Sayed-Amir Marashi

Associate Professor in University of Tehran

Associate Professor In Department of Biotechnology In University of Tehran

 

Research interest(s):

  • Bioinformatics
  • Computational Biology
  • Systems Biology
  • Genomics
  • Biotechnology

 

Recent Papers:

  • Marashi, Sayed-Amir,  M Rezaei Tavirani ,  H Zali , and  MA Shokrgozar . “Mitochondrial DNA might be influenced in calprotectin – induced cell death.” EXCLI Journal 7, no. — (2008): 163-168.
  • Amir Lakizadeh, and Sayed-Amir Marashi. “ADDITION OF CONTACT NUMBER INFORMATION CAN IMPROVE PROTEIN SECONDARY STRUCTURE PREDICTION BY NEURAL NETWORKS.” EXCLI Journal 8, no. — (2009): 66-73.
  • Marashi, Sayed-Amir, and A Bockmayr . “Flux coupling analysis of metabolic networks is sensitive to missing reactions.” Bio Systems 103, no. 1 (2011): 57-66.
  • , Laszlo David, Sayed-Amir Marashi, Abdelhalim Larhlimi , Bettina Mieth , and Alexander Bockmayr . “FFCA : a feasibility – based method for flux coupling analysis of metabolic networks.” BMC BIOINFORMATICS 12, no. — (2011): -.
  • Marashi, Sayed-Amir, Laszlo David , and Alexander Bockmayr . “Analysis of metabolic subnetworks by flux cone projection.” ALGORITHMS FOR MOLECULAR BIOLOGY 7, no. 1 (2012): 17.
  • Marashi, Sayed-Amir, Laszlo David , and Alexander Bockmayr . “On flux coupling analysis of metabolic subsystems.” JOURNAL OF THEORETICAL BIOLOGY 302, no. — (2012): 62-69.
  • Jafari, Mohieddin, Mehdi Mirzaie, Mehdi Sadeghi, Sayed-Amir Marashi, and Mostafa Rezaei-Tavirani. “Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data.” BIOCHIMICA ET BIOPHYSICA ACTA PROTEINS AND PROTEOMICS 1834, no. 6 (2013): 1063-1069.
  • Jafari, Mohieddin, Mehdi Sadeghi, Mehdi Mirzaie, Sayed-Amir Marashi, and . “Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks.” Mitochondrion 13, no. 6 (2013): 668-675.
  • Jafari, Mohieddin, mehdi sadeghi, Mehdi Mirzaie, Sayed-Amir Marashi, and Mostafa Rezaei-Tavirani. “Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks.” Mitochondrion 13, no. 6 (2013): 668–675.
  • Marashi, Sayed-Amir, Hawa Kouhestani, and . “Studying the relationship between robustness against mutations in metabolic networks and lifestyle of organisms.” THESCIENTIFICWORLDJOURNAL 2013, no. 1 (2013): 615697.
  • Tabe-Bordbar, Shayan, and Sayed-Amir Marashi. “Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism.” BIOTECHNOLOGY LETTERS 35, no. 12 (2013): 2039-2044.
  • Babaei, Parizad, Tahereh Ghasemi-Kahrizsangi, and Sayed-Amir Marashi. “Modeling the differences in biochemical capabilities of Pseudomonas species by flux balance analysis: How good are genome-scale metabolic networks at predicting the differences?.” THESCIENTIFICWORLDJOURNAL 2014, no. 1 (2014): 416289.
  • Marashi, Sayed-Amir, and Mojtaba Tefagh. “A mathematical approach to emergent properties of metabolic networks: Partial coupling relations, hyperarcs and flux ratios.” JOURNAL OF THEORETICAL BIOLOGY 355, no. – (2014): 185-193.
  • Heydari, Mahdi, Sayed-Amir Marashi, Ruzbeh Tusserkani, and Mehdi Sadeghi. “Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.” Bio Systems 124, no. 1 (2014): 86-94.
  • Hadi, Mahdieh, and Sayed-Amir Marashi. “Reconstruction of a generic metabolic network model of cancer cells.” Molecular BioSystems 10, no. 11 (2014): 3014.
