Journal Paper

1. "AmiR-P3: An AI-based microRNA prediction pipeline in plants"
   سبحان عطائی, جعفر احمدی, Sayed Amir Marashi, Ilia Abolhassani
   PLoS One, Vol. 19, No 8, 2024
2. "RT-DOb, a switch gene for the gene pair {Csf1r, Milr1}, can influence the onset of Alzheimer’s disease by regulating communication between mast cell and microglia"
   Nasibeh Khayer, Nasrin Motamed, Sayed Amir Marashi, Fatemeh Goshadrou
   PLoS One, Vol. 18, No 7, 2023
3. "Glucose Metabolism: Optimizing Regenerative Functionalities of Mesenchymal Stromal Cells Postimplantation"
   Guotian Luo, Pauline Wosinski, Giuliana E. Salazar-Noratto, Morad Bensidhoum, Rena Bizios, Sayed Amir Marashi, Esther Potier, Puyi Sheng, Herve Petite
   Tissue Engineering Part B-Reviews, Vol. 29, No 1, pp.47-61, 2023
4. "Genome-scale metabolic model-based engineering of Escherichia coli enhances recombinant single-chain antibody fragment production"
   Aidin Behravan, Atieh Hashemi, Sayed Amir Marashi, Fouladiha Hamideh
   BIOTECHNOLOGY LETTERS, Vol. 44, No 12, 2022
5. "The assessment of essential genes in the stability of PPI networks using critical node detection problem"
   Javad Rezaei, Fatemeh Zare-Mirakabad, Sayed Amir Marashi, Seyed Ali MirHassani
   AUT Journal of Mathematics and Computing, Vol. 3, No 1, pp.59-76, 2022
6. "A Constraint-based modeling approach to reach an improved chemically defined minimal medium for recombinant antiEpEX-scFv production by Escherichia coli"
   Aidin Behravan, Atieh Hashemi, Sayed Amir Marashi
   BIOCHEMICAL ENGINEERING JOURNAL, Vol. 179, No 1, 2022
7. "Critical assessment of genome-scale metabolic models of Arabidopsis thaliana"
   Javad Zamani Amirzakaria, Sayed Amir Marashi, Mohammad Ali Malbo0bi, Tahmineh Lohrasebi, Esmail Forouzan
   Molecular Omics, Vol. 18, No 4, pp.328-335, 2022
8. "In silico prediction of enzymatic reactions catalyzed by acid phosphatases"
   Javad Zamani Amirzakaria, Mohammadali Malboobi, Sayed Amir Marashi, Tahmineh Lohrasebi
   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, Vol. 39, No 11, pp.3900-3911, 2021
9. "Systematically gap-filling the genome-scale metabolic model of CHO cells"
   Fouladiha Hamideh, Sayed Amir Marashi, Shangzhong Li., Zerong Li, Helen O. Masson, Behrouz Vaziri, Nathan E. Lewis
   BIOTECHNOLOGY LETTERS, Vol. 43, No 1, pp.73-87, 2021
10. "EIA-CNDP: An Exact Iterative Algorithm for Critical Node Detection Problem"
    Javad Rezaei, Fatemeh Zare-Mirakabad, Seyed Ali MirHassani, Sayed Amir Marashi
    COMPUTERS & OPERATIONS RESEARCH, Vol. 127, No 1, 2021
11. "A system architecture for parallel analysis of flux-balanced metabolic pathways"
    Mona Arabzadeh, Mehdi Sedighi, Morteza Saheb Zamani, Sayed Amir Marashi
    COMPUTATIONAL BIOLOGY AND CHEMISTRY, Vol. 88, No 88, 2020
12. "Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases"
    Nasibeh Khayer, Mehdi Mirzaei Azad, Sayed Amir Marashi, maryam jalesi
    PLoS One, Vol. 15, No 9, 2020
13. "NDDSA: A network- and domain-based method for predicting drug-side effect associations"
    Soheila Shabanimashcool, Sayed Amir Marashi, Sajjad Gharaghani
    INFORMATION PROCESSING & MANAGEMENT, Vol. 57, No 6, 2020
14. "A Systems-Based Approach for Cyanide Overproduction by Bacillus megaterium for Gold Bioleaching Enhancement"
    Javad Aminian-Dehkordi, سیدمحمد موسوی , Sayed Amir Marashi, آرزو جعفری, Ivan Mijakovic
    FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, Vol. 8, No 1, 2020
