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Compiled Books:

Next Generation Sequencing and Sequence Assembly

Next Generation Sequencing and Sequence Assembly: methodologies and algorithms.


Ali Masoudi-Nejad, Zahra Narimani, Nazanin Hosseinkhan.

SpringerBriefs in Systems Biology. 2013
Next Generation Sequencing and Sequence Assembly

Microscopic Scale of the Cancer Systems Biology.


Ali Masoudi-Nejad, Gholamreza Bidkhori, Saman Hosseini Ashtiani, Ali Najafi.

SpringerBriefs in Systems Biology. 2014

Contributed Chapters

  1. Ali Masoudi-Nejad, Ali Salehzadeh, Shiva Akbari, Yazdan Asgari. Integration of Metabolic Knowledge for Genome-scale Metabolic Reconstruction.Invited chapter in book “Biological Knowledge Discovery Handbook: Preprocessing, Mining and Post processing of Biological Data ".ISBN: 978-1-1181-3273-9. John Wiley 2014.
  2. Ali Masoudi-Nejad, Susumu Goto, Takashi Endo and Minoru Kanehisa. KEGG/EGENES resource for plant bioinformatics in post-sequence era. Invited chapter in book “Plant Bioinformatics”. Humana Press. 2014.
  3. Bahman Yari, DaryanazDargahi, NimaAghaeepour and Ali Masoudi-Nejad. Support Vector Clustering: From Local Constraint to Global Stability. Invited chapter in book "Foundations of Computational Intelligence. Volume 6: Data Mining ". Springer 2009.
  4. Saeed Omidi and Ali Masoudi-Nejad. Network Evolution: Theory and Mechanisms. Invited chapter in book “Computational Network Analysis". Springer 2009

Published / Accepted Papers

  1. DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing.Z Ghorbanali, F Zare-Mirakabad, N Salehi, M Akbari, A Masoudi-Nejad.
    BMC bioinformatics 24 (1), 374, 2023.
  2. Computational-based strategies to deal with liver injuries induced by the repurposed drugs against SARS-CoV-2.N Bakhtiyari, S Parvizpour, Y Masoudi-Sobhanzadeh, A Masoudi-Nejad.
    Informatics in Medicine Unlocked, 101336, 2023.
  3. DeepTraSynergy: drug combinations using multimodal deep learning with transformers.F Rafiei, H Zeraati, K Abbasi, JB Ghasemi, M Parsaeian, ....
    Bioinformatics 39 (8), btad438, 2023.
  4. A deep learning-based framework for predicting survival-associated groups in colon cancer by integrating multi-omics and clinical data.S Salimy, H Lanjanian, K Abbasi, M Salimi, A Najafi, L Tapak, ....
    Heliyon 9 (7), 2023.
  5. DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs.Z Ghorbanali, F Zare-Mirakabad, M Akbari, N Salehi, A Masoudi-Nejad.
    Journal of Chemical Information and Modeling 63 (8), 2532-2545, 2023.
  6. Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players.MM Naghizadeh, B Bakhshandeh, F Noorbakhsh, M Yaghmaie, ....
    Systems Biology in Reproductive Medicine, 1-12, 2023.
  7. Parallel molecular alteration between Alzheimer’s disease and major depressive disorder in the human brain dorsolateral prefrontal cortex: An insight from gene expression and ….S Rastad, N Barjaste, H Lanjanian, A Moeini, F Kiani, A Masoudi-Nejad.
    Genes & Genetic Systems 97 (6), 311-324, 2022.
  8. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers.SS Moravveji, S Khoshbakht, M Mokhtari, M Salimi, H Lanjanian, ....
    BMC Genomic Data 23 (1), 1-9, 2022.
  9. Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug–gene interaction networks analysis.H MotieGhader, P Tabrizi-Nezhadi, M Deldar Abad Paskeh, B Baradaran, ....
    Scientific Reports 12 (1), 9417, 2022.
  10. mRNA–miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis.Z Abedi, H MotieGhader, SS Hosseini, MA Sheikh Beig Goharrizi, ....
    Scientific reports 12 (1), 5885, 2022.
  11. Re-wiring and gene expression changes of AC025034. 1 and ATP2B1 play complex roles in early-to-late breast cancer progression.S Khoshbakht, M Mokhtari, SS Moravveji, S Azimzadeh Jamalkandi, ....
    BMC Genomic data 23 (1), 6, 2022.
  12. Identifying common signatures and potential therapeutic biomarkers in COPD and lung cancer using miRNA-mRNA co-expression networks.A Fathinavid, Z Mousavian, A Najafi, S Nematzadeh, M Salimi, ....
    Informatics in Medicine Unlocked 34, 101115, 2022.
  13. Pan-cancer analysis of biological events on cell cycle instability in gastrointestinal cancers with integrative scoring method.SS Moravveji, S Khoshbakht, M Mokhtari, M Salimi, A Masoudi-Nejad.
    Genomics 114 (1), 253-265, 2022.
  14. A fuzzy logic-based computational method for the repurposing of drugs against COVID-19.Y Masoudi-Sobhanzadeh, H Esmaeili, A Masoudi-Nejad.
    BioImpacts: BI 12 (4), 315, 2022.
  15. Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer.S Khoshbakht, S Azimzadeh Jamalkandi, A Masudi-Nejad.
    BMC medical genomics 14, 1-12, 2021.
  16. Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis.A Fathinavid, MZ Ghobadi, A Najafi, A Masoudi-Nejad.
    BMC genomic data 22, 1-14, 2021.
  17. Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries.Y Masoudi-Sobhanzadeh, A Salemi, MM Pourseif, B Jafari, Y Omidi, ....
