Publications

Patent

• Motamedian E., Sarmadi M., Derakhshan E., ‘Systemic process of microorganism culture generation to improve the production of a bio-based product”, Registration No.: 96042, 2018. . Evaluated by: Iranian Research Organization for Science and Technology (http://dx.doi.org/10.22104/IROST.1397.209).
• Motamedian E., Taheri E. and Bagheri F., “Growth inhibition of a drug-resistant cancer cell using drugs screened by a system-oriented strategy”, Registration No.: 91805, 2017. Evaluated by: Iranian Research Organization for Science and Technology (http://dx.doi.org/10.22104/IROST.1396.204).

Journal Papers

• Salehabadi, E., Motamedian, E., & Shojaosadati, S. A. (2022). Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PloS one, 17(3), e0254270.
• Savizi, I. S. P., Maghsoudi, N., Motamedian, E., Lewis, N. E., & Shojaosadati, S. A. (2022). Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Applied microbiology and biotechnology, 1-14.
• Peighami, R., Rasekh, B., Motamedian, E., Yazdian, F., & Khodaverdi, H. (2022). Investigating the ability of sulfur-oxidizing strains in biodesulfurisation of sulfide-containing streams, screening the most capable strain and determining the optimum condition for elemental sulfur recovery from sulfide using response surface method. Fuel, 309, 121985.
• Firoozabadi H., Mardanpour M. M. and E. Motamedian (2021). A system-oriented strategy to enhance electron production of Synechocystis sp. PCC6803 in bio-photovoltaic devices: experimental and modeling insights. Scientific Reports, 11, 12294. https://doi.org/10.1038/s41598-021-91906-9.
• Ghaffarinasab, S., & Motamedian, E. (2021). Improving ethanol production by studying the effect of pH using a modified metabolic model and a systemic approach. Biotechnology and Bioengineering, http://doi.org/10.1002/bit.27800.
• Savizi, I. S. P., Motamedian, E., Lewis, N. E., Jimenez del Val, I., & Shojaosadati, S. A. (2021). An integrated modular framework for modeling the effect of ammonium on the sialylation process of monoclonal antibodies produced by CHO cells. Biotechnology Journal, 2100019.
• Ardalani, O., Motamedian, E., & Hamedi, J. (2021). Reconstruction and validation of genome-scale metabolic model of L. lactis subsp. lactis NCDO 2118 and in silico analysis for succinate and Gamma-aminobutyric acid overproduction. Biochemical Engineering Journal, 107967.
• Pedram, N., Rashedi, H., & Motamedian, E. (2020). A systematic strategy using a reconstructed genome-scale metabolic network for pathogen Streptococcus pneumoniae D39 to find novel potential drug targets. Pathogens and Disease, 78(6), ftaa051.
• Karimian, E. and Motamedian, E. (2020) ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities. Scientific Reports, 10, 8695 . https://doi.org/10.1038/s41598-020-65659-w.
• Malek Shahkouhi A. and Motamedian E. (2020) Reconstruction of a two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413, PLOS ONE, 15(1): e0227977. DOI:10.1371/journal.pone.0227977.
• Rezazadeh M., Babaeipour V., Motamedian E. (2020) Reconstruction, verification and in-silico analysis of a genome-scale metabolic model of bacterial cellulose producing Komagataeibacter xylinus, Bioprocess and Biosystems Engineeringing, 43, 1017–1026.
• Motamedian, E., Sarmadi, M., Derakhshan, E., (2019) Development of a regulatory defined medium using a system-oriented strategy to reduce the intracellular constraints. Process Biochemistry.
• Babazadegan, M. A., Motamedian, E., (2019) Applying a system-oriented method for culture medium design to improve bio-ethanol production by Synechocystis. Journal of Applied Research of Chemical-Polymer Engineering. 7, 55-67.
• Jamialahmadi, O., Hashemi-Najafabadi, S., Motamedian, E., Romeo, S., Bagheri, F. (2019) A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism, PLoS computational biology. 15, e1006936.
• Mekanik M., Motamedian E., Fotovat R., Jafarian V. (2019) Reconstruction of a genome-scale metabolic model for Auxenochlorella protothecoides to study hydrogen production under anaerobiosis using multiple optimal solutions. International Journal of Hydrogen Energy. 44,2580-2591.
• Jelokhani niaraki S. , Tahmoorespur M. , Minuchehr Z. , Motamedian E. , Nassiri M. (2019) Reconstruction and analysis of the genome-scale metabolic network of Streptococcus bovis B315 involved in lactic acid production in the rumen. Animal Science Journal, 121, 103-116. DOI: 10.22092/ASJ.2018.116808.1595
• Motamedian, E., & Naeimpoor, F. (2018) LAMOS: a linear algorithm to identify the origin of multiple optimal flux distributions in metabolic networks. Computers & Chemical Engineering. https://doi.org/10.1016/j.compchemeng.2018.06.014
• Motamedian, E, Taheri, E, Bagheri, F. (2017) Proliferation inhibition of cisplatin-resistant ovarian cancer cells using drugs screened by integrating a metabolic model and transcriptomic data, Cell Proliferation. , e12370. https://doi.org/10.1111/cpr.12370.
• Motamedian, E., Mohammadi, M., Shojaosadati, S. A., Heydari, M. (2017) TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data, Bioinformatics. btw772.
• Jamialahmadi, O., Motamedian, E. and Hashemi-Najafabadi, S. (2016) BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases. Molecular BioSystems, 12, 3459-3466.
• Motamedian, E., Saeidi, M. and Shojaosadati, S. (2016) Reconstruction of a charge balanced genome-scale metabolic model to study the energy-uncoupled growth of Zymomonas mobilis ZM1, Molecular BioSystems, 12, 1241-1249.
• Motamedian, E., Ghavami, G. and Sardari, S. (2015) Investigation on metabolism of cisplatin resistant ovarian cancer using a genome scale metabolic model and microarray data. Iranian journal of basic medical sciences, 18, 267.
• Irani, Z.A., Maghsoudi, A., Shojaosadati, S.A. and Motamedian, E. (2015) Development and in silico analysis of a new nitrogen-limited feeding strategy for fed-batch cultures of Pichia pastorisbased on a simple pH-control system, Biochemical Engineering Journal, 98, 1-9.
• Motamedian, E. (2015) A new algorithm to find all alternate optimal flux distributions of a metabolic network. Computers & Chemical Engineering, 73, 64-69.
• Motamedian, E. and Naeimpoor, F. (2011) Prediction of proton exchange and bacterial growth on various substrates using constraint-based modeling approach. Biotechnology and Bioprocess Engineering, 16, 875-884.
• Motamedian, E. and Naeimpoor, F. (2011) Flux distribution in Bacillus subtilis: inspection on plurality of optimal solutions. Iranian journal of biotechnology, 9, 260-266.