15. "A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4"
    Hoda Nouri, Fouladiha Hamideh, Hamid Moghimi, Sayed Amir Marashi
    Scientific Reports, Vol. 10, No 1, 2020
16. "A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production"
    Fouladiha Hamideh, Sayed Amir Marashi, Fatemeh Torkashvand, فریدون مهبودی , Nathan Lewis, Behrouz Vaziri
    BIOPROCESS AND BIOSYSTEMS ENGINEERING, Vol. 43, No 8, pp.1381-1389, 2020
17. "Beyond Taxonomic Analysis of Microbiomes: A Functional Approach for Revisiting Microbiome Changes in Colorectal Cancer"
    Mohammad Hossein Norouzi-Beirami, Sayed Amir Marashi, Ali Mohammad Banaei Moghaddam, Kaveh Kavousi
    Frontiers in Microbiology, Vol. 10, No 10, 2020
18. "Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319"
    Javad Aminian-Dehkordi, Seyyed Mohammad Mousavi, آرزو جعفری, Ivan Mijakovic, Sayed Amir Marashi
    Scientific Reports, Vol. 9, No 1, 2019
19. "Cancer driver gene discovery in transcriptional regulatory networks using influence maximization approach"
    Majid Rahimi, Babak Teimourpour, Sayed Amir Marashi
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 114, No 1, 2019
20. "Acetic acid uptake rate controls H2 production in Chlamydomonas-bacteria co-cultures"
    Neda Fakhimi, Omid Tavakoli, Sayed Amir Marashi, Hamid Moghimi, Mohammad Reza Mehrnia, Alexandra Dubini, David Gonzalez Ballester
    Algal Research-Biomass Biofuels and Bioproducts, Vol. 42, 2019
21. "The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency"
    Meisam Yousefi, Sayed Amir Marashi, Ali Sharifi-zarchi, Sara Taleahmad
    Cell and Bioscience, Vol. 9, No 1, 2019
22. "Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes"
    Nasibeh Khayer, Mehdi Mirzaei Azad, Sayed Amir Marashi, Mostafa Rezaei-tavirani, Fatemeh Goshadrou
    Expert Review of Proteomics, Vol. 16, No 2, pp.161-169, 2018
23. "Accounting for robustness in modeling signal transduction responses"
    Mohammad Omid Oftadeh, Sayed Amir Marashi
    JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, Vol. 38, pp.442-447, 2018
24. "Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications"
    Tahereh Ghasemi-kahrizsangi, Sayed Amir Marashi, Zhaleh Hosseini
    Iranian Journal of Biotechnology, Vol. 16, No 3, 2018
25. "A graph-based approach to analyze flux-balanced pathways in metabolic networks"
    Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed Amir Marashi
    BIOSYSTEMS, Vol. 165, No 165, pp.40-51, 2018
26. "Applications of a metabolic network model of mesenchymal stem cells for controlling cell proliferation and differentiation"
    Hamideh Fouladiha, Sayed Amir Marashi, Mohammd Ali Shokrgozar, Mehdi Farokhi, Amir Atashi
    CYTOTECHNOLOGY, Vol. 70, No 1, 2017
27. "Three-way interaction model to trace the mechanisms involved in Alzheimer’s disease transgenic mice"
    Nasibeh Khayer, Sayed Amir Marashi, Mahdi Mirzayi, Fatemeh Goshadrou
    PLoS One, Vol. 12, No 9, 2017
28. "A multiscale agent-based framework integrated with a constraint-based metabolic network model of cancer for simulating avascular tumor growth"
    Mehrdad Ghadiri, Mahshid Heidari, Sayed Amir Marashi, Seyed Hasan Mousavi
    Molecular BioSystems, Vol. 13, No 9, pp.1888-1897, 2017
29. "A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia"
    Arvand Asghari, Sayed Amir Marashi, Naser Ansari Pour
    Systems Biology in Reproductive Medicine, Vol. 63, No 2, pp.100-112, 2017
30. "Biomedical applications of cell- and tissue-specific metabolic network models"