    Briefings in bioinformatics 22 (6), bbab113, 2021.
  18. A propagation-based seed-centric local community detection for multilayer environment: The case study of colon adenocarcinoma.E Pournoor, Z Mousavian, A Nowzari-Dalini, A Masoudi-Nejad.
    Plos one 16 (8), e0255718, 2021.
  19. High-throughput analysis of the interactions between viral proteins and host cell RNAs.H Lanjanian, S Nematzadeh, S Hosseini, M Torkamanian-Afshar, F Kiani, ....
    Computers in biology and medicine 135, 104611, 2021.
  20. In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm.M Torkamanian-Afshar, S Nematzadeh, M Tabarzad, A Najafi, ....
    Molecular diversity 25, 1395-1407, 2021.
  21. A multimodal deep learning-based drug repurposing approach for treatment of COVID-19.SA Hooshmand, M Zarei Ghobadi, SE Hooshmand, ....
    Molecular diversity 25, 1717-1730, 2021.
  22. DNA methylation association with stage progression of head and neck squamous cell carcinoma.V Ghafarpour, M Khansari, AM Banaei-Moghaddam, A Najafi, ....
    Computers in Biology and Medicine 134, 104473, 2021.
  23. Nodes with the highest control power play an important role at the final level of cooperation in directed networks.A Ebrahimi, M Yousefi, F Shahbazi, MA Sheikh Beig Goharrizi, ....
    Scientific Reports 11 (1), 13668, 2021.
  24. Revealing transcriptional and post-transcriptional regulatory mechanisms of γ-glutamyl transferase and keratin isoforms as novel cooperative biomarkers in low-grade glioma and ….F Mottaghitalab, H Lanjanian, A Masoudi-Nejad.
    Genomics 13 (4), 2623-2633, 2021.
  25. Distinguishing drug/non-drug-like small molecules in drug discovery using deep belief network.SA Hooshmand, SA Jamalkandi, SM Alavi, A Masoudi-Nejad.
    Molecular Diversity 25, 827-838, 2021.
  26. Deep learning in drug target interaction prediction: current and future perspectives.K Abbasi, P Razzaghi, A Poso, S Ghanbari-Ara, A Masoudi-Nejad.
    Current Medicinal Chemistry 28 (11), 2100-2113, 2021.
  27. Comparison of COPD and Lung Cancer Mechanisms for Identifying MicroRNA Biomarkers By The Reconstruction of miRNA-mRNA Co-Expression Network.A Fathinavid, Z Mousavian, A Najafi, A Masoudi-Nejad.
    …, 2021.
  28. A machine learning method based on the genetic and world competitive contests algorithms for selecting genes or features in biological applications.Y Masoudi-Sobhanzadeh, H Motieghader, Y Omidi, A Masoudi-Nejad.
    Scientific Reports 11 (1), 3349, 2021.
  29. ParaKavosh: A Parallel Algorithm for Finding Biological Network Motifs.ZRM Kashani, A Masoudi-Nejad, A Nowzari-Dalini.
    2020 11th International Conference on Information and Knowledge Technology …, 2020.
  30. Appropriate time to apply control input to complex dynamical systems.A Ebrahimi, A Nowzari-Dalini, M Jalili, A Masoudi-Nejad.
    Scientific Reports 10 (1), 22035, 2020.
  31. Design of a bioinformatics model to predict drug compound properties and its application in inhibition of HIV replication and BACE-1.K Abbasi, A Masoudi-Nejad.
    Genetic Engineering and Biosafety Journal 9 (2), 181-193, 2020.
  32. ParaKavosh: A Parallel Algorithm for Finding Biological Network Motifs.Z Razaghi-Moghadam, A Masoudi-Nejad, A Nowzari-Dalini.
    …, 2020.
  33. Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm.Y Masoudi-Sobhanzadeh, A Masoudi-Nejad.
    BMC bioinformatics 21, 1-21, 2020.
  34. Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis.M Maghsoudloo, S Azimzadeh Jamalkandi, A Najafi, A Masoudi-Nejad.
    Molecular Medicine 26 (1), 1-19, 2020.
  35. Target controllability with minimal mediators in complex biological networks.A Ebrahimi, A Nowzari-Dalini, M Jalili, A Masoudi-Nejad.
    Genomics 112 (6), 4938-4944, 2020.
  36. An efficient hybrid feature selection method to identify potential biomarkers in common chronic lung inflammatory diseases.M Maghsoudloo, SA Jamalkandi, A Najafi, A Masoudi-Nejad.
    Genomics 112 (5), 3284-3293, 2020.
  37. mRNA and microRNA selection for breast cancer molecular subtype stratification using meta-heuristic based algorithms.H MotieGhader, Y Masoudi-Sobhanzadeh, SH Ashtiani, A Masoudi-Nejad.
    Genomics 112 (5), 3207-3217, 2020.
  38. DeepCDA: deep cross-domain compound–protein affinity prediction through LSTM and convolutional neural networks.K Abbasi, P Razzaghi, A Poso, M Amanlou, JB Ghasemi, ....
    Bioinformatics 36 (17), 4633-4642, 2020.
  39. Synthetic Repurposing of Drugs in Hypertension: a Datamining Method Based on Association Rules and a Novel Discrete Algorithm.Y Masoudi-Sobhanzadeh, A Masoudi-Nejad.
    …, 2020.
  40. RPINBASE: an online toolbox to extract features for predicting RNA-protein interactions.M Torkamanian-Afshar, H Lanjanian, S Nematzadeh, M Tabarzad, ....
    Genomics 112 (3), 2623-2632, 2020.
