مقالات علمی چاپ شده در مجلات

1. "AmiR-P3: An AI-based microRNA prediction pipeline in plants"
   Ilia Abolhassani, Sayed Amir Marashi, جعفر احمدی, سبحان عطائی
   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"
   Fatemeh Goshadrou, Sayed Amir Marashi, Nasrin Motamed, Nasibeh Khayer
   PLoS One, Vol. 18, No 7, 2023
3. "Glucose Metabolism: Optimizing Regenerative Functionalities of Mesenchymal Stromal Cells Postimplantation"
   Sayed Amir Marashi, Puyi Sheng, Esther Potier, Rena Bizios, Morad Bensidhoum, Giuliana E. Salazar-Noratto, Pauline Wosinski, Guotian Luo, 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"
   Sayed Amir Marashi, Fouladiha Hamideh, Atieh Hashemi, Aidin Behravan
   BIOTECHNOLOGY LETTERS, Vol. 44, No 12, 2022
5. "The assessment of essential genes in the stability of PPI networks using critical node detection problem"
   Seyed Ali MirHassani, Sayed Amir Marashi, Fatemeh Zare-Mirakabad, Javad Rezaei
   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"
   Sayed Amir Marashi, Atieh Hashemi, Aidin Behravan
   BIOCHEMICAL ENGINEERING JOURNAL, Vol. 179, No 1, 2022
7. "Critical assessment of genome-scale metabolic models of Arabidopsis thaliana"
   Esmail Forouzan, Tahmineh Lohrasebi, Mohammad Ali Malbo0bi, Sayed Amir Marashi, Javad Zamani Amirzakaria
   Molecular Omics, Vol. 18, No 4, pp.328-335, 2022
8. "In silico prediction of enzymatic reactions catalyzed by acid phosphatases"
   Tahmineh Lohrasebi, Sayed Amir Marashi, Mohammadali Malboobi, Javad Zamani Amirzakaria
   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, Vol. 39, No 11, pp.3900-3911, 2021
9. "EIA-CNDP: An Exact Iterative Algorithm for Critical Node Detection Problem"
   Sayed Amir Marashi, Seyed Ali MirHassani, Fatemeh Zare-Mirakabad, Javad Rezaei
   COMPUTERS & OPERATIONS RESEARCH, Vol. 127, No 1, 2021
10. "Systematically gap-filling the genome-scale metabolic model of CHO cells"
    Nathan E. Lewis, Behrouz Vaziri, Helen O. Masson, Zerong Li, Shangzhong Li., Sayed Amir Marashi, Fouladiha Hamideh
    BIOTECHNOLOGY LETTERS, Vol. 43, No 1, pp.73-87, 2021
11. "A system architecture for parallel analysis of flux-balanced metabolic pathways"
    Mehdi Sedighi, Morteza Saheb Zamani, Sayed Amir Marashi, Mona Arabzadeh
    COMPUTATIONAL BIOLOGY AND CHEMISTRY, Vol. 88, No 88, 2020
12. "Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases"
    maryam jalesi, Sayed Amir Marashi, Mehdi Mirzaei Azad, Nasibeh Khayer
    PLoS One, Vol. 15, No 9, 2020
13. "NDDSA: A network- and domain-based method for predicting drug-side effect associations"
    Sayed Amir Marashi, Sajjad Gharaghani, Soheila Shabanimashcool
    INFORMATION PROCESSING & MANAGEMENT, Vol. 57, No 6, 2020
14. "A Systems-Based Approach for Cyanide Overproduction by Bacillus megaterium for Gold Bioleaching Enhancement"
    سیدمحمد موسوی , Javad Aminian-Dehkordi, Ivan Mijakovic, آرزو جعفری, Sayed Amir Marashi
    FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, Vol. 8, No 1, 2020
15. "A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4"
    Sayed Amir Marashi, Hamid Moghimi, Fouladiha Hamideh, Hoda Nouri
    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 , Behrouz Vaziri, Nathan Lewis
    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"
    Ali Mohammad Banaei Moghaddam, Sayed Amir Marashi, Kaveh Kavousi, Mohammad Hossein Norouzi-Beirami
    Frontiers in Microbiology, Vol. 10, No 10, 2020
18. "Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319"
    Sayed Amir Marashi, Ivan Mijakovic, آرزو جعفری, Seyyed Mohammad Mousavi, Javad Aminian-Dehkordi
    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"
    Sayed Amir Marashi, David Gonzalez Ballester, Alexandra Dubini, Mohammad Reza Mehrnia, Hamid Moghimi, Omid Tavakoli, Neda Fakhimi
    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"