    Hamideh Fouladiha, Sayed Amir Marashi
    JOURNAL OF BIOMEDICAL INFORMATICS, Vol. 68, No 68, pp.35-49, 2017
31. "Discovering missing reactions of metabolic networks by using gene co-expression data"
    Zhaleh Hosseini, Sayed Amir Marashi
    Scientific Reports, Vol. 7, No 1, 2017
32. "Confronting Metabolic-Related Conditions by Constraint-Based Simulations: A Review"
    Sayed Amir Marashi
    Bioinformatics and Biocomputational Research, Vol. 1, No 2, pp.63-66, 2016
33. "In silico prediction of specific pathways that regulate mesangial cell proliferation in IgA nephropathy"
    Elham Sadat Mirfazeli, Sayed Amir Marashi, Shiva Kalantari
    MEDICAL HYPOTHESES, Vol. 97, No 1, pp.38-45, 2016
34. "A kidney-specific genome-scale metabolic network model for analyzing focal segmental glomerulosclerosis"
    Salma Sohrabi-jahromi, Sayed Amir Marashi, Shiva Kalantari
    MAMMALIAN GENOME, Vol. 27, No 2, pp.158-167, 2016
35. "Indirect role of microRNAs and transcription factors in the regulation of importantcancer genes: A network biology approach"
    Mehdi Ahmadi, Rahim Jafari, Sayed Amir Marashi, Ali Farazmand
    CELLULAR AND MOLECULAR BIOLOGY, Vol. 61, No 6, pp.100-107, 2015
36. "CAMWI: Detecting Protein Complexes Using Weighted Clustering Coefficient and Weighted Density"
    Amir Lakizadeh, Saeed Jalili, Sayed Amir Marashi
    COMPUTATIONAL BIOLOGY AND CHEMISTRY, Vol. 58, No 1, pp.231-240, 2015
37. "Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells"
    Hamideh Fouladiha, Sayed Amir Marashi, محمدعلی شکرگزار
    CELL PROLIFERATION, Vol. 48, No 8, pp.475-485, 2015
38. "PCD-GED: Protein complex detection considering PPI dynamics based on time series gene expression data"
    Amir Lakizadeh, Saeed Jalili, Sayed Amir Marashi
    JOURNAL OF THEORETICAL BIOLOGY, Vol. 378, No 1, 2015
39. "Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks"
    Mehdi Ahmadi, Rahim Jafari, Sayed Amir Marashi, Ali Farazmand
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 63, No 1, 2015
40. "On correlated reaction sets and coupled reaction sets in metabolic networks"
    Sayed Amir Marashi, Zhaleh Hosseini
    Journal of Bioinformatics and Computational Biology, Vol. 13, No 4, 2015
41. "Hierarchical organization of fluxes in Escherichia coli metabolic network: Using flux coupling analysis for understanding the physiological properties of metabolic genes"
    Zhaleh Hosseini, Sayed Amir Marashi
    GENE, Vol. 561, No 2, pp.199-208, 2015
42. "FCDECOMP: Decomposition of metabolic networks based on flux coupling relations"
    Abolfazl Rezvan, Sayed Amir Marashi, چنگیز اصلاح چی
    Journal of Bioinformatics and Computational Biology, Vol. 12, No 5, 2014
43. "Reconstruction of a generic metabolic network model of cancer cells"
    Mahdieh Hadi, Sayed Amir Marashi
    Molecular BioSystems, Vol. 10, No 11, 2014
44. "Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals"
    Mahdi Heydari, Sayed Amir Marashi, Ruzbeh Tusserkani, Mehdi Sadeghi
    BIOSYSTEMS, Vol. 124, No 1, pp.86-94, 2014
45. "A mathematical approach to emergent properties of metabolic networks: Partial coupling relations, hyperarcs and flux ratios"
    Sayed Amir Marashi, Mojtaba Tefagh
    JOURNAL OF THEORETICAL BIOLOGY, Vol. 355, pp.185-193, 2014
46. "Modeling the differences in biochemical capabilities of Pseudomonas species by flux balance analysis: How good are genome-scale metabolic networks at predicting the differences?"