  41. Identification of key components in colon adenocarcinoma using transcriptome to interactome multilayer framework.E Pournoor, Z Mousavian, AN Dalini, A Masoudi-Nejad.
    Scientific reports 10 (1), 4991, 2020.
  42. Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.N Poorinmohammad, J Hamedi, A Masoudi-Nejad.
    Scientific reports 10 (1), 3787, 2020.
  43. Drug databases and their contributions to drug repurposing.Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad.
    Genomics 112 (2), 1087-1095, 2020.
  44. Introducing a panel for early detection of lung adenocarcinoma by using data integration of genomics, epigenomics, transcriptomics and proteomics.N Haghjoo, A Masoudi-Nejad.
    Experimental and molecular pathology 112, 104360, 2020.
  45. Transcription Factors and microRNA Genes Regulatory Network Construction Under Drought Stress in Sesame (Sesamum indicum L.).MA Baghery, SK Kazemitabar, A Dehestani, P Mehrabanjoubani, ....
    …, 2020.
  46. Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia.Z Mousavian, A Nowzari-Dalini, Y Rahmatallah, A Masoudi-Nejad.
    Molecular Medicine 25, 1-12, 2019.
  47. Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data.A Khosravi, B Jayaram, B Goliaei, A Masoudi-Nejad.
    Molecular Medicine 25, 1-11, 2019.
  48. FeatureSelect: a software for feature selection based on machine learning approaches.Y Masoudi-Sobhanzadeh, H Motieghader, A Masoudi-Nejad.
    BMC bioinformatics 20 (1), 1-17, 2019.
  49. Deep transferable compound representation across domains and tasks for low data drug discovery.K Abbasi, A Poso, J Ghasemi, M Amanlou, A Masoudi-Nejad.
    Journal of chemical information and modeling 59 (11), 4528-4539, 2019.
  50. Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues.N Barjaste, M Shahhoseini, P Afsharian, A Sharifi-Zarchi, ....
    Journal of Assisted Reproduction and Genetics 36, 1743-1752, 2019.
  51. Network-based expression analyses and experimental validations revealed high co-expression between Yap1 and stem cell markers compared to differentiated cells.F Dehghanian, Z Hojati, F Esmaeili, A Masoudi-Nejad.
    Genomics 111 (4), 831-839, 2019.
  52. GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes.A Meshkin, A Shakery, A Masoudi-Nejad.
    Genomics 111 (4), 612-618, 2019.
  53. Trader as a new optimization algorithm predicts drug-target interactions efficiently.Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad.
    Scientific reports 9 (1), 9348, 2019.
  54. Detection of novel biomarkers for early detection of non-muscle-invasive bladder cancer using competing endogenous RNA network analysis.M Kouhsar, S Azimzadeh Jamalkandi, A Moeini, A Masoudi-Nejad.
    Scientific reports 9 (1), 8434, 2019.
  55. DrugR+: a comprehensive relational database for drug repurposing, combination therapy, and replacement therapy.Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad.
    Computers in biology and medicine 109, 254-262, 2019.
  56. Systematic analysis of genes and diseases using PheWAS-Associated networks.A Khosravi, M Kouhsar, B Goliaei, B Jayaram, A Masoudi-Nejad.
    Computers in Biology and Medicine 109, 311-321, 2019.
  57. Novel putative drugs and key initiating genes for neurodegenerative disease determined using network‐based genetic integrative analysis.Z Mortezaei, JB Cazier, AA Mehrabi, C Cheng, A Masoudi‐Nejad.
    Journal of Cellular Biochemistry 120 (4), 5459-5471, 2019.
  58. Novel potential drugs for therapy of age-related molecular degeneration using protein-protein interaction network (PPI) analysis.Z Abedi, H MotieGhader, M Maghsoudloo, MA Sheikh Beig Goharrizi, ....
    J Ophthalmic Optom Sci 3, 11-23, 2019.
  59. Disease global behavior: a systematic study of the human interactome network reveals conserved topological features among categories of diseases.E Pournoor, N Elmi, Y Masoudi-Sobhanzadeh, A Masoudi-Nejad.
    Informatics in Medicine Unlocked 17, 100249, 2019.
  60. Catbnet: A multi network analyzer for comparing and analyzing the topology of biological networks.E Pournoor, N Elmi, A Masoudi-Nejad.
    Current Genomics 20 (1), 69-75, 2019.
  61. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma.S Alaei, B Sadeghi, A Najafi, A Masoudi-Nejad.
    Genomics 111 (1), 76-89, 2019.
  62. Block alignment: New representation and comparison method to study evolution of genomes.MNA Lanjanian H, Nowzari A, Hosseinkhan N, Masoudi-Nejad A.
    Genomics, https://www.ncbi.nlm.nih.gov/pubmed/3044, 2018.
  63. Cattle infection response network and its functional modules.H Beiki, A Pakdel, AN Javaremi, A Masoudi-Nejad, JM Reecy.
    BMC immunology 19 (1), 2, 2018.
  64. Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer.F Dehghanian, Z Hojati, N Hosseinkhan, Z Mousavian, A Masoudi-Nejad.
    Computers in Biology and Medicine 99, 76-84, 2018.
  65. SCAN-Toolbox: structural COBRA add-on (SCAN) for analysing large metabolic networks.Y Asgari, Z Zabihinpour, A Masoudi-Nejad.
    Current Bioinformatics 13 (1), 100-107, 2018.
  66. The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation.A Masoudi-Nejad.
    Brieflands, 2018.
  67. Comparison of gene co-expression networks in Pseudomonas aeruginosa and Staphylococcus aureus reveals conservation in some aspects of virulence.N Hosseinkhan, Z Mousavian, A Masoudi-Nejad.
