Articles in International Scientific Journals
22 articles in peer reviewed journals, with 410 citations (Web of Science), 646 citations (Google Scholar)  |
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Computational systems biology of metabolism in infection (Book Chapter)
- Computational Glioscience, Springer, submitted
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Genome-scale brain metabolic networks as scaffolds for the systems biology of neurodegenerative diseases: mapping metabolic alterations (Book Chapter)
- Systems Neuroscience, Springer, submitted
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Constraint-Based Modeling of Metabolic Interactions in and between Astrocytes and Neurons (Book Chapter)
- Computational Glioscience, Springer, submitted
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Reconstructed metabolic network models predict flux-level metabolic reprogramming of glioblastoma
- Frontiers in Neuroscience, 10:156 (2016)
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Data-based reconstruction of gene regulatory networks of fungal pathogens
- Frontiers in Microbiology, 7:570 (2016)
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Editorial: Computational Systems Biology of Pathogen-Host Interactions
- Frontiers in Microbiology, 7:21 (2016)
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Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach
- Scientific Reports, 5:14563 (2015)
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A review on computational systems biology of pathogen–host interactions
- Frontiers in Microbiology, 6:235, (2015), Citation: 20
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Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation
- Frontiers in Bioengineering and Biotechnology, 2:62, (2014)
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Biyolojik Ağların Modellenmesi (Book Chapter)
- Biyomedikal Mühendisliğin Temelleri (Foundations of Biomedical Engineering), Eds. M.H. Asyalı, S. Kara, B. Yılmaz, Nobel Kitap, Ankara, 523-560, (2014)
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The role of flexibility and optimality in the prediction of Intracellular Fluxes of microbial cell metabolism
- Molecular Biosystems, 10, 2459-2465, (2014)
- Systematic Analysis of Transcription-Level Effects of Neurodegenerative Diseases on Human Brain Metabolism by a Newly Reconstructed Brain-Specific Metabolic Network
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Sparsity as cellular objective to infer directed metabolic networks from steady-state metabolome data: A theoretical analysis
- PLoS ONE, 8:12, e84505, (2013)
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PHISTO: Pathogen-Host Interaction Search Tool
- Bioinformatics, 29:1357-1358, (2013), Citation: 22
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Infection strategies of bacterial and viral pathogens through pathogen-host protein protein interactions
- Frontiers in Microbiology, 3:46, (2012), Citation: 26
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Metabolic network discovery through reverse engineering of metabolome data
- Metabolomics, 5: 318-329, (2009), Citation: 23
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2007
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Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
- BMC Systems Biology, 1:18, (2007), Citation: 25
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Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains
- Biotechnology Progress, 23: 320-326, (2007), Citation: 17
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Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia
- Theoretical Biology & Medical Modelling, 4:48, (2007), Citation: 26
2006
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Integration of metabolome data with metabolic networks reveals reporter reactions
- Molecular Systems Biology, 2:50, (2006), Citation: 91
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Analysis of enzymopathies in the human red blood cells by constraint based stoichiometric modeling approaches
- Computational Biology and Chemistry, 30: 327-338 (2006)
2005
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Modelling of calcium dynamics in brain energy metabolism and Alzheimer's disease
- Computational Biology and Chemistry, 29: 151-162 (2005)
2004
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Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
- Biotechnology & Bioengineering, 86: 251-260 (2004), Citation: 43
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Metabolic pathway analysis of enzyme-deficient human red blood cells
- Biosystems, 78: 49-67, (2004), Citation: 24
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Flux analysis of the recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimum ethanol production
- Process Biochemistry, 39: 2097-2108 (2004), Citation: 13
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Transfer function approach in structured modeling of recombinant yeast utilizing starch
- Process Biochemistry, 39: 1237-1248 (2004)