    Sara Taleahmad, Ali Sharifi-zarchi, Sayed Amir Marashi, Meisam Yousefi
    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"
    Sayed Amir Marashi, Fatemeh Goshadrou, Mostafa Rezaei-tavirani, Mehdi Mirzaei Azad, Nasibeh Khayer
    Expert Review of Proteomics, Vol. 16, No 2, pp.161-169, 2018
23. "Accounting for robustness in modeling signal transduction responses"
    Sayed Amir Marashi, Mohammad Omid Oftadeh
    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"
    Zhaleh Hosseini, Sayed Amir Marashi, Tahereh Ghasemi-kahrizsangi
    Iranian Journal of Biotechnology, Vol. 16, No 3, 2018
25. "A graph-based approach to analyze flux-balanced pathways in metabolic networks"
    Sayed Amir Marashi, Mehdi Sedighi, Morteza Saheb Zamani, Mona Arabzadeh
    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"
    Amir Atashi, Mehdi Farokhi, Mohammd Ali Shokrgozar, Sayed Amir Marashi, Hamideh Fouladiha
    CYTOTECHNOLOGY, Vol. 70, No 1, 2017
27. "Three-way interaction model to trace the mechanisms involved in Alzheimer’s disease transgenic mice"
    Sayed Amir Marashi, Fatemeh Goshadrou, Mahdi Mirzayi, Nasibeh Khayer
    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"
    Seyed Hasan Mousavi, Mahshid Heidari, Mehrdad Ghadiri, Sayed Amir Marashi
    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"
    Naser Ansari Pour, Arvand Asghari, Sayed Amir Marashi
    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"
    Shiva Kalantari, Elham Sadat Mirfazeli, Sayed Amir Marashi
    MEDICAL HYPOTHESES, Vol. 97, No 1, pp.38-45, 2016
34. "A kidney-specific genome-scale metabolic network model for analyzing focal segmental glomerulosclerosis"
    Shiva Kalantari, Salma Sohrabi-jahromi, Sayed Amir Marashi
    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"
    Ali Farazmand, Rahim Jafari, Mehdi Ahmadi, Sayed Amir Marashi
    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, محمدعلی شکرگزار, Sayed Amir Marashi
    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, Ali Farazmand, Sayed Amir Marashi
    COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 63, No 1, 2015
40. "On correlated reaction sets and coupled reaction sets in metabolic networks"
    Zhaleh Hosseini, Sayed Amir Marashi
    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. "Reconstruction of a generic metabolic network model of cancer cells"
    Sayed Amir Marashi, Mahdieh Hadi
    Molecular BioSystems, Vol. 10, No 11, 2014
43. "FCDECOMP: Decomposition of metabolic networks based on flux coupling relations"
    Abolfazl Rezvan, چنگیز اصلاح چی , Sayed Amir Marashi
    Journal of Bioinformatics and Computational Biology, Vol. 12, No 5, 2014
44. "Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals"
    Mahdi Heydari, Ruzbeh Tusserkani, Mehdi Sadeghi, Sayed Amir Marashi
    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"
    Mojtaba Tefagh, Sayed Amir Marashi
    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?"
    Tahereh Ghasemi-kahrizsangi, Parizad Babaei, 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"
    Hawa Kouhestani, مجید مهدوی, Sayed Amir Marashi
    THESCIENTIFICWORLDJOURNAL, Vol. 2013, No 1, 2013
49. "Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks"
    Mostafa Rezaei-tavirani, Mehdi Mirzaie, Mehdi Sadeghi, Mohieddin Jafari, Sayed Amir Marashi
    MITOCHONDRION, Vol. 13, No 6, 2013
50. "Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks"
    Mehdi Mirzaie, Mehdi Sadeghi, Mohieddin Jafari, مصطفی رضایی طاویرانی, Sayed Amir Marashi
    MITOCHONDRION, Vol. 13, No 6, pp.668-675, 2013
51. "Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data"
    Mehdi Sadeghi, Mostafa Rezaei-tavirani, Mehdi Mirzaie, Mohieddin Jafari, Sayed Amir Marashi
    BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, Vol. 1834, No 6, pp.1063-1069, 2013