    Parizad Babaei, Tahereh Ghasemi-kahrizsangi, Sayed Amir Marashi
    THESCIENTIFICWORLDJOURNAL, Vol. 2014, No 1, 2014
47. "Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism"
    Shayan Tabe-bordbar, Sayed Amir Marashi
    BIOTECHNOLOGY LETTERS, Vol. 35, No 12, pp.2039-2044, 2013
48. "Studying the relationship between robustness against mutations in metabolic networks and lifestyle of organisms"
    Sayed Amir Marashi, Hawa Kouhestani, مجید مهدوی
    THESCIENTIFICWORLDJOURNAL, Vol. 2013, No 1, 2013
49. "Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks"
    Mohieddin Jafari, Mehdi Sadeghi, Mehdi Mirzaie, Sayed Amir Marashi, Mostafa Rezaei-tavirani
    MITOCHONDRION, Vol. 13, No 6, 2013
50. "Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks"
    Mohieddin Jafari, Mehdi Sadeghi, Mehdi Mirzaie, Sayed Amir Marashi, مصطفی رضایی طاویرانی
    MITOCHONDRION, Vol. 13, No 6, pp.668-675, 2013
51. "Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data"
    Mohieddin Jafari, Mehdi Mirzaie, Mehdi Sadeghi, Sayed Amir Marashi, Mostafa Rezaei-tavirani
    BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, Vol. 1834, No 6, pp.1063-1069, 2013
52. "On flux coupling analysis of metabolic subsystems"
    Sayed Amir Marashi, Laszlo David , Alexander Bockmayr
    JOURNAL OF THEORETICAL BIOLOGY, Vol. 302, pp.62-69, 2012
53. "Analysis of metabolic subnetworks by flux cone projection"
    Sayed Amir Marashi, Laszlo David , Alexander Bockmayr
    Algorithms for Molecular Biology, Vol. 7, No 1, 2012
54. "FFCA : a feasibility - based method for flux coupling analysis of metabolic networks"
    Laszlo David , Sayed Amir Marashi, Abdelhalim Larhlimi , Bettina Mieth , Alexander Bockmayr
    BMC BIOINFORMATICS, Vol. 12, 2011
55. "Flux coupling analysis of metabolic networks is sensitive to missing reactions"
    Sayed Amir Marashi, A Bockmayr
    BIOSYSTEMS, Vol. 103, No 1, pp.57-66, 2011
56. "ADDITION OF CONTACT NUMBER INFORMATION CAN IMPROVE PROTEIN SECONDARY STRUCTURE PREDICTION BY NEURAL NETWORKS"
    Amir Lakizadeh , Sayed Amir Marashi
    EXCLI Journal, Vol. 8, pp.66-73, 2009
57. "Mitochondrial DNA might be influenced in calprotectin - induced cell death"
    Sayed Amir Marashi, M Rezaei Tavirani , H Zali , Ma Shokrgozar
    EXCLI Journal, Vol. 7, pp.163-168, 2008
58. "Utilization of CTAnalyzer algorithm to identify pri-microRNA candidate sequences in the genome of Azadirachta indica"
    سبحان عطائی, جعفر احمدی, Sayed Amir Marashi
    ژنتیک نوین, Vol. 16, No 4, 2022
59. "A Multivariate Bayesian Model for Gene Networks"
    Abdollah Safari, Ali Sharifi, Hamid Pezeshk, Peyman Nickchi, Sayed Amir Marashi, Changiz Eslahchi
    Journal of Statistical Sciences, Vol. 6, No 2, pp.187-200, 2012

Conference Paper

1. "A method to visualize pseudo-potential landscape of high-dimensional Boolean networks"
   Mohammad Taheri Ledari, Sayed Amir Marashi, Kaveh Kavousi
   3rd International & 12th Iranian Conference on Bioinformatics, 2024
2. "Feature set prioritization of metagenomes for predicting colorectal cancer based on multiple human gut microbiome datasets"
   Zahra Tavakkol-Hamedani, Sayed Amir Marashi, Kaveh Kavousi