    Gene 639, 1-10, 2018.
  68. Link prediction potentials for biological networks.S Sulaimany, M Khansari, A Masoudi-Nejad.
    International Journal of Data Mining and Bioinformatics 20 (2), 161-184, 2018.
  69. The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation.M Dehghan-Shasaltaneh, H Lanjanian, GH Riazi, A Masoudi-Nejad.
    Iranian Journal of Pharmaceutical Research: IJPR 17 (1), 63, 2018.
  70. The Nature of Withdrawal Right in Electronic Contracts.سعیده باقری اصل, حیدر باقری اصل, ناصر مسعودی, ابراهیم شعاریان ستاری‎.
    فصلنامه مطالعات فقه و حقوق اسلامی 9 (17), 7-32‎, 2017.
  71. Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions.D Salimi, A Moeini, A Masoudi-Nejad.
    Genes & genomics 40 (12), 1363-1371, 2017.
  72. Task modulates functional connectivity networks in free viewing behavior.H Seidkhani, AR Nikolaev, RN Meghanathan, H Pezeshk, ....
    NeuroImage 159, 289-301, 2017.
  73. Biogeography, distribution and conservation status of maples (Acer L.) in Iran.M Mohtashamian, F Attar, K Kavousi, A Masoudi-Nejad.
    Trees 31, 1583-1598, 2017.
  74. Inhibitory effects of lactic acid bacteria isolated from traditional fermented foods against aflatoxigenic Aspergillus spp..M Ebrahimi, M Khomeiri, A Masoudi-Nejad, A Sadeghi, B Sadeghi, ....
    Comparative Clinical Pathology 26, 1083-1092, 2017.
  75. Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study.Z Mortezaei, H Lanjanian, A Masoudi-Nejad.
    Genomics 109 (3-4), 158-164, 2017.
  76. Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis.E Khodadadi, AA Mehrabi, A Najafi, S Rastad, A Masoudi-Nejad.
    Physiology and Molecular Biology of Plants 23, 331-342, 2017.
  77. Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data.Z Narimani, H Beigy, A Ahmad, A Masoudi-Nejad, H Fröhlich.
    PloS one 12 (2), e0171240, 2017.
  78. Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia.Z Mousavian, A Nowzari-Dalini, RW Stam, Y Rahmatallah, ....
    Cellular Oncology 40, 33-45, 2017.
  79. A hybrid gene selection algorithm for microarray cancer classification using genetic algorithm and learning automata.H Motieghader, A Najafi, B Sadeghi, A Masoudi-Nejad.
    Informatics in Medicine Unlocked 9, 246-254, 2017.
  80. mRNA–miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation.H Motieghader, M Kouhsar, A Najafi, B Sadeghi, A Masoudi-Nejad.
    Molecular BioSystems 13 (10), 2168-2180, 2017.
  81. Sequential and mixed genetic algorithm and learning automata (SGALA, MGALA) for feature selection in QSAR.H MotieGhader, S Gharaghani, Y Masoudi-Sobhanzadeh, ....
    Iranian journal of pharmaceutical research: IJPR 16 (2), 533, 2017.
  82. Micromorphological studies of leaf epidermal features in populations of maples (Acer L.) from Iran..M Mohtashamian, F Attar, K Kavousi, A Masoudi-Nejad.
    Phytotaxa 299 (1), 36-54, 2017.
  83. Predicting brain network changes in Alzheimer's disease with link prediction algorithms.S Sulaimany, M Khansari, P Zarrineh, M Daianu, N Jahanshad, ....
    Molecular BioSystems 13 (4), 725-735, 2017.
  84. Large-scale gene co-expression network as a source of functional annotation for cattle genes.H Beiki, A Nejati-Javaremi, A Pakdel, A Masoudi-Nejad, ZL Hu, JM Reecy.
    BMC genomics 17 (1), 1-13, 2016.
  85. CeFunMO: A centrality based method for discovering functional motifs with application in biological networks.M Kouhsar, Z Razaghi-Moghadam, Z Mousavian, A Masoudi-Nejad.
    Computers in Biology and Medicine 76, 154-159, 2016.
  86. Reconstruction and topology analysis of metabolic network involved in Bos Taurus milk production.S Ghorbani, M Tahmoorespur, A Masoudi-nejad, MR Nasiri, Y Asgari, ....
    Animal Sciences Journal 29 (110), 167-180, 2016.
  87. Determination of the best concentration of streptozotocin to create a diabetic brain using histological techniques.M Dehghan-Shasaltaneh, N Naghdi, S Choopani, L Alizadeh, B Bolouri, ....
    Journal of Molecular Neuroscience 59, 24-35, 2016.
  88. Flow of Information in Biological Systems..A Masoudi-Nejad, H Zenil.
    Seminars in Cell & Developmental Biology 51, 1-2, 2016.
  89. Information theory in systems biology. Part II: protein–protein interaction and signaling networks.Z Mousavian, J Díaz, A Masoudi-Nejad.
    Seminars in cell & developmental biology 51, 14-23, 2016.
  90. Information theory in systems biology. Part I: Gene regulatory and metabolic networks.Z Mousavian, K Kavousi, A Masoudi-Nejad.
    Seminars in cell & developmental biology 51, 3-13, 2016.
  91. Drug–target interaction prediction from PSSM based evolutionary information.Z Mousavian, S Khakabimamaghani, K Kavousi, A Masoudi-Nejad.
    Journal of pharmacological and toxicological methods 78, 42-51, 2016.
  92. Protein clustering and interactome analysis in Parkinson and Alzheimer's diseases.M Rezaei-Tavirani, M Zamanian-Azodi, S Rajabi, A Masoudi-Nejad, ....
