 1, No 1, 2019
63. "Systematic analysis of genes and diseases using PheWAS-Associated networks"
    Ali Khosravi, Morteza Kouhsar, Bahram Golyaei, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 1, No 1, 2019
64. "FeatureSelect: a software for feature selection based on machine learning approaches"
    Yosef Masoudi-Sobhanzadeh, Habib Mottighader, Ali Masoudi-Nejad
    BMC BIOINFORMATICS, Vol. 20, No 1, 2019
65. "CatbNet: A Multi Network Analyzer for Comparing and Analyzing the Topology of Biological Networks"
    Ehsan Pournoor, naser Elmi, Ali Masoudi-Nejad
    CURRENT GENOMICS, Vol. 20, No 1, pp.69-75, 2019
66. "Disease global behavior: A systematic study of the human interactome network reveals conserved topological features among categories of diseases"
    Ehsan Pournoor, naser Elmi, Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad
    Informatics in Medicine Unlocked, Vol. 17, No 1, 2019
67. "Block alignment: New representation and comparison method to study evolution of genomes"
    Hossein Lenjanian, Abbas Nouzari Dalini, Nazanin Hosseinkhan, Ali Masoudi-Nejad
    GENOMICS, Vol. 111, No 6, pp.1-4, 2018
68. "Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis"
    Zahra Mortezaei, Ali Ashraf Mehrabi, JBC Cazier, Ali Masoudi-Nejad
    JOURNAL OF CELLULAR BIOCHEMISTRY, Vol. 120, No 4, pp.5459-5471, 2018
69. "Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions"
    Dariush Salimi, Ali Moeini, Ali Masoudi-Nejad
    Genes & Genomics, Vol. 40, No 12, pp.1363-1371, 2018
70. "Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer"
    Fariba Dehghanian, Zohreh Hojati, Nazanin Hosseinkhan, Zeinabsadat Mousavianhor, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 99, pp.76-84, 2018
71. "Link prediction potentials for biological networks: a computational view"
    Sadegh Sulaimany, Mohammad Khansari, Ali Masoudi-Nejad
    International Journal of Data Mining and Bioinformatics, Vol. 2, No 10, pp.32-45, 2018
72. "Network-based expression analyses and experimental validations revealed high co-expression between Yap1 and stem cell markers compared to differentiated cells"
    Fariba Dehghanian, Zohreh Hojati, Fariba Esmaeili, Ali Masoudi-Nejad
    GENOMICS, Vol. 1, No 1, 2018
73. "GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes"
    Alireza Meshkin, Azadeh Shakery, Ali Masoudi-Nejad
    GENOMICS, Vol. 1, No 1, 2018
74. "SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large Metabolic Networks"
    Yazdan Asgari, Zahra Zabihin Pour, Ali Masoudi-Nejad
    Current Bioinformatics, Vol. 13, No 1, pp.100-107, 2018
75. "Cattle infection response network and its functional modules"
    Hamid Beiki, Abas Pakdl, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, James Reecy
    BMC IMMUNOLOGY, Vol. 19, No 1, 2018
76. "Comparison of gene co-expression networks in Pseudomonas aeruginosa and Staphylococcus aureus reveals conservation in some aspects of virulence"
    Nazanin Hosseinkhan, Zeinabsadat Mousavianhor, Ali Masoudi-Nejad
    GENE, Vol. 639, No 639, pp.1-10, 2018
77. "LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma"
    Shervin Alaei, Balal Sadeghi, Ali Najafi, Ali Masoudi-Nejad
    GENOMICS, Vol. 1, No 1, 2018
78. "The Importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation"
    Marziye Dehghan, Hossein Lenjanian, Gholam Hosein Riyazi, Ali Masoudi-Nejad
    Iranian Journal of Pharmaceutical Research, Vol. 1, No 1, 2017
79. "Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study"
    Zahra Mortezaei, Hossein Lenjanian, Ali Masoudi-Nejad
    GENOMICS, Vol. 109, pp.158-164, 2017
80. "Inhibitory effects of lactic acid bacteria isolated from traditional fermented foods against aflatoxigenic Aspergillus spp."
