All Stories

  1. SynCoKnock: a computational workflow for,knockout-based design of two-strain microbial,co-cultures to optimize target metabolite production and engineer cross-feeding

    Article • January 2026, Elsevier

    Dr Sayed-Amir Marashi

  2. Calibrating a parameterized stochastic Boolean network model of gene regulation using a single steady-state gene expression profile

    Article • Mathematical Biosciences, November 2025, Elsevier

    Dr Sayed-Amir Marashi

  3. Genome-Scale Metabolic Modeling Identifies Synergistic Metabolites that Enhance 5-Fluorouracil Efficacy in Colon Cancer.

    Article • Iranian Biomedical Journal, September 2025, National Academy of Sciences of Tajikistan

    Dr Sayed-Amir Marashi

  4. pastboon: an R package to simulate parameterized stochastic Boolean networks

    Article • Bioinformatics Advances, December 2024, Oxford University Press (OUP)

    Dr Sayed-Amir Marashi

  5. AmiR-P3: An AI-based microRNA prediction pipeline in plants

    Article • PLOS One, August 2024, PLOS

    Dr Sayed-Amir Marashi

  6. 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

    Article • PLOS One, July 2023, PLOS

    Dr Sayed-Amir Marashi

  7. Genome-scale metabolic model-based engineering of Escherichia coli enhances recombinant single-chain antibody fragment production

    Article • Biotechnology Letters, September 2022, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  8. On the role of oxygen and glucose in bone marrow-derived mesenchymal stem cell proliferation

    Article • January 2022, Wiley

    Dr Sayed-Amir Marashi

  9. Computational modeling of the evolutionary transition from C3 to C4 photosynthesis

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr Sayed-Amir Marashi

  10. Critical assessment of genome-scale metabolic models of Arabidopsis thaliana

    Article • Molecular Omics, January 2022, Royal Society of Chemistry

    Dr Sayed-Amir Marashi

  11. Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria

    Article • PLOS One, December 2021, PLOS

    Dr Sayed-Amir Marashi

  12. Transcriptome Meta-Analysis Suggests the Existence of Two Molecular Subtypes in Alzheimer’s Disease

    Article • May 2021, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  13. A constraint-based modeling approach to reach an improved chemically defined minimal medium for recombinant antiEpEX-scFv production by Escherichia coli

    Article • April 2021, Wiley

    Dr Sayed-Amir Marashi

  14. CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data

    Article • NAR Genomics and Bioinformatics, January 2021, Oxford University Press (OUP)

    Dr Sayed-Amir Marashi

  15. Systematically gap-filling the genome-scale metabolic model of CHO cells

    Article • Biotechnology Letters, October 2020, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  16. Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases

    Article • PLOS One, September 2020, PLOS

    Dr Sayed-Amir Marashi

  17. In silico prediction of enzymatic reactions catalyzed by acid phosphatases

    Article • Journal of Biomolecular Structure and Dynamics, July 2020, Taylor & Francis

    Dr Sayed-Amir Marashi

  18. A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer’s disease

    Article • Scientific Reports, May 2020, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  19. A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4

    Article • Scientific Reports, May 2020, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  20. Systematically gap-filling the genome-scale model of CHO cells

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Dr Sayed-Amir Marashi

  21. Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

    Article • Scientific Reports, December 2019, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  22. A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Dr Sayed-Amir Marashi

  23. The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency

    Article • Cell & Bioscience, August 2019, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  24. SAFEPPP: a Simple And Fast method to Find and analyze Extreme Points of a metabolic Phenotypic Phase Plane

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Sayed-Amir Marashi

  25. A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber

    Article • PLOS One, May 2019, PLOS

    Dr Sayed-Amir Marashi

  26. Accounting for robustness in modeling signal transduction responses

    Article • Journal of Receptors and Signal Transduction, February 2019, Taylor & Francis

    Dr Sayed-Amir Marashi

  27. Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes

    Article • Expert Review of Proteomics, December 2018, Taylor & Francis

    Dr Sayed-Amir Marashi, Mostafa Rezaei Tavirani, Nasibeh Khayer

  28. Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

    Article • Iranian Journal of Biotechnology, August 2018, American Journal of Life Science Researches