    Archives of Iranian Medicine 19 (2), 0-0, 2016.
  93. Computational Detection of piRNA in Human Using Support Vector Machine.A Seyeddokht Dehbar, AA Aslaminejad, A Masoudi-Nejad, M Nassiri, ....
    پژوهش های تولیدات دامی 8‎, 2016.
  94. A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production.R Mohammadi, J Fallah-Mehrabadi, G Bidkhori, J Zahiri, MJ Niroomand, ....
    Molecular BioSystems 12 (8), 2552-2561, 2016.
  95. Computational detection of piRNA in human using support vector machine.A Seyeddokht, AA Aslaminejad, A Masoudi-Nejad, M Nassiri, J Zahiri, ....
    Avicenna Journal of Medical Biotechnology 8 (1), 36, 2016.
  96. Systems Biology, Synthetic Biology and Electronic Plant.A Masoudi Nejad, M Torkaman Momeni, E Zangene.
    Science Cultivation 6 (1), 65-70, 2015.
  97. Analysis of the enzyme network involved in cattle milk production using graph theory.S Ghorbani, M Tahmoorespur, AM Nejad, M Nasiri, Y Asgari.
    Molecular Biology Research Communications 4 (2), 93, 2015.
  98. Alterations in cancer cell metabolism: the Warburg effect and metabolic adaptation.Y Asgari, Z Zabihinpour, A Salehzadeh-Yazdi, F Schreiber, ....
    Genomics 105 (5-6), 275-281, 2015.
  99. Microscopic Scale of Cancer Systems Biology.A Masoudi-Nejad, G Bidkhori, SH Ashtiani, A Najafi.
    Springer, 2015.
  100. Cancer modeling and network biology: Accelerating toward personalized medicine.A Masoudi-Nejad, E Wang.
    Seminars in cancer biology 30, 1-3, 2015.
  101. Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data.E Wang, N Zaman, S Mcgee, JS Milanese, A Masoudi-Nejad, ....
    Seminars in cancer biology 30, 4-12, 2015.
  102. Cancer systems biology and modeling: microscopic scale and multiscale approaches.A Masoudi-Nejad, G Bidkhori, SH Ashtiani, A Najafi, JH Bozorgmehr, ....
    Seminars in cancer biology 30, 60-69, 2015.
  103. Metabolic cancer biology: structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment.A Masoudi-Nejad, Y Asgari.
    Seminars in cancer biology 30, 21-29, 2015.
  104. Co-expressional conservation in virulence and stress related genes of three Gammaproteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa.N Hosseinkhan, P Zarrineh, H Rokni-Zadeh, MR Ashouri, ....
    Molecular BioSystems 11 (11), 3137-3148, 2015.
  105. Cancer Modeling.A Masoudi-Nejad, G Bidkhori, SH Ashtiani, A Najafi.
    Microscopic Scale of Cancer Systems Biology, 41-61, 2015.
  106. Case Study: Modeling and Comparison of NSCLC and Normal EGFR Signaling.A Masoudi-Nejad, G Bidkhori, SH Ashtiani, A Najafi.
    Microscopic Scale of Cancer Systems Biology, 63-77, 2015.
  107. Formalisms for Molecular Modeling and Simulation.A Masoudi-Nejad, G Bidkhori, SH Ashtiani, A Najafi.
    Microscopic Scale of Cancer Systems Biology, 1-39, 2015.
  108. LocFuse: human protein–protein interaction prediction via classifier fusion using protein localization information.J Zahiri, M Mohammad-Noori, R Ebrahimpour, S Saadat, JH Bozorgmehr, ....
    Genomics 104 (6), 496-503, 2014.
  109. 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, AA Saboury, A Masoudi-Nejad.
    PloS one 9 (11), e111686, 2014.
  110. Analysis of genome-scale expression network in four major bacterial residents of cystic fibrosis lung.N Hosseinkhan, P Zarrineh, A Masoudi-Nejad.
    Current Genomics 15 (5), 408-418, 2014.
  111. Centrality measures in biological networks.M Ghasemi, H Seidkhani, F Tamimi, M Rahgozar, A Masoudi-Nejad.
    Current Bioinformatics 9 (4), 426-441, 2014.
  112. Drug–target interaction prediction via chemogenomic space: learning-based methods.Z Mousavian, A Masoudi-Nejad.
    Expert opinion on drug metabolism & toxicology 10 (9), 1273-1287, 2014.
  113. Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at ….P Zarrineh, A Sanchez-Rodriguez, N Hosseinkhan, Z Narimani, K Marchal, ....
    PLoS One 9 (8), e102871, 2014.
  114. BosFinder: a novell pre‐microRNA gene prediction algorithm in Bos taurus.B Sadeghi, H Ahmadi, S Azimzadeh‐Jamalkandi, MR Nassiri, ....
    Animal genetics 45 (4), 479-484, 2014.
  115. Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard.A Najafi, A Masoudi-Nejad, AA Imani Fooladi, M Ghanei, MR Nourani.
    Journal of receptors and signal transduction 34 (4), 283-289, 2014.
  116. Pathway reconstruction of airway remodeling in chronic lung diseases: a systems biology approach.A Najafi, A Masoudi-Nejad, M Ghanei, MR Nourani, A Moeini.
    PloS one 9 (6), e100094, 2014.
  117. Cuckoo search epistasis: a new method for exploring significant genetic interactions.M Aflakparast, H Salimi, A Gerami, MP Dubé, S Visweswaran, ....
    Heredity 112 (6), 666-674, 2014.
  118. Genome scale modeling in systems biology: algorithms and resources.A Najafi, G Bidkhori, J H Bozorgmehr, I Koch, A Masoudi-Nejad.