    Maryam Ebrahimi, Morteza Khamiri, Ali Masoudi-Nejad, Alireza Sadeghi
    Comparative Clinical Pathology, Vol. 26, No 5, pp.1083-1092, 2017
81. "Biogeography, distribution and conservation status of maples (Acer L.) in Iran"
    Mojgan Sadat Mohtashamian, Farideh Attar, Kaveh Kavousi, Ali Masoudi-Nejad
    TREES-STRUCTURE AND FUNCTION, Vol. 31, No 3, pp.1-16, 2017
82. "Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis"
    Ehsan Khodadadi, Ali Ashraf Mehrabi, Ali Najafi, Saber Rastad, Ali Masoudi-Nejad
    PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS, Vol. 23, No 2, 2017
83. "Sequential and Mixed Genetic Algorithm and Learning Automata (SGALA, MGALA) for Feature Selection in QSAR"
    Habib Motieghader, Sajjad Gharaghani, Yosef Masoudi-sobhanzadeh, Ali Masoudi-Nejad
    Iranian Journal of Pharmaceutical Research, Vol. 16, No 2, pp.533-553, 2017
84. "Micromorphological studies of leaf epidermal features in populations of maples (Acer L.) from Iran"
    Mojgan Sadat Mohtashamian, Farideh Attar, Kaveh Kavousi, Ali Masoudi-Nejad
    Phytotaxa, Vol. 299, No 1, 2017
85. "Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data"
    Zahra Narimani, حمید بیگی , Ashar Ahmad, Ali Masoudi-Nejad, Holger Frohlich
    PLoS One, Vol. 12, No 2, 2017
86. "Predicting brain network changes in Alzheimer's disease with link prediction algorithms"
    Sadegh Sulaimany, Mohammad Khansari, Peyman Zarrineh, Madelaine Daianu, Neda Jahanshad, Paul M. Thompson, Ali Masoudi-Nejad
    Molecular BioSystems, Vol. 13, No 4, pp.725-735, 2017
87. "mRNA–miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation"
    Habib Mottighader, Morteza Kouhsar, Ali Najafi, Balal Sadeghi, Ali Masoudi-Nejad
    Molecular BioSystems, Vol. 13, No 10, pp.2168-2180, 2017
88. "A hybrid gene selection algorithm for microarray cancer classification using genetic algorithm and learning automata"
    Habib Mottighader, Ali Najafi, Balal Sadeghi, Ali Masoudi-Nejad
    Informatics in Medicine Unlocked, Vol. 9, No 1, pp.246-254, 2017
89. "Large-scale gene co-expression network as a source of functional annotation for cattle genes"
    Hamid Beiki, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, Zhi-liang Hu, James M Reecy, Abbas Pakdel
    BMC GENOMICS, Vol. 17, No 1, 2016
90. "Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia"
    Zeinab Moosavian, Abbas Nouzari Dalini, Ronald Stam, Yasir Rahmatallah, Ali Masoudi-Nejad
    CELLULAR ONCOLOGY, Vol. 40, No 1, pp.33-45, 2016
91. "CeFunMO: A centrality based method for discovering functional motifs with application in biological networks"
    Morteza Kouhsar, Zahra Razaghi Moghadam Kashani, Zaynab Mousavian, Ali Masoudi-Nejad
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 76, No 1, pp.154-159, 2016
92. "theory in systems biology. : Gene regulatory and metabolic networks"
    Zeinabsadat Mousavianhor, Kaveh Kavousi, Ali Masoudi-Nejad
    SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, Vol. 1, No 51, 2016
93. "Drug–target interaction prediction from PSSM based evolutionary information"
    Zeinab Moosavian, Sahan Khakabimamaghani, Kaveh Kavousi, Ali Masoudi-Nejad
    JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS, Vol. 78, No 2, pp.42-51, 2016
94. "Information theory in systems biology. Part II: protein–protein interaction and signaling networks"
    Zeinabsadat Mousavianhor, Jose Diaz, Ali Masoudi-Nejad
    SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, Vol. 51, No 1, pp.14-23, 2016
95. "Flow of Information in Biological Systems"
    Ali Masoudi-Nejad, Hector Zenil
    SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, Vol. 51, No 2, pp.1-2, 2016
96. "Protein Clustering and Interactome Analysis in Parkinson and Alzheimer's Diseases"
    Mostafa Rezaei-tavirani, Mona Zamanian-azodi, Sepideh Rajabi, Ali Masoudi-Nejad, Mohammad Rostami-nejad, Sara Rahmatirad
