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List of works by Sayed-Amir Marashi

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

scientific article published on 09 May 2019

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

scientific article published on 11 January 2018

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

scientific article published on 29 February 2016

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

scientific article published on 19 April 2014

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

scientific article published on 20 May 2020

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

scientific article published on 24 July 2017

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

scientific article

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

scientific article published on 08 May 2020

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

scientific article published on 13 January 2017

A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins

scientific article

Accounting for robustness in modeling signal transduction responses

scientific article published on 01 October 2018

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

scientific article

Analysis of metabolic subnetworks by flux cone projection.

scientific article published on 29 May 2012

Application of beta-lactamase-dependent prodrugs in clostridial-directed enzyme therapy (CDEPT): a proposal.

scientific article

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

scientific article

Beta-sheet capping: signals that initiate and terminate beta-sheet formation.

scientific article published on 11 October 2007

Binding of Tris to Bacillus licheniformis alpha-amylase can affect its starch hydrolysis activity

scientific article

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

scientific article

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

scientific article published on 06 January 2021

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

scientific article

Conformational study of human serum albumin in pre-denaturation temperatures by differential scanning calorimetry, circular dichroism and UV spectroscopy.

scientific article published on September 2006

Correlations between genomic GC levels and optimal growth temperatures are not 'robust'.

scientific article published in December 2004

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

scientific article

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

scientific article published on 21 May 2015

Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study

scientific article published in December 2007

Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks

scientific article

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

scientific article published on February 13, 2013

FCDECOMP: decomposition of metabolic networks based on flux coupling relations

scientific article published in October 2014

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

scientific article published on June 15, 2011

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

scientific article published in December 2013

Flux coupling analysis of metabolic networks is sensitive to missing reactions ⬇️

scientific article published on October 1, 2010

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

scientific article published in 2022

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

scientific article published on 25 August 2015

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

scientific article published on 14 February 2015

How reliable re-adjustment is: correspondence regarding A. Fuglsang, "The 'effective number of codons' revisited".

scientific article

Impact of RNA structure on the prediction of donor and acceptor splice sites

scientific article

Impact of Wikipedia on citation trends

scientific article

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

scientific article

In silico prediction of enzymatic reactions catalyzed by acid phosphatases

scientific article published on 02 July 2020

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

scientific article published on 20 October 2016

Indirect role of microRNAs and transcription factors in the regulation of important cancer genes: A network biology approach

scientific article published on 30 October 2015

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

scientific article published on 10 December 2019

Modeling directed ligand passage toward enzyme active site by a 'double cellular automata' model.

scientific article published in July 2005

Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences?

scientific article published on 24 February 2014

Nanotechnology helps medicine: nanoscale swimmers and their future applications.

scientific article

On correlated reaction sets and coupled reaction sets in metabolic networks

scientific article published on 30 January 2015

On flux coupling analysis of metabolic subsystems

scientific article published on 3 March 2012

On the identity of "citers": are papers promptly recognized by other investigators?

scientific article

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

scientific article published on 28 November 2006

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

scientific article

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

scientific article

Reconstruction of a generic metabolic network model of cancer cells.

scientific article published in November 2014

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals

scientific article

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

scientific article published on 17 September 2020

Studying the relationship between robustness against mutations in metabolic networks and lifestyle of organisms

scientific article published on 14 November 2013

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

scientific article published on 10 October 2020

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

scientific article published on 29 August 2019

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

scientific article published on 21 September 2017

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

scientific article published on 24 December 2018

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