    Current genomics 15 (2), 130-159, 2014.
  119. Human RNAi pathway: crosstalk with organelles and cells.S Azimzadeh Jamalkandi, E Azadian, A Masoudi-Nejad.
    Functional & integrative genomics 14, 31-46, 2014.
  120. Influence of Cr dopant on the microstructure and optical properties of ZnO nanorods.S Safa, NA MASOUDI.
    JOURNAL OF ADVANCED MATERIALS AND PROCESSING (JOURNAL OF MATERIALS SCIENCE …, 2014.
  121. Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: A Systems.A Najafi, A Masoudi-Nejad, M Ghanei, MR Nourani, A Moeini.
    …, 2014.
  122. Informative Bayesian Model Selection: a method for identifying interactions in genome-wide data.M Aflakparast, A Masoudi-Nejad, JH Bozorgmehr, S Visweswaran.
    Molecular BioSystems 10 (10), 2654-2662, 2014.
  123. Extracting a cancer model by enhanced ant colony optimisation algorithm.R Shamsaee, M Fathy, A Masoudi-Nejad.
    International Journal of Data Mining and Bioinformatics 10 (1), 83-97, 2014.
  124. Integration of Metabolic Knowledge for Genome‐Scale Metabolic Reconstruction.A Masoudi‐Nejad, A Salehzadeh‐Yazdi, S Akbari‐Birgani, Y Asgari.
    Biological Knowledge Discovery Handbook, 1023-1048, 2013.
  125. Drug-target and disease networks: polypharmacology in the post-genomic era.A Masoudi-Nejad, Z Mousavian, JH Bozorgmehr.
    In silico pharmacology 1, 1-4, 2013.
  126. Computational structure analysis of biomacromolecule complexes by interface geometry.S Mahdavi, A Salehzadeh-Yazdi, A Mohades, A Masoudi-Nejad.
    Computational Biology and Chemistry 47, 16-23, 2013.
  127. Controllability in cancer metabolic networks according to drug targets as driver nodes.Y Asgari, A Salehzadeh-Yazdi, F Schreiber, A Masoudi-Nejad.
    PloS one 8 (11), e79397, 2013.
  128. Discovering dominant pathways and signal–response relationships in signaling networks through nonparametric approaches.I Nassiri, A Masoudi-Nejad, M Jalili, A Moeini.
    Genomics 102 (4), 195-201, 2013.
  129. PPIevo: Protein–protein interaction prediction from PSSM based evolutionary information.J Zahiri, O Yaghoubi, M Mohammad-Noori, R Ebrahimpour, ....
    Genomics 102 (4), 237-242, 2013.
  130. C-element: A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks.M Ghasemi, M Rahgozar, G Bidkhori, A Masoudi-Nejad.
    Plos one 8 (9), e72366, 2013.
  131. Computational prediction of protein–protein interaction networks: algorithms and resources.J Zahiri, J Hannon Bozorgmehr, A Masoudi-Nejad.
    Current genomics 14 (6), 397-414, 2013.
  132. Mineral metabolism during in vitro root development in microcuttings of Juglans regia L. cultivars.M Cheniany, H Ebrahimzadeh, A Masoudi-Nejad, K Vahdati.
    7th International Walnut Symposium, 2013.
  133. Quatexelero: an accelerated exact network motif detection algorithm.S Khakabimamaghani, I Sharafuddin, N Dichter, I Koch, A Masoudi-Nejad.
    PloS one 8 (7), e68073, 2013.
  134. Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma.G Bidkhori, Z Narimani, S Hosseini Ashtiani, A Moeini, A Nowzari-Dalini, ....
    PloS one 8 (7), e67552, 2013.
  135. Next generation sequencing and sequence assembly: methodologies and algorithms.A Masoudi-Nejad, Z Narimani, N Hosseinkhan.
    Springer Science & Business Media, 2013.
  136. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.H Ahmadi, A Ahmadi, S Azimzadeh-Jamalkandi, MA Shoorehdeli, ....
    Genomics 101 (2), 94-100, 2013.
  137. Controllability in Cancer Metabolic Networks According to Drug Targets as Driver.Y Asgari, A Salehzadeh-Yazdi, F Schreiber, A Masoudi-Nejad.
    …, 2013.
  138. A Sequence Motif Associated with Intrinsic Mutation Hot-Spots in Human Cancers.I Nassiri, E Azadian, A Masoudi-Nejad.
    J Proteomics Bioinform 6, 183-86, 2013.
  139. Nonparametric Computing Dominant Signaling Pathways and Signal-Response Relationships in Signaling Networks.I Nassiri, A Masoudi-Nejad, M Jalili, A Moeini.
    …, 2013.
  140. Protein-Protein Interaction Network Clustering Using Particle Swarm Optimization.I Sharafuddin, M Mirzaei, M Rahgozar, A Masoudi-Nejad.
    IWBBIO, 317-324, 2013.
  141. Emergence of Next-Generation Sequencing.A Masoudi-Nejad, Z Narimani, N Hosseinkhan, A Masoudi-Nejad, ....
    Next Generation Sequencing and Sequence Assembly: Methodologies and …, 2013.
  142. De novo assembly algorithms.A Masoudi-Nejad, Z Narimani, N Hosseinkhan, A Masoudi-Nejad, ....
    Next Generation Sequencing and Sequence Assembly: Methodologies and …, 2013.
  143. The Assembly of Sequencing Data.A Masoudi-Nejad, Z Narimani, N Hosseinkhan, A Masoudi-Nejad, ....
    Next Generation Sequencing and Sequence Assembly: Methodologies and …, 2013.