    Archives of Iranian Medicine, Vol. 1, No 19, 2016
97. "Determination of the Best Concentration of Streptozotocin to Create a Diabetic Brain Using Histological Techniques"
    Marzieh Dehghan-shasaltaneh, Nasser Naghdi, Samira Choopani, Leila Alizadeh, Bahram Bolouri, Ali Masoudi-Nejad, Gholam Hosein Riyazi
    JOURNAL OF MOLECULAR NEUROSCIENCE, Vol. 59, No 1, pp.24-35, 2016
98. "A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production"
    Reza Mohammadi, Jalil Fallah Mehrabadi, Gholamreza Bidkhori, Javad Zahiri, Mohammad Javad Niroomand, Ali Masoudi-Nejad
    Molecular BioSystems, Vol. 12, No 8, pp.2552-2561, 2016
99. "Computational detection of piRNA in human using support vector machine"
    Atefeh Seyeddokht, Ali Asghar Aslami Nejad, Ali Masoudi-Nejad, Mohammad Reza Nasiri, Javad Zahiri, Balal Sadeghi
    AVICENNA JOURNAL OF MEDICAL BIOTECHNOLOGY, Vol. 8, No 1, 2016
100. "Analysis of the enzyme network involved in cattle milk production using graph theory"
     شعله قربانی , Ali Masoudi-Nejad, Mojtaba Tahmoorespur, محمدرضا نصیری , Yazdan Asgari
     Molecular Cell Biology Research Communications, Vol. 4, No 2, pp.93-103, 2015
101. "Alterations in cancer cell metabolism: The Warburg effect and metabolic adaptation"
     Yazdan Asgari, Zahra Zabihinpour, Ali Salehzadeh-yazdi, Falk Schreiber, Ali Masoudi-Nejad
     GENOMICS, Vol. 105, pp.275-281, 2015
102. "Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data"
     Edwin Wang, Naif Zaman, Shauna Mcgee, Jean-sebastien Milanese, Ali Masoudi-Nejad, Maureen Oconnor-mccourt
     SEMINARS IN CANCER BIOLOGY, Vol. 30, No 1, pp.4-12, 2015
103. "Cancer modeling and network biology: Accelerating toward personalized medicine"
     Ali Masoudi-Nejad, Edwin Wang
     SEMINARS IN CANCER BIOLOGY, Vol. 30, No 1, pp.1-3, 2015
104. "Co-expressional conservation in virulence and stress related genes of three Gammaproteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa"
     Nazanin Hossein Khan, Peyman Zarrineh, Hassan Roknizadeh, Mohammad Reza Ashouri, Ali Masoudi-Nejad
     Molecular BioSystems, Vol. 11, No 11, pp.3137-3148, 2015
105. "LocFuse: Human Protein- Protein Interaction Prediction via Classifier Fusion Using Proteins Localization Information"
     Javad Zahiri, Morteza Mohammad Nouri, Reza Ebrahimpour, Samaneh Saadat, Joseph H.bozorgmehr, Talyana Goldberg, Ali Masoudi-Nejad
     GENOMICS, Vol. 1, No 104, pp.496-503, 2014
106. "Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung"
     Nazanin Hossein Khan, Peyman Zarrineh, Ali Masoudi-Nejad
     CURRENT GENOMICS, Vol. 15, No 5, pp.408-418, 2014
107. "Drug–target interaction prediction via chemogenomic space: learning-based methods"
     Zaynab Mousavian, Ali Masoudi-Nejad
     Expert Opinion on Drug Metabolism and Toxicology, Vol. 10, No 9, pp.1273-1287, 2014
108. "Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles"
     Peyman Zarrineh, Aminael Sa Nchez-rodrguez, Nazanin Hosseinkhan, Zahra Narimani, Kathleen Marchal, Ali Masoudi-Nejad
     PLoS One, Vol. 9, No 8, pp.101-113, 2014
109. "Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: A Systems Biology Approach"
     Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad Reza Nourani, Ali Moeini
     PLoS One, Vol. 9, No 6, pp.806-810, 2014
110. "BosFinder: a novell pre-microRNA gene prediction algorithm in Bos taurus"
     Balal Sadeghi, Hamed Ahmadi, Sadegh Azimzadeh-jamalkand, Mohemmad Reza Nassiri, Ali Masoudi-Nejad
     ANIMAL GENETICS, Vol. 45, No 4, pp.479-484, 2014
111. "Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard"
     Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohammad Bagher Rezaee
     JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, Vol. 34, No 4, pp.283-289, 2014
112. "Centrality Measures in Biological Networks"
