Ali Masoudi-Nejad

1. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy

Zohrab Beigi Yasaman, Lanjanian Hossein, Fayazi Reyhane, Salimi Mahdieh, Haji Molla Hoseyni Behnaz, Noroozizadeh Mohammad Hafez, Masoudi-Nejad Ali (2025)., molecular biomedicine, 5(1).

2. Interplay of lung microbiome and epigenetics in former smokers: A machine learning and fuzzy logic approach on COPD progression

Taherkhani Hamidreza, KavianFar Azadeh, Lenjanian Hossein, حسین خان نازنین, Salimi Mahdieh, Nematzadeh Sajjad, Naghizadeh Mohammad Mehdi, عظیم زاده جمالکندی صادق, Masoudi-Nejad Ali (2025)., Heliyon, 11(5), e42944.

3. Keystone bacteria dynamics in chronic obstructive pulmonary disease (COPD): Towards differential diagnosis and probiotic candidates

KavianFar Azadeh, Taherkhani Hamidreza, Lenjanian Hossein, AminNezhad Sargol, احمدی علی, عظیم زاده جمالکندی صادق, Masoudi-Nejad Ali (2025)., Heliyon, 11(4), e42719.

1. HLAPepBinder: An Ensemble Model for The Prediction Of HLA-Peptide Binding

سعادتی مهسا, Zare-Mirakabad Fatemeh, Masoudi-Nejad Ali, Farahanchi Baradaran Mohammad, حسین خان نازنین (2024)., Iranian Journal of Biotechnology, 22(4).

2. CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction

Rafiei Fatemeh, زراعتی حجت, Abasi Karim, Razzaghi Parvin, Ghasemi Jahan Bakhsh, Parsaeian Mahboubeh, Masoudi-Nejad Ali (2024)., Journal of Chemical Information and Modeling, 64(7), 2577-2585.

3. Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome

Taherkhani Hamidreza, KavianFar Azadeh, AminNezhad Sargol, Lanjanian Hossein, احمدی علی, عظیم زاده جمالکندی صادق, Masoudi-Nejad Ali (2024)., Heliyon, 10(4), e24775.

4. Restoring the epigenetic landscape of lung microbiome: potential therapeutic approach for chronic respiratory diseases

Taherkhani Hamidreza, KavianFar Azadeh, احمدی علی, Salimi Mahdieh, Lenjanian Hossein, Masoudi-Nejad Ali (2024)., BMC Pulmonary Medicine, 24(1).

1. Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation

ShariatMadar Taleghani AliReza, Zohrab Beigi Yasaman, Zare-Mirakabad Fatemeh, Masoudi-Nejad Ali (2023)., Scientific Reports, 13(1).

2. Food co-consumption network as a new approach to dietary pattern in non-alcoholic fatty liver diseas

Naghizadeh Mohammad Mehdi, Osati Saeed, Homayounfar Reza, Masoudi-Nejad Ali (2023)., Scientific Reports, 13(1).

3. Identifying common signatures and potential therapeutic biomarkers in COPD and lung cancer using miRNA-mRNA co-expression networks

Fathinavid Amirhossein, Mousavianhor Zeinabsadat, Najafi Ali, Nematzadeh Sajjad, Salimi Mahdieh, Masoudi-Nejad Ali (2023)., Informatics in Medicine Unlocked, 34(1), 101115.

4. DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing

Ghorbanali Zahra, Zare-Mirakabad Fatemeh, Salehi Najmeh, Masoudi-Nejad Ali (2023)., BMC BIOINFORMATICS, 24(1).

5. Computational-based strategies to deal with liver injuries induced by the repurposed drugs against SARS-CoV-2

Bakhtiyari Nasim, Parvizpour Sepideh, Masoudi sobhanzadeh Yosef, Masoudi-Nejad Ali (2023)., Informatics in Medicine Unlocked, 41(1), 101336.

6. DeepTraSynergy: drug combinations using multimodal deep learning with transformers

Rafiei Fatemeh, Zeraati Hojjat, Abbasi Karim, Ghasemi Jahan Bakhsh, Parsaeian Mahboubeh, Masoudi-Nejad Ali (2023)., BIOINFORMATICS, 39(8).

7. A deep learning-based framework for predicting survival-associated groups in colon cancer by integrating multi-omics and clinical data

Salimy Siamak, Lanjanian Hossein, Abbasi Karim, Salimi Mahdieh, Najafi Ali, Tapak Leili, Masoudi-Nejad Ali (2023)., Heliyon, 9(7), e17653.

8. DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs

GhorbanAli Zahra, Zare-Mirakabad Fatemeh, اکبری محمد, Salehi Najmeh, Masoudi-Nejad Ali (2023)., Journal of Chemical Information and Modeling, 63(8), 2532-2545.

9. Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players

Naghizadeh Mohammad Mehdi, Bakhshandeh Behnaz, Noorbakhsh Farshid, Yaghmaie Marjan, Masoudi-Nejad Ali (2023)., Systems Biology in Reproductive Medicine, ND(ND), 1-12.

1. 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

Rastad Saber, Barjaste Nadia, Lanjanian Hossein, Moeini Ali, Kiani Farzad, Masoudi-Nejad Ali (2022)., GENES & GENETIC SYSTEMS, 97(6), 311-324.

2. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers

Moravveji Sayyed Sajjad, Khoshbakht Samane, Mokhtari Majid, Salimi Mahdieh, Lanjanian Hossein, Nematzadeh sajad, Torkamanianafshar Mahsa, Masoudi-Nejad Ali (2022)., BMC Genomic Data, 23(1).

3. Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug–gene interaction networks analysis

Motieghader Habib, Tabrizi Nezhadi Parinaz, Deldar Abad Paskeh Mahshid, برادران بهزاد, Mokhtarzadeh Ahad, Hashemi Mehrdad, Lanjanian Hossein, Jazayeri seyed Mehdi, Maleki Masoud, Khodadadi Ehsan, Nematzadeh Sajjad, Kiani Farzad, Maghsoudloo Mazaher, Masoudi-Nejad Ali (2022)., Scientific Reports, 12(1).

4. mRNA–miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis

Abedi Zahra, Mottighader Habib, Hosseini Seyedh Sahar, Sheikh Beig Goharrizi Mohammad Ali, Masoudi-Nejad Ali (2022)., Scientific Reports, 12(1).

5. Re-wiring and gene expression changes of AC025034.1 and ATP2B1 play complex roles in early-to-late breast cancer progression

Khoshbakht Samane, Mokhtari Majid, Moravveji Sayyed Sajjad, Azimzadeh-Jamalkandi Sadegh, Masoudi-Nejad Ali (2022)., BMC Genomic Data, 23(1).

6. Pan-cancer analysis of biological events on cell cycle instability in gastrointestinal cancers with integrative scoring method

Moravveji Sayyed Sajjad, Khoshbakht Samane, Mokhtari Majid, Salimi Mahdieh, Masoudi-Nejad Ali (2022)., GENOMICS, 114(1), 253-265.

1. Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

Khoshbakht Samane, Azimzadeh-Jamalkandi Sadegh, Masoudi-Nejad Ali (2021)., BMC MEDICAL GENOMICS, 14(1).

2. Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis

Fathinavid Amirhossein, Zarei Ghobadi Mohadeseh, Najafi Ali, Masoudi-Nejad Ali (2021)., BMC Genomic Data, 22(1).

3. A fuzzy logic-based computational method for the repurposing of drugs against COVID-19

Masoudi-Sobhanzadeh Yosef, Esmaeili Hosein, Masoudi-Nejad Ali (2021)., BioImpacts, 11(5).