  • Hosseini, Zhaleh, and Sayed-Amir Marashi. “Hierarchical organization of fluxes in Escherichia coli metabolic network: Using flux coupling analysis for understanding the physiological properties of metabolic genes.” Gene 561, no. 2 (2015): 199-208.
  • Marashi, Sayed-Amir, and Zhaleh Hosseini. “On correlated reaction sets and coupled reaction sets in metabolic networks.” Journal of Bioinformatics and Computational Biology 13, no. 4 (2015): 1571003.
  • Ahmadi, Mehdi, Rahim Jafari, Sayed-Amir Marashi, and Ali Farazmand. “Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks.” COMPUTERS IN BIOLOGY AND MEDICINE 63, no. 1 (2015): 83.
  • Lakizadeh, Amir, Saeed Jalili, and Sayed-Amir Marashi. “PCD-GED: Protein complex detection considering PPI dynamics based on time series gene expression data.” JOURNAL OF THEORETICAL BIOLOGY 378, no. 1 (2015): 31.
  • Fouladiha, Hamideh, Sayed-Amir Marashi, and . “Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells.” Cell Proliferation 48, no. 8 (2015): 475-485.
  • Lakizadeh, Amir, Saeed Jalili, and Sayed-Amir Marashi. “CAMWI: Detecting Protein Complexes Using Weighted Clustering Coefficient and Weighted Density.” Computational Biology and Chemistry 58, no. 1 (2015): 231-240.
  • Ahmadi, Mehdi, Rahim Jafari, Sayed-Amir Marashi, and Ali Farazmand. “Indirect role of microRNAs and transcription factors in the regulation of importantcancer genes: A network biology approach.” Cellular and Molecular Biology 61, no. 6 (2015): 100-107.
  • Sohrabi-Jahromi, Salma, Sayed-Amir Marashi, and Shiva Kalantari. “A kidney-specific genome-scale metabolic network model for analyzing focal segmental glomerulosclerosis.” Mammalian Genome 27, no. 2 (2016): 158-167.
  • Mirfazeli, Elham Sadat, Sayed-Amir Marashi, and Shiva Kalantari. “In silico prediction of specific pathways that regulate mesangial cell proliferation in IgA nephropathy.” Medical Hypotheses 97, no. 1 (2016): 38-45.
  • Hosseini, Zhaleh, and Sayed-Amir Marashi. “Discovering missing reactions of metabolic networks by using gene co-expression data.” Scientific Reports 7, no. 1 (2017): 41774.
  • Fouladiha, Hamideh, and Sayed-Amir Marashi. “Biomedical applications of cell- and tissue-specific metabolic network models.” JOURNAL OF BIOMEDICAL INFORMATICS 68, no. 68 (2017): 35-49.
  • Asghari, Arvand, Sayed-Amir Marashi, and Naser Ansari-Pour. “A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia.” Systems biology in reproductive medicine 63, no. 2 (2017): 100-112.
  • Khayer, Nasibeh, Sayed-Amir Marashi, Mahdi Mirzayi, and Fatemeh Goshadrou. “Three-way interaction model to trace the mechanisms involved in Alzheimer’s disease transgenic mice.” PLOS ONE 12, no. 9 (2017): e0184697.
  • Ghadiri, Mehrdad, Mahshid Heidari, Sayed-Amir Marashi, and Seyed Hasan Mousavi. “A multiscale agent-based framework integrated with a constraint-based metabolic network model of cancer for simulating avascular tumor growth.” Molecular BioSystems 13, no. 9 (2017): 1888-1897.
  • Fouladiha, Hamideh, Sayed-Amir Marashi, Mohammd ali Shokrgozar, Mehdi Farokhi, and Amir Atashi. “Applications of a metabolic network model of mesenchymal stem cells for controlling cell proliferation and differentiation.” CYTOTECHNOLOGY 70, no. 1 (2017): 1.

 

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