     Mahdiyeh Ghasemi, Hossein Seidkhani, Maseud Rahgozar, Ali Masoudi-Nejad
     Current Bioinformatics, Vol. 8, No 5, 2014
113. "Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach"
     A.. Salehzadeh-yazdi, Y.. Asgari, Ali Akbar Saboury, Ali Masoudi-Nejad
     PLoS One, Vol. 9, No 1, pp.1-12, 2014
114. "Genome Scale Modeling in Systems Biology: Algorithms and Resources"
     Ali Najafi, Gholamreza Bidkhori, Joseph H. Bozorgmehr, Ina Koch, Ali Masoudi-Nejad
     CURRENT GENOMICS, Vol. 15, No 2, pp.130-159, 2014
115. "Cancer systems biology and modeling: Microscopic scale and multiscale approaches"
     Ali Masoudi-Nejad, Gholamreza Bidkhori, Saman Hosseini Ashtiani, Ali Najafi, Joseph Bozorgmehr, Edwin Wang
     SEMINARS IN CANCER BIOLOGY, Vol. هنوز در مرحله چاپ قبل از انتشار, 2014
116. "Cuckoo search epistasis: a new method for exploring significant genetic interactions"
     Mehran Aflakparast, Abbas Gerami, M. P Dubec, sss Viswesvaran, Ali Masoudi-Nejad
     HEREDITY, Vol. 112, No 6, pp.666-674, 2014
117. "Metabolic Cancer Biology: Structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment"
     Ali Masoudi-Nejad, Yazdan Asgari
     SEMINARS IN CANCER BIOLOGY, Vol. هنوز در مرحله چاپ قبل از انتشار, 2014
118. "Informative Bayesian Model Selection: a method for identifying interactions in genome-wide data"
     Mehran Aflakparst, Ali Masoudi-Nejad, Joseph Bozorgmehr, Shyam Visweswaran
     Molecular BioSystems, Vol. 10, No 10, 2014
119. "Extracting a cancer model by enhanced ant colony optimisation algorithm"
     رضا شمسایی, محمد فتحی, Ali Masoudi-Nejad
     International Journal of Data Mining and Bioinformatics, Vol. 10, No 1, 2014
120. "Drug-target and disease networks: polypharmacology in the post-genomic era"
     Ali Masoudi-Nejad, Zeinab Moosavian, Joseph Hanon Bozorgmehr
     In Silico Biology, Vol. 1, No 1, 2013
121. "Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes"
     Yazdan Asgari, Ali Salehzadeh-Yazdi, فالک شرایبر, Ali Masoudi-Nejad
     PLoS One, Vol. 8, No 11, 2013
122. "Human RNAi pathway: crosstalk with organelles and cells"
     Sadegh Azimzadeh-Jamalkandi, Esmaeel Azadian, Ali Masoudi-Nejad
     FUNCTIONAL & INTEGRATIVE GENOMICS, Vol. 14, No 1, pp.31-46, 2013
123. "PPIevo: Protein-Protein interaction prediction from PSSM based evolutionary information"
     Javad Zahiri, Omid Yaghoubi, Morteza Mohammad Nouri, Reza Ebrahimpour, Ali Masoudi-Nejad
     GENOMICS, Vol. 102, No 4, pp.237-242, 2013
124. "Discovering dominant pathways and signal–response relationships in signaling networks through nonparametric approaches"
     ایثار نصیری, Ali Masoudi-Nejad, مهدی جلیلی, Ali Moeini
     GENOMICS, Vol. 102, No 4, pp.195-201, 2013
125. "C-element : A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks"
     Mahdiyeh Ghasemi, Maseud Rahgozar, Gholamreza Bidkhori, Ali Masoudi-Nejad
     PLoS One, Vol. 8, No 9, pp.121-132, 2013
126. "Computational Prediction of Protein–Protein Interaction Networks: Algorithms and Resources"
     Javad Zahiri, Joseph Hanon Bozorgmehr, Ali Masoudi-Nejad
     CURRENT GENOMICS, Vol. 14, No 6, pp.397-414, 2013
127. "QuateXelero: An Accelerated Exact Network Motif Detection Algorithm"
     Sahand Khakabimamaghani, Ali Masoudi-Nejad, Norbert Dichter, Ina Koch
     PLoS One, Vol. 8, No 7, 2013
128. "Reconstruction of an Integrated Genome-Scale CoExpression Network Reveals Key Modules Involved in Lung Adenocarcinoma"
     Gholamreza Bidkhori, Zahra Narimani, Saman Hosseini Ashtiani, Ali Moeini, Abbas Nouzari Dalini, Ali Masoudi-Nejad
     PLoS One, Vol. 8, No 7, pp.1-10, 2013
129. "Normalized Similarity Index : An adjusted index to prioritize article citations"
     Isar Nasiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini
     Journal of Informetrics, Vol. 7, No 1, pp.91-98, 2013
130. "HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens."