   2nd International & 11th Iranian Conference on Bioinformatics, 2023
3. "DEVELOPMENT OF NEW C4 CROPS"
   Sayed Amir Marashi, Armin Dadras, Ali Mohammad Banaei Moghaddam
   3rd International Cukurova Agriculture and Veterinary Congress, 2021
4. "Why some human genes can be deleted from genome? A systems biology approach"
   Sayed Amir Marashi, Mohammad Sababi, Naser Ansari Pour
   Data-Driven Biotechnology, 2017
5. "On the applications of a metabolic network model of mesenchymal stem cells"
   Hamideh Fouladiha, Sayed Amir Marashi, Mohammad Ali Shokrgozar, Mehdi Farokhi
   41st FEBS Congress, Molecular and Systems Biology for a Better Life, 2016
6. "On the Applicability of Metabolic Network Models in Biotechnology: Comparing the in silico and in vitro biochemical capabilities of Bacillus subtilis and Bacillus megaterium using genome-scale metabolic network models"
   Tahereh Ghasemi-kahrizsangi, Zhaleh Hosseini, Sayed Amir Marashi
   The Second Iranian International Conference on Systems Biology, 2015
7. "Asymmetric Distribution of Important Reactions in E. coli Metabolic Network"
   Salma Sohrabi-jahromi, Sayed Amir Marashi
   6th European Conference on Prokaryotic and Fungal Genomics, 2015
8. "Gap Filling of Metabolic Networks Using Flux Coupling Analysis and Expression Profiles of Metabolic Genes"
   Zhaleh Hosseini, Sayed Amir Marashi
   4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), 2015
9. "Genome-Scale Metabolic Network of Pseudomonas stutzeri A1501: Reconstruction and Experimental Validation"
   Parizad Babaei, Sayed Amir Marashi, Sedigheh Asad
   5th Iran Conference on Bioinformatics, 2014
10. "CSC: A new approach to spectral clustering of gene expression data"
    Samira Mali, Mir Mohsen Pedram, Sayed Amir Marashi
    5th Iran Conference on Bioinformatics, 2014
11. "Computing elementary flux modes based on flux balance analysis"
    Sayed Amir Marashi, Shayan Tabe-bordbar
    Cell Factories and Biosustainability 2013, 2013
12. "On emergent properties in constraint-based models of metabolic networks"
    Sayed Amir Marashi, مجتبی تفاق
    COBRA2012, 2012
13. "Systems-level modeling for forward and inverse metabolic engineering"
    Sayed Amir Marashi
    The 3rd Iranian Conference on Systems Biology, 2018
14. "Comparison of triad significance profiles for E. coli metabolic network using "mass-balances" vs. "switch" randomization"
    Farnaz Mohammadi, Sayed Amir Marashi
    The 3rd Iranian Conference on Systems Biology, 2018
15. "An updated version of the genome-scale model of CHO cells"
    Hamideh Fouladiha, Sayed Amir Marashi
    The 3rd Iranian Conference on Systems Biology, 2018
16. "Mixed-integer linear programming approach for modeling and solving bioinformatics problems"
    Sayed Amir Marashi
    7th Iranian Conference on Bioinformatics, 2018
17. "In silico prediction of preferred substrate of some HAD-Related Acid Phosphatase of A. thaliana"
    Javad Zamani Amirzakaria, Mohammad Ali Malbo0bi, Sayed Amir Marashi, Tahmineh Lohrasebi
    7th Iranian Conference on Bioinformatics, 2018
18. "Comparing flux coupling and flux correlation"
    Sayed Amir Marashi, Zhaleh Hosseini
    The Fourth National Bioinformatics Congress, 2012