  144. Next-Generation Sequencing Methodologies.A Masoudi-Nejad, Z Narimani, N Hosseinkhan, A Masoudi-Nejad, ....
    Next Generation Sequencing and Sequence Assembly: Methodologies and …, 2013.
  145. Normalized Similarity Index: An adjusted index to prioritize article citations.I Nassiri, A Masoudi-Nejad, M Jalili, A Moeini.
    Journal of Informetrics 7 (1), 91-98, 2013.
  146. Modeling and analysis of abnormality detection in biomolecular nano-networks.S Ghavami, F Lahouti, A Masoudi-Nejad.
    Nano Communication Networks 3 (4), 229-241, 2012.
  147. Modeling of tumor progression in NSCLC and intrinsic resistance to TKI in loss of PTEN expression.G Bidkhori, A Moeini, A Masoudi-Nejad.
    PloS one 7 (10), e48004, 2012.
  148. Molecular epidemiology of hepatitis C virus among injection drug users in Iran: a slight change in prevalence of HCV genotypes over time.K Samimi-Rad, M Nasiri Toosi, A Masoudi-Nejad, A Najafi, R Rahimnia, ....
    Archives of virology 157, 1959-1965, 2012.
  149. Building blocks of biological networks: a review on major network motif discovery algorithms.A Masoudi-Nejad, F Schreiber, ZRM Kashani.
    IET systems biology 6 (5), 164-174, 2012.
  150. Hubs and Non-hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation.A Salehzadeh-Yazdi, A Masoudi-Nejad, AA Saboury, S Akbari-Birgani.
    2012 23rd International Workshop on Database and Expert Systems Applications …, 2012.
  151. Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae.M Darabi, A Masoudi-Nejad, G Nemat-Zadeh.
    Molecular biology reports 39, 8925-8935, 2012.
  152. CytoKavosh: a Cytoscape plug-in for finding network motifs in large biological networks.A Masoudi-Nejad, M Ansariola, Z Razaghi Moghadam Kashani, ....
    Public Library of Science 7 (8), e43287, 2012.
  153. Proteomics Databases and Websites.M Jafari, A Masoudi-Nejad.
    Archives of Advances in Biosciences 3 (3), 2012.
  154. Nonparametric simulation of signal transduction networks with semi-synchronized update.I Nassiri, A Masoudi-Nejad, M Jalili, A Moeini.
    PLoS One 7 (6), e39643, 2012.
  155. Computational analyses for identification novel microRNAs from cattle and sheep.B Sadeghi, M Nassiri, A Masoudi-Nejad, M Tahmoorespour, H Dehghani, ....
    Journal of Cell and Molecular Research 4 (2), 62-67, 2012.
  156. Expression of chalcone synthase influences flavonoid content and frequency of rhizogenesis in microshoots of Juglans regia L..M Cheniany, H Ebrahimzadeh, A Masoudi-nejad.
    Plant Cell, Tissue and Organ Culture (PCTOC) 109, 51-59, 2012.
  157. Finding protein complexes via fuzzy learning vector quantization algorithm.H Ravaee, A Masoudi-Nejad, A Moeini.
    Protein-Protein Interactions-Computational and Experimental Tools, 273-284, 2012.
  158. Computational analysis of RNA–protein interaction interfaces via the Voronoi diagram.S Mahdavi, A Mohades, AS Yazdi, S Jahandideh, A Masoudi-Nejad.
    Journal of theoretical biology 293, 55-64, 2012.
  159. Comparing carbohydrate enzymes activity in Eurygaster integriceps Putton (Hemiptera: Scutelleridae), Rhopalosiphum padi L.(Homoptera: Aphididae) and Haplothrips tritici Kurd ….S Seddigh, A Masoudi-Nejad, B Tafaghodinia, S Imani.
    Munis Entomology & Zoology 7 (1), 344-351, 2012.
  160. Finding exact and solo LTR-retrotransposons in biological sequences using SVM.DH TORABI, NALI MASOUDI, F Zare.
    IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE) 31 (262), 111-116, 2012.
  161. Patterns prediction of chemotherapy sensitivity in cancer cell lines using FTIR spectrum, neural network and principal components analysis.R Zendehdel, A Masoudi-Nejad, FH Shirazi.
    Iranian Journal of Pharmaceutical Research: IJPR 11 (2), 401, 2012.
  162. Cisplatin resistant patterns in ovarian cell line using FTIR and principle component analysis.R Zendehdel, A Masoudi-Nejad, J Mohammadzadeh, FH Shirazi.
    Iranian Journal of Pharmaceutical Research: IJPR 11 (1), 235, 2012.
  163. Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.A Masoudi-Nejad, S Movahedi, R Jáuregui.
    BMC genomics 12 (1), 1-11, 2011.
  164. Emerging roles of epigenetic mechanisms in Parkinson’s disease.E Habibi, A Masoudi-Nejad, HM Abdolmaleky, SJ Haggarty.
    Functional & integrative genomics 11, 523-537, 2011.
  165. RNAi pathway integration in Caenorhabditis elegans development.S Azimzadeh Jamalkandi, A Masoudi-Nejad.
    Functional & integrative genomics 11, 389-405, 2011.
  166. gpaligner: A fast algorithm for global pairwise alignment of dna sequences.DM HADIAN, NALI MASOUDI, MM MOHAMAD.
    IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE) 30 (258), 139-146, 2011.
  167. Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems.GR DAIE, H Mirhendi, SA Ghiasian, NA MASOUDI, H Shokri, M Soltani, ....
    IRANIAN JOURNAL OF VETERINARY RESEARCH (IJVR) 12 (437), 309-316, 2011.