     Hamed Ahmadi, ali ahmadi, Sadegh Azimzadeh-Jamalkandi, Mehdi Aliyari Shore Deli, Ali Salehzadeh-Yazdi, Gholamreza Bidkhori, Ali Masoudi-Nejad
     GENOMICS, Vol. 1, No 1, 2012
131. "Computational Analyses for Identification Novel MicroRNAs from Cattle and Sheep"
     Balal Sadeghi, Mohammad Reza Nasiri, Ali Masoudi-Nejad, Mojtaba Tahmoorespour, Hesam Dehghani, Hamed Ahmadi
     Journal of Cell and Molecular Research, Vol. 4, No 4, 2012
132. "Patterns Prediction of Chemotherapy Sensitivity in Cancer Cell lines Using FTIR Spectrum, Neural Network and Principal Components Analysis"
     رضوان زنده دل, Ali Masoudi-Nejad, Seed Farshad Hoseini Shirazi
     Iranian Journal of Pharmaceutical Research, Vol. 1, No 1, 2012
133. "Molecular epidemiology of hepatitis C virus among injection drug users in Iran: a slight change in prevalence of HCV genotypes over time"
     Katrin Samimi Rad , Mohsaen Nasiri Toosi , Ali Masoudi-Nejad, Ali Najafi , Ramin Rahimnia , Fereshte Asgari , Alireza Namazi Shabestari , Gholamreza Hassanpour , Seyed Moayed Alavian , Fateme Asghari
     ARCHIVES OF VIROLOGY, Vol. 157, No 10, pp.1959-1965, 2012
134. "Building blocks of biological networks : a review on major network motif discovery algorithms"
     Ali Masoudi-Nejad, Falk Schreiber , Zahra Razaghi Moghadam Kashani
     IET Systems Biology, Vol. 6, No 5, pp.164-174, 2012
135. "Candidate gene prioritization"
     Ali Masoudi-Nejad, Alireza Meshkin , Behzad Haji Eghrari , Gholam Reza Bidkhori
     MOLECULAR GENETICS AND GENOMICS, Vol. 287, No 9, pp.679-698, 2012
136. "Bioinformatics study of the 3 - hydroxy - 3 - methylglotaryl - coenzyme A reductase ( HMGR ) gene in Gramineae"
     Maryam Darabi , Ali Masoudi-Nejad, Ghorbanali Nemat Zadeh
     MOLECULAR BIOLOGY REPORTS, Vol. 39, No 9, pp.8925-8935, 2012
137. "Gene Encoding and Bioinformatics Analysis of Protein Structure of B-Galactosidase from Bird Cherry oat Aphid"
     ثمین صدیق, Ali Masoudi-Nejad, Alireza Bandani, سهراب ایمانی, بهرام تفقدی نیا
     Archives des Maladies Professionnelles et de l Environnement, Vol. 65, No 8, pp.381-390, 2012
138. "Nonparametric simulation of signal transduction networks with semi - synchronized update"
     Isar Nasiri, Ali Masoudi-Nejad, Mehdi Jalili , Ali Moeini
     PLoS One, Vol. 7, No 6, 2012
139. "Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae"
     Maryam Darabi, Ali Izadi Darbandi, Ali Masoudi-Nejad, Mohammad Reza Naghavi, قربانعلی نعمت زاده
     MOLECULAR BIOLOGY REPORTS, Vol. 39, No 9, pp.8925-8935, 2012
140. "Computational Analysis of RNA - Protein Interaction interfaces via the Voronoi Diagram"
     Sedigheh Mahdavi , Ali Mohades , Ali Salehzadeh Yazdi , Samad Jahandideh , Ali Masoudi-Nejad
     JOURNAL OF THEORETICAL BIOLOGY, Vol. 293, pp.55-64, 2012
141. "Emerging Roles of Epigenetic Mechanisms in Parkinsons disease"
     Ehsan Habibi , Ali Masoudi-Nejad, Hm Abdolmaleky , Sj Haggarty
     FUNCTIONAL & INTEGRATIVE GENOMICS, Vol. 11, No 4, pp.523-537, 2012
142. "Modeling of Tumor Progression in NSCLC and Intrinsic Resistance to TKI in Loss of PTEN Expression"
     Gholamreza Bidkhori, Ali Moeini, Ali Masoudi-Nejad
     PLoS One, Vol. 7, No 10, 2012
143. "Expression of chalcone synthase influences flavonoid content and frequency of rhizogenesis in microshoots of Juglans regia L"
     Monireh Cheniany , Hasan Ebrahimzade Maboud, Ali Masoudi-Nejad
     PLANT CELL TISSUE AND ORGAN CULTURE, Vol. 109, No 1, pp.51-59, 2012
144. "Cisplatin Resistant Patterns in Ovarian Cell Line Using FTIR and Principle Component Analysis"
     Rezvan Zendehdel , Ali Masoudi-Nejad, Javad Mohammadzadeh , Farshad Shirazi
     Iranian Journal of Pharmaceutical Research, Vol. 11, No 1, pp.235-240, 2012
145. "Proteomics Databases and Websites"
     Mohieddin Jafari , Ali Masoudi-Nejad
     JOURNAL OF PARAMEDICAL SCIENCES, Vol. 3, No 3, pp.44-51, 2012
146. "CytoKavosh : A Cytoscape Plug - In for Finding Network Motifs in Large Biological Networks"
     Mitra Ansari , Ali Salehzade Yazdi , Sahand Khak Abi , Ali Masoudi-Nejad, Zahra Razaghi Moghadam Kashani