    Dr Sayed-Amir Marashi

  29. A graph-based approach to analyze flux-balanced pathways in metabolic networks

    Article • Biosystems, March 2018, Elsevier

    Dr Sayed-Amir Marashi

  30. Applications of a metabolic network model of mesenchymal stem cells for controlling cell proliferation and differentiation

    Article • Cytotechnology, October 2017, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  31. Three-way interaction model to trace the mechanisms involved in Alzheimer’s disease transgenic mice

    Article • PLOS One, September 2017, PLOS

    Dr Sayed-Amir Marashi

  32. Biomedical applications of cell- and tissue-specific metabolic network models

    Article • Journal of Biomedical Informatics, April 2017, Elsevier

    Dr Sayed-Amir Marashi

  33. Discovering missing reactions of metabolic networks by using gene co-expression data

    Article • Scientific Reports, February 2017, Nature

    Dr Sayed-Amir Marashi

  34. A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia

    Article • Systems Biology in Reproductive Medicine, January 2017, Taylor & Francis

    Dr Sayed-Amir Marashi

  35. A multiscale agent-based framework integrated with a constraint-based metabolic network model of cancer for simulating avascular tumor growth

    Article • Molecular BioSystems, January 2017, Royal Society of Chemistry

    Dr Sayed-Amir Marashi

  36. In silico prediction of specific pathways that regulate mesangial cell proliferation in IgA nephropathy

    Article • Medical Hypotheses, December 2016, Elsevier

    Dr Sayed-Amir Marashi

  37. A network biology approach to understanding the importance of chameleon proteins in human physiology and pathology

    Article • Amino Acids, November 2016, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  38. A kidney-specific genome-scale metabolic network model for analyzing focal segmental glomerulosclerosis

    Article • Mammalian Genome, February 2016, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  39. CAMWI: Detecting protein complexes using weighted clustering coefficient and weighted density

    Article • Computational Biology and Chemistry, October 2015, Elsevier

    Dr Sayed-Amir Marashi

  40. PCD-GED: Protein complex detection considering PPI dynamics based on time series gene expression data

    Article • Journal of Theoretical Biology, August 2015, Elsevier

    Dr Sayed-Amir Marashi

  41. On correlated reaction sets and coupled reaction sets in metabolic networks

    Article • Journal of Bioinformatics and Computational Biology, August 2015, World Scientific Pub Co Pte Lt

    Dr Sayed-Amir Marashi

  42. Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks

    Article • Computers in Biology and Medicine, August 2015, Elsevier

    Dr Sayed-Amir Marashi

  43. Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells

    Article • Cell Proliferation, July 2015, Wiley

    Dr Sayed-Amir Marashi

  44. Hierarchical organization of fluxes in Escherichia coli metabolic network: Using flux coupling analysis for understanding the physiological properties of metabolic genes

    Article • Gene, May 2015, Elsevier

    Dr Sayed-Amir Marashi

  45. Can scientific journals be classified based on their ‘citation profiles’?

    Article • South African Journal of Science, March 2015, Academy of Science of South Africa

    Dr Sayed-Amir Marashi

  46. Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

    Article • Molecular BioSystems, January 2015, Royal Society of Chemistry

    Dr Sayed-Amir Marashi

  47. Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals

    Article • Biosystems, October 2014, Elsevier

    Dr Sayed-Amir Marashi

  48. FCDECOMP: Decomposition of metabolic networks based on flux coupling relations

    Article • Journal of Bioinformatics and Computational Biology, October 2014, World Scientific Pub Co Pte Lt

    Dr Sayed-Amir Marashi

  49. A mathematical approach to emergent properties of metabolic networks: Partial coupling relations, hyperarcs and flux ratios

    Article • Journal of Theoretical Biology, August 2014, Elsevier

    Dr Sayed-Amir Marashi

  50. Reconstruction of a generic metabolic network model of cancer cells

    Article • Molecular BioSystems, January 2014, Royal Society of Chemistry

    Dr Sayed-Amir Marashi

  51. Modeling the Differences in Biochemical Capabilities ofPseudomonasSpecies by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

    Article • The Scientific World JOURNAL, January 2014, Hindawi Publishing Corporation