Conference Papers

• Maryam Mohammadi, Ehsan Motamedian, Seyed Abbas Shojaosadati (2018), Adding New Constraints to Incorporate Transcriptional Regulatory and Metabolic Networks of E. coli on Binary Substrates, 10^th international chemical engineering congress, Isfahan, Iran.
• Elham Taheri, Ehsan Motamedian, Fatemeh Bagheri (2015), A Bi-Level Integration Algorithm for Simultaneous Modeling of Multiple Cells, 4^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg, Germany.
• Maryam Mohammadi, Ehsan Motamedian, Seyed Abbas Shojaosadati (2015), Integration of Metabolic and Regulatory Networks with Incorporating Gene Expression Data, 16th International Conference on Systems Biology (ICSB 2015), Singapore.
• Elham Taheri, Ehsan Motamedian, Fatemeh Bagheri (2015), Finding essential genes for proliferation of cancer cell by integration of transcription data into a human metabolic model, 16th International Conference on Systems Biology (ICSB 2015), Singapore.
• Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati (2014), Integration of Microarray Data into a Genome-Scale Metabolic Model to Study Flux Distribution after Gene Knockout, International Science Index Vol: 8 No: 11 Part XVII, Istanbul, Turkey.
• Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati (2014), Reconstruction of a Genome-Scale Metabolic Model to Simulate Uncoupled Growth of Zymomonas mobilis, International Science Index Vol: 8 No: 11 Part XVII, Istanbul, Turkey.
• Ehsan Motamedian (2014), Effect of Variable Fluxes on Optimal Flux Distribution in a Metabolic Network, International Science Index Vol: 8 No: 11 Part XVII, Istanbul, Turkey.
• Ehsan Motamedian, Fereshteh Naeimpoor (2010), Comparison of Bacillus subtilis Growth on Different Nitrogen Sources using Flux Balance Analysis. 13^th Iranian National Chemical Engineering Congress & 1^st International Regional Chemical and Petroleum Engineering, Kermanshah, Iran, October 25-28.