     PLoS One, Vol. 7, No 8, 2012
147. "Finding Exact and Solo LTR - Retrotransposons in Biological Sequences Using SVM"
     Torabi Dashti Hesam , Ali Masoudi-Nejad, Zare Fatemeh
     IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING-INTERNATIONAL ENGLISH EDITION, Vol. 31, No 2, pp.111-116, 2012
148. "Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems"
     Hossein Mirhendi , Roshanak Daie Ghazvini , Seyyed Ali Ghiasian , Ali Masoudi-Nejad, Hojjatollah Shokri , Minoo Soltani , Siamak Haddadi , Alireza Khosravi
     Iranian Journal of Veterinary Research, Vol. 20, No 4, pp.309-316, 2011
149. "Effect of expression of chalcone synthase gene on flavonoids content and rooting ability in Juglans regia L"
     Hasan Ebrahimzade Maboud, منیره چنیانی , Ali Masoudi-Nejad
     PLANT CELL TISSUE AND ORGAN CULTURE, Vol. 1, No 1, 2011
150. "RNAi Pathway Integration in Caenorhabditis elegans Development"
     Sadegh Azimzadeh Jamalkandi , Ali Masoudi-Nejad
     FUNCTIONAL & INTEGRATIVE GENOMICS, Vol. 11, No 3, pp.389-405, 2011
151. "Integration and Reduction of Microarray Data Using Information Theory Approach"
     رضا شمسایی , محمود فتحی , Ali Masoudi-Nejad
     IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING-INTERNATIONAL ENGLISH EDITION, Vol. 4, No 29, 2011
152. "MINING BIOLOGICAL REPETITIVE SEQUENCES USING SUPPORT VECTOR MACHINES AND FUZZY SVM"
     Torabi Dashti , Ali Masoudi-Nejad
     IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING-INTERNATIONAL ENGLISH EDITION, Vol. 29, No 4, 2011
153. "Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties"
     Ali Masoudi-Nejad, Sara Movahedi , Ruy Uregui
     BMC GENOMICS, Vol. 12, No 1, 2011
154. "gpALIGNER : a fast algorithm for global pairwise alignment of DNA sequences"
     Mostafa Hadian Dehkordi , Ali Masoudi-Nejad, Morteza Mohamad Mouri
     IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING-INTERNATIONAL ENGLISH EDITION, Vol. 30, No 2, pp.139-146, 2011
155. "COMPARING CARBOHYDRATE ENZYMES ACTIVITY IN EURYGASTER INTEGRICEPS PUTTON ( HEMIPTERA : SCUTELLERIDAE ) , RHOPALOSIPHUM PADI L . ( HOMOPTERA : APHIDIDAE ) AND HAPLOTHRIPS TRITICI KURD . ( PHLAEOTHRIPIDAE : THYSANOPTERA ) AS A COMPLEX PEST ON WHEAT"
     Samin Seddigh , Ali Masoudi-Nejad, Bahram Tafaghodinia , Sohrab Imani
     Munis Entomology & Zoology Journal, Vol. 7, No 1, 2011
156. "Effect of endogenous phenols and some antioxidant enzyme activities on rooting of Persian walnut ( Juglans regia L. )"
     Monireh Cheniany , Hassan Ebrahimzadeh , Ali Masoudi-Nejad, Kourosh Vahdati, Charles Leslie
     African Journal of Plant Science, Vol. 4, No 12, pp.479-487, 2010
157. "Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD - PCR"
     Alireza Khosravi, Foroogh Behzad , Azar Sabokbar , حجت اله شکری, Siamak Haddadi , Ali Masoudi-Nejad
     JOURNAL OF BASIC MICROBIOLOGY, Vol. 50, No 1, pp.68-73, 2010
158. "Computational methodologies for analyzing modeling and controlling gene regulatory networks"
     Zahra Zamani , Amirhossein Hajihosseini, Ali Masoudi-Nejad
     Biomedical Engineering and Computational Biology, Vol. -, No 2, pp.47-62, 2010
159. "Application of near - infrared spectroscopy and support vector machine in detection of HIV - 1 infection"
     Aliasghar Rahimi , Mirza Khalil Bahmani , Ali Masoudi-Nejad, Mojtaba Saadati , Ayob Khosravi , Azizollah Shafi Khani , Javad Mohamadzadeh
     مجله پزشکی کوثر, Vol. 15, No 1, pp.23-29, 2010
160. "N4 A Precise and Highly Sensitive Promoter Predictor Using Neural Network fed by Nearest Neighbors"
     Amjad Askary , Ali Masoudi-Nejad, Saeed Omidi , Roozbeh Sharafi , Amir Mizbani , Sobhan Naderi Parizi , Malihe Purmasjedi
     GENES & GENETIC SYSTEMS, Vol. 84, No 1, pp.425-430, 2009
161. "Reconstruction of Arabidopsis thaliana Fully - Integrated Small RNA Pathway"
     Sa Jamalkandi , Ali Masoudi-Nejad
     FUNCTIONAL & INTEGRATIVE GENOMICS, Vol. 9, No 4, pp.419-32, 2009
162. "Kavosh a new algorithm for finding network motifs"
     Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabiyan, Elahe Allahi, Abbas Nouzari Dalini, الناز صابری انصاری , سحر اسدی , شاهین محمدی, Ali Masoudi-Nejad
     BMC BIOINFORMATICS, Vol. 10, No 318, 2009
163. "MODA An Efficient Algorithm for Network Motif Discovery in Biological Networks"
     Saeed Omidi , F Schreiber , Ali Masoudi-Nejad
     GENES & GENETIC SYSTEMS, Vol. 84, No 5, pp.385-395, 2009
164. "Kavosh: a new algorithm for finding network motifs"
     Zahra Razaghi Moghadam Kashani, Ali Masoudi-Nejad, Elahe Allahi, Hayedeh Ahrabiyan, الناز صابری انصاری
     BMC BIOINFORMATICS, Vol. 10, No 1, pp.1-12, 2009
165. "A New Approach for Touching Cells Segmentation"
     Shihrin Nasr Isfahani , Atefeh Mirsafian , Ali Masoudi-Nejad
     BioMedical Engineering and Informatics, 2008. BMEI 2008. International Conference on, Vol. 1, pp.816-820, 2008
166. "Molecular Typing of Iranian Cladosporium Isolates Using RAPD - PCR"
     Siamak Haddadi , Alireza Khosravi, Mina Rostami Beshman, Minoo Soltani , Saeed Soltani , Ali Masoudi-Nejad
     Advances in Biochemical Engineering-Biotechnology, Vol. 7, No 4, pp.763-768, 2008
167. "Importance of 273rd residue in proteolytic processing for production of functional TSGA10 protein"
     Mohammad Modarressi , Fariba Ranjzad , Majid Tavallaei , A Asadi , H Zaim Kohan , Ali Masoudi-Nejad
     Bioscience Hypotheses, Vol. 1, No 6, 2008
168. "KEGG bioinformatics resource for plant genomics research"
     Ali Masoudi-Nejad, S Goto , Tr Endo , M Kanehisa
     Methods in Molecular Biology, Vol. 406, pp.437-458, 2007
169. "EGassembler : online bioinformatics service for large - scale processing clustering and assembling ESTs and genomic DNA fragments"
     Ali Masoudi-Nejad, K Tonomura , S Kawashima , Y Moriya , M Suzuki , M Itoh , M Kanehisa , T Endo , S Goto
     NUCLEIC ACIDS RESEARCH, Vol. 34, pp.459-462, 2006
170. "An alternative to radiation hybrid mapping for large - scale genome analysis"
     Ali Masoudi-Nejad, Shuhei Nasuda , Marie Therese Bihoreau , Robbie Waugh , Takashi Ryu Endo
     MOLECULAR GENETICS AND GENOMICS, Vol. 274, No 6, pp.589-594, 2005
171. "Developing a novel algorithm to predict diagnostic biomarkers in lung cancer"
     Morteza Piadeh kouhsar, Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad
     ژنتیک نوین, Vol. 16, No 2, 2021
172. "Population growth model of the carob moth, Ectomyelois ceratoniae (Lepidoptera: Pyralidae) under field conditions"
     Kobra Fotouhi, Seyed Hossein Goldansaz, مسعود امیرمعافی , Vahid Hosseininaveh, Ali Masoudi-Nejad
     Journal of Entomological Society of Iran, Vol. 41, No 1, pp.1-10, 2021
173. "Design of a bioinformatics model to predict drug compound properties and its application in inhibition of HIV replication and BACE-1"
     Karim Abasi, Ali Masoudi-Nejad
     Genetic Engineering and Biosafety Journal, Vol. 9, No 2, 2021
174. "Foodomics: A new approach to the influence of nutrition on the health of biological systems"
     Ali Masoudi-Nejad, Faezeh Mottaghitalab, Ali Akbar Moosavi Movahhedi
     Science Cultivation, Vol. 9, No 1, 2018
175. "Detecting of Functional Short Non-Coding RNAs using Bioinformatics Methods in Sheep and Goat"
     Atefeh Seyeddokht, Hamed Ahmadi, Ali Asghar Aslami Nejad, Ali Masoudi-Nejad, Mohammad Reza Nasiri, Balal Sadeghi
     Research On Animal Production(Scientific and Research), Vol. 8, No 15, pp.161-170, 2017
176. "Detection of Functional RNA Using Bioinformatics"
     Atefeh Seyeddokht, Hamed Ahmadi, Ali Asghar Aslami Nejad, Ali Masoudi-Nejad, Mohammad Nasirifard, Balal Sadeghi
     Research On Animal Production(Scientific and Research), Vol. 8, No 15, 2017
177. "Reconstruction and Topology Analysis of Metabolic Networks Involved in Bos Taurus Milk Production"
     Sholeh Ghorbani, Mojtaba Tahmoorespour, Ali Masoudi-Nejad, Mahammadreza Nasiri, Ehsan Moetamedian
     Animal Science Journal, Vol. 11, No 110, 2016
178. "Systems Biology, Synthetic Biology and Electronic Plants"
     [] [], Mojgan Torkaman Momeni, Ali Masoudi-Nejad
     Science Cultivation, Vol. 6, No 1, 2015

Conference Paper