52. "On flux coupling analysis of metabolic subsystems"
    Laszlo David , Alexander Bockmayr , Sayed Amir Marashi
    JOURNAL OF THEORETICAL BIOLOGY, Vol. 302, pp.62-69, 2012
53. "Analysis of metabolic subnetworks by flux cone projection"
    Laszlo David , Alexander Bockmayr , Sayed Amir Marashi
    Algorithms for Molecular Biology, Vol. 7, No 1, 2012
54. "FFCA : a feasibility - based method for flux coupling analysis of metabolic networks"
    Laszlo David , Abdelhalim Larhlimi , Alexander Bockmayr , Bettina Mieth , Sayed Amir Marashi
    BMC BIOINFORMATICS, Vol. 12, 2011
55. "Flux coupling analysis of metabolic networks is sensitive to missing reactions"
    A Bockmayr , Sayed Amir Marashi
    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"
    M Rezaei Tavirani , H Zali , Ma Shokrgozar , Sayed Amir Marashi
    EXCLI Journal, Vol. 7, pp.163-168, 2008
58. "استفاده از الگوریتم CTAnalyzer به منظور شناسایی توالی های کاندید pri-microRNA در ژنوم Azadirachta indica"
    سیدامیر مرعشی، جعفر احمدی، سبحان عطائی
    ژنتیک نوین، نسخه 16، شماره 4، 1400
59. "یک الگوی چند متغیری بیزی برای شبکه های ژنی"
    علی شریفی، عبدالله صفری، چنگیز اصلاح چی، پیمان نیک چی، سیدامیر مرعشی، حمید پزشک
    مجله علوم آماری، نسخه 6، شماره 2، صفحات:187-200، 1391

مقالات علمی ارائه شده در همایش‌ها

1. "Feature set prioritization of metagenomes for predicting colorectal cancer based on multiple human gut microbiome datasets"
   Kaveh Kavousi, Zahra Tavakkol-Hamedani, Sayed Amir Marashi
   2nd International & 11th Iranian Conference on Bioinformatics, 2023
2. "DEVELOPMENT OF NEW C4 CROPS"
   Sayed Amir Marashi, Ali Mohammad Banaei Moghaddam, Armin Dadras
   3rd International Cukurova Agriculture and Veterinary Congress, 2021
3. "Why some human genes can be deleted from genome? A systems biology approach"
   Mohammad Sababi, Naser Ansari Pour, Sayed Amir Marashi
   Data-Driven Biotechnology, 2017
4. "On the applications of a metabolic network model of mesenchymal stem cells"
   Hamideh Fouladiha, Mohammad Ali Shokrgozar, Mehdi Farokhi, Sayed Amir Marashi
   41st FEBS Congress, Molecular and Systems Biology for a Better Life, 2016
5. "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
6. "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
7. "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
8. "Genome-Scale Metabolic Network of Pseudomonas stutzeri A1501: Reconstruction and Experimental Validation"
   Parizad Babaei, Sedigheh Asad, Sayed Amir Marashi
   5th Iran Conference on Bioinformatics, 2014
9. "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
10. "Computing elementary flux modes based on flux balance analysis"
    Shayan Tabe-bordbar, Sayed Amir Marashi
    Cell Factories and Biosustainability 2013, 2013
11. "On emergent properties in constraint-based models of metabolic networks"
    Sayed Amir Marashi, مجتبی تفاق
    COBRA2012, 2012
12. "اSystems-level modeling for forward and inverse metabolic engineering"
    سیدامیر مرعشی
    سومین کنفرانس زیست شناسی سامانه های ایران، 1396
13. "ارائه نسخه ای جدید از مدل شبکه متابولیکی ژنوم مقیاس سلول های CHO"
    سیدامیر مرعشی، حمیده فولادیها
    سومین کنفرانس زیست شناسی سامانه های ایران، 1396
14. "مقایسه پروفایل های معنی داری سه تایی در شبکه متابولیکی E.coli با استفاده از تصادفی سازی موازنه جرم"
    سیدامیر مرعشی، فرناز محمدی
    سومین کنفرانس زیست شناسی سامانه های ایران، 1396
15. "رویکرد برنامه ریزی خطی صحیح برای مدلسازی و حل مسائل بیوانفورماتیک"
    سیدامیر مرعشی
    هفتمین همایش بیوانفورماتیک ایران، 1396
16. "اIn silico prediction of preferred substrate of some HAD-Related Acid Phosphatase of A. thaliana"
    تهمینه لهراسبی، سیدامیر مرعشی، محمد علی ملبوبی، جواد زمانی امیرزکریا
    هفتمین همایش بیوانفورماتیک ایران، 1396
17. "بررسی مقایسه ای دو مفهوم همراهی شارها و همبستگی شارها در شبکه های متابولیکی"
    ژاله حسینی، سیدامیر مرعشی
    چهارمین همایش ملی بیوانفورماتیک ایران، 1391