  168. Effect of endogenous phenols and some antioxidant enzyme activities on rooting of Persian walnut (Juglans regia L.).M Cheniany, H Ebrahimzadeh, A Masoudi-nejad, K Vahdati, C Leslie.
    Afr J Plant Sci 4 (12), 479-487, 2010.
  169. Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD‐PCR.A Khosravi, F Behzad, A Sabokbar, H Shokri, S Haddadi, ....
    Journal of basic microbiology 50 (S1), S68-S73, 2010.
  170. Relationship between Endogenous Free IAA Levels and Peroxidase Activities during Root Development from Shoot Microcuttings of Persian Walnut Varieties.M Cheniany, H Ebrahimzadeh, A Masoudi-Nejad, K Vahdati.
    28th International Horticultural Congress, 2010.
  171. Improved immune genetic algorithm for clustering protein-protein interaction network.H Ravaee, A Masoudi-Nejad, S Omidi, A Moeini.
    2010 IEEE International Conference on BioInformatics and BioEngineering, 174-179, 2010.
  172. Integration and Reduction of Microarray Gene Expressions Using an Information Theory Approach.R Shamsaee, M Fathy, NALI MASOUDI.
    IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE) 29 (4), 19-29, 2010.
  173. Mining biological repetitive sequences using support vector machines and fuzzy SVM.DH TORABI, NALI MASOUDI.
    IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE) 29 (4), 1-17, 2010.
  174. Network evolution: theory and mechanisms.S Omidi, A Masoudi-Nejad.
    Computational Social Network Analysis: Trends, Tools and Research Advances …, 2010.
  175. computational Methodologies for Analyzing, Modeling and controlling Gene Regulatory networks.Z Zamani, A Hajihosseini, A Masoudi-Nejad.
    Biomedical Engineering and Computational Biology 2, BECB. S5594, 2010.
  176. Kavosh: a new algorithm for finding network motifs.ZRM Kashani, H Ahrabian, E Elahi, A Nowzari-Dalini, ES Ansari, S Asadi, ....
    BMC bioinformatics 10 (1), 1-12, 2009.
  177. Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway.SA Jamalkandi, A Masoudi-Nejad.
    Functional & integrative genomics 9, 419-432, 2009.
  178. Support vector clustering: from local constraint to global stability.BYS Khanloo, D Dargahi, N Aghaeepour, A Masoudi-Nejad.
    Foundations of Computational, IntelligenceVolume 6: Data Mining, 209-227, 2009.
  179. N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighbors.A Askary, A Masoudi-Nejad, R Sharafi, A Mizbani, SN Parizi, ....
    Genes & genetic systems 84 (6), 425-430, 2009.
  180. MODA: an efficient algorithm for network motif discovery in biological networks.S Omidi, F Schreiber, A Masoudi-Nejad.
    Genes & genetic systems 84 (5), 385-395, 2009.
  181. Dissection of rye chromosome 1R in common wheat [Triticum aestivum].M Tsuchida, T Fukushima, S Nasuda, A Masoudi-Nejad, G Ishikawa, ....
    Genes and Genetic Systems (Japan), 2008.
  182. Dissection of rye chromosome 1R in common wheat.M Tsuchida, T Fukushima, S Nasuda, A Masoudi-Nejad, G Ishikawa, ....
    Genes & Genetic Systems 83 (1), 43-53, 2008.
  183. EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.A Masoudi-Nejad, S Goto, R Jauregui, M Ito, S Kawashima, Y Moriya, ....
    Plant Physiology 144 (2), 857-866, 2007.
  184. KEGG bioinformatics resource for plant genomics research.A Masoudi-Nejad, S Goto, TR Endo, M Kanehisa.
    Plant Bioinformatics: Methods and Protocols, 437-458, 2007.
  185. EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.A Masoudi-Nejad, K Tonomura, S Kawashima, Y Moriya, M Suzuki, M Itoh, ....
    Nucleic acids research 34 (suppl_2), W459-W462, 2006.
  186. An alternative to radiation hybrid mapping for large-scale genome analysis in barley.A Masoudi-Nejad, S Nasuda, MT Bihoreau, R Waugh, TR Endo.
    Molecular Genetics and Genomics 274, 589-594, 2005.
  187. The kingdom of Plantae EST Indices: a resource for plant genomics community.A Masoudi-Nejad, R Jauregui, S Kawashima, S Goto, M Kanehisa, ....
    Genome Informatics, 16-18, 2004.
  188. MOLECULAR GENETICS AND GENOMICS STUDIES USING GAMETOCIDAL CHROMOSOMES.A Masoudi-Nejad.
    Kyoto University, 2003.
  189. Molecular cloning, sequencing, and chromosome mapping of a 1A-encoded ω-type prolamin sequence from wheat.A Masoudi-Nejad, S Nasuda, A Kawabe, TR Endo.
    Genome 45 (4), 661-669, 2002.
  190. Transfer of rye chromosome segments to wheat by a gametocidal system.A Masoudi-Nejad, S Nasuda, RA McIntosh, TR Endo, TR Endo.
    Chromosome Research 10, 349-357, 2002.
  191. Deep Learning in Drug Target Interaction Prediction: Current and Future Perspective.AMN Karim Abbasi, Parvin Razzaghi, Antti Poso, Saber Ghanbari-Ara.
    Current Medicinal Chemistry, DOI : 10.2174/092986732766620090714101, None.
  192. Informatics in Medicine Unlocked.E Pournoor, N Elmi, Y Masoudi-Sobhanzadeh, A Masoudi-Nejad.
    …, None.
  193. Bioinformatics in the post-genomics era: Towards Biology of the Systems.A Masoudi-Nejad.
    …, None.