1. "ParaKavosh: A Parallel Algorithm for Finding Biological Network Motifs"
   Zahra Razaghi Moghadam Kashani, Ali Masoudi-Nejad, Abbas Nouzari Dalini
   11 International Conference on Information and Knowledge Technology, 2020
2. "Functional Connectivity networks in free"
   Hossein Seidkhani, Hamid Pezeshk, Ali Masoudi-Nejad
   6th Neuroscience congress of Iran, 2017
3. "Biological Networks and NetworksBiology: a cancer story"
   Ali Masoudi-Nejad
   International congress Networks Biology, 2015
4. "Systems Biology: Making sense of the biological systems"
   Ali Masoudi-Nejad
   11th International symposium on programming and systems, 2013
5. "Protein-Protein Interaction Network Clustering Using Particle Swarm Optimization"
   Iman Sharafuddin, Mehrdad Mirzaii, Maseud Rahgozar, Ali Masoudi-Nejad
   IWBBIO 2013, 2013
6. "Modeling of tumor progression in non-small-cell lung cancer (NSCLC"
   Ali Masoudi-Nejad, Gholamreza Bidkhori
   4th Conference on Systems Biology of Mammalian Cells 2012, 2012
7. "Using GO annotation clustering to improve protein-protein interaction prediction"
   Javad Zahiri, Mohammad Hossein Karimi-jafari, Aabasali Emamjomeh, Ali Masoudi-Nejad, رضا ابراهیم پور
   4th Conference on Systems Biology of mammalian Cells, 2012
8. "Hubs and Non-Hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation"
   Ali Salehzadeh-Yazdi, Ali Masoudi-Nejad, Ali Akbar Saboury
   BIOKDD 2012, 2012
9. "Modeling and Analysis of Abnormality Detection in Biomolecular Nano-Networks"
   Farshad Lahouti, سیدسیاوش قوامی رودسری , Ali Masoudi-Nejad
   2nd IEEE International Workshop on Molecular and Nanoscale Communications.June 11 2012 Ottawa Canada, 2012
10. "Reconstruction of CNV-related co-expression"
    Gholamreza Bidkhori, Zahra Narimani, Ali Masoudi-Nejad
    4th Conference on Systems Biology of Mammalian Cells 2012, 2012
11. "A novel ensemble learning for protein protein interaction"
    Javad Zahiri, Mohammad Hossein Karimi-jafari, علیرضا ابراهیم پور, Ali Masoudi-Nejad
    4th Conference on Systems Biology of Mammalian Cells 2012, 2012
12. "Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network"
    حمید روایی, Ali Masoudi-Nejad, سعید امیدی, Ali Moeini
    10th International Conference on Bioinformatics and Bioengineering, 2010
13. "Endogenous phenolic contents peroxidase and polyphenoloxidase activities in shoot microcuttings from Persian walnut cultivars"
    منیره چنیانی, Hasan Ebrahimzade Maboud, Ali Masoudi-Nejad, Kourosh Vahdati
    6th International Walnut Symposium, 2009
14. "A Parallel algorithm for finding network motifs"
    زهرا رزاقی مقدم کاشانی, Hayedeh Ahrabiyan, Abbas Nouzari Dalini, الناز انصاری صابری, شاهین محمدی, افشین احمدیان, Ali Masoudi-Nejad
    The 2th iranian conference on bioinformatics, 2008
15. "A novel and efficient algorithm for finding network motifs"
    زهرا رزاقی مقدم کاشانی, Hayedeh Ahrabiyan, افشین احمدیان, Ali Masoudi-Nejad, Abbas Nouzari Dalini, الناز انصاری صابری, سحر اسدی, شاهین محمدی
    The 2th iranian conference on bioinformatics, 2008
16. "Alignment of protein-ptotein interaction networks by using genetic algorithm"
    زهرا رزاقی مقدم کاشانی, Hayedeh Ahrabiyan, Abbas Nouzari Dalini, سحر اسدی, افشین احمدیان, Ali Masoudi-Nejad
    The 2th iranian conference on bioinformatics, 2008
17. "Study of total protein and some antioxidant enzymes and their relationship with growth changes during in-vitro culture of walnut cultivars"
    Monireh Cheniani, Hasan Ebrahimzade Maboud, Ali Masoudi-Nejad, Kourosh Vahdati
    Fifteenth National and Third International Conference of Biology, 2008
18. "Mutant Plant sensetivity to environmental stress"
    Younes Mirzaei, Reza Shirzadian Khorramabad, Mohammad Mahdi Sohani, Ali Masoudi-Nejad
    12th Iranian genetics Congress, 2012
19. "Study of total protein and some antioxidant enzymes and their relationship with growth changes during in-vitro culture of walnut cultivars"
    Hasan Ebrahimzade Maboud, Monireh Cheniani, Ali Masoudi-Nejad, Kourosh Vahdati
    The 15th National & 3rd International Conference of Biology of Iran, 2008