    Dr Sayed-Amir Marashi

  52. Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks

    Article • Mitochondrion, November 2013, Elsevier

    Dr Sayed-Amir Marashi

  53. Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism

    Article • Biotechnology Letters, September 2013, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  54. Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, June 2013, Elsevier

    Dr Sayed-Amir Marashi

  55. Studying the Relationship between Robustness against Mutations in Metabolic Networks and Lifestyle of Organisms

    Article • The Scientific World JOURNAL, January 2013, Hindawi Publishing Corporation

    Dr Sayed-Amir Marashi

  56. On flux coupling analysis of metabolic subsystems

    Article • Journal of Theoretical Biology, June 2012, Elsevier

    Dr Sayed-Amir Marashi

  57. Analysis of Metabolic Subnetworks by Flux Cone Projection

    Article • Algorithms for Molecular Biology, May 2012, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  58. Flux coupling analysis of metabolic networks is sensitive to missing reactions

    Article • Biosystems, January 2011, Elsevier

    Dr Sayed-Amir Marashi

  59. FFCA: a feasibility-based method for flux coupling analysis of metabolic networks

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  60. Binding of Tris to Bacillus licheniformis α-Amylase Can Affect Its Starch Hydrolysis Activity

    Article • Protein & Peptide Letters, February 2008, Bentham Science Publishers

    Dr Sayed-Amir Marashi

  61. Impact of residue accessible surface area on the prediction of protein secondary structures

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  62. β-Sheet capping: Signals that initiate and terminate β-sheet formation

    Article • Journal of Structural Biology, January 2008, Elsevier

    Dr Sayed-Amir Marashi

  63. A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  64. Evolution of ‘Ligand-Diffusion Chreodes’ on Protein-Surface Models: A Genetic-Algorithm Study

    Article • Chemistry & Biodiversity, December 2007, Wiley

    Dr Sayed-Amir Marashi

  65. Adaptation of proteins to different environments: A comparison of proteome structural properties in Bacillus subtilis and Escherichia coli

    Article • Journal of Theoretical Biology, January 2007, Elsevier

    Dr Sayed-Amir Marashi

  66. On the mechanism of apoptosis-inducing activity of human calprotectin: Zinc sequestration, induction of a signaling pathway, or something else?

    Article • Medical Hypotheses, January 2007, Elsevier

    Dr Sayed-Amir Marashi

  67. Conformational Study of Human Serum Albumin in Pre-denaturation Temperatures by Differential Scanning Calorimetry, Circular Dichroism and UV Spectroscopy

    Article • BMB Reports, September 2006, Korean Society for Biochemistry and Molecular Biology - BMB Reports

    Dr Sayed-Amir Marashi

  68. Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks

    Article • Computational Biology and Chemistry, February 2006, Elsevier

    Dr Sayed-Amir Marashi

  69. Application of β-lactamase-dependent prodrugs in clostridial-directed enzyme therapy (CDEPT): A proposal

    Article • Medical Hypotheses, January 2006, Elsevier

    Dr Sayed-Amir Marashi

  70. Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

    Dr Sayed-Amir Marashi

  71. Modeling directed ligand passage toward enzyme active site by a ‘double cellular automata’ model

    Article • Biochemical and Biophysical Research Communications, July 2005, Elsevier

    Dr Sayed-Amir Marashi

  72. On the identity of “citers”: Are papers promptly recognized by other investigators?

    Article • Medical Hypotheses, January 2005, Elsevier

    Dr Sayed-Amir Marashi

  73. Nanotechnology helps medicine: Nanoscale swimmers and their future applications

    Article • Medical Hypotheses, January 2005, Elsevier

    Dr Sayed-Amir Marashi

  74. Why major nonenzymatic glycation sites of human serum albumin are preferred to other residues?

    Article • Medical Hypotheses, January 2005, Elsevier

    Dr Sayed-Amir Marashi

  75. Correlations between genomic GC levels and optimal growth temperatures are not ‘robust’

    Article • Biochemical and Biophysical Research Communications, December 2004, Elsevier

    Dr Sayed-Amir Marashi

  76. How reliable re-adjustment is: correspondence regarding A. Fuglsang, “The ‘effective number of codons’ revisited”

    Article • Biochemical and Biophysical Research Communications, November 2004, Elsevier

    Dr Sayed-Amir Marashi