Browsing Bergen Open Research Archive by Author "Fallahi, Shirin"
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A comparison of Monte Carlo sampling methods for metabolic network models
Fallahi, Shirin; Skaug, Hans J.; Alendal, Guttorm (Journal article; Peer reviewed, 2020)Reaction rates (fluxes) in a metabolic network can be analyzed using constraint-based modeling which imposes a steady state assumption on the system. In a deterministic formulation of the problem the steady state assumption ... -
Dynamic modelling of biochemical reaction networks and sampling methods for constraint-based models
Fallahi, Shirin (Doctoral thesis, 2021-02-05)This dissertation is a partial fulfillment of the requirements for the degree of Doctor of Philosophy (PhD). This study is carried out at the Department of Mathematics, University of Bergen. The subject of the thesis is ... -
Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod
Eide, Marta; Goksøyr, Anders; Yadetie, Fekadu; Gilabert, Alejandra; Bartosova, Zdenka; Frøysa, Håvard Guldbrandsen; Fallahi, Shirin; Zhang, Xiaokang; Blaser, Nello; Jonassen, Inge; Bruheim, Per; Alendal, Guttorm; Brun, Morten; Porte, Cinta; Karlsen, Odd André (Journal article; Peer reviewed, 2023-03-22)Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in ... -
New Conceptual Toxicokinetic Model to Assess Synergistic Mixture Effects between the Aromatic Hydrocarbon β-Naphthoflavone and the Azole Nocodazole on the CYP1A Biomarker in a Fish Cell Line
Fallahi, Shirin; Mlnaříková, Marie; Alvord, Charlotte; Alendal, Guttorm; Frøysa, Håvard G; Lundh, Thorbjörn; Celander, Malin C. (Journal article; Peer reviewed, 2020)Toxicokinetic interactions with catabolic cytochrome P450 (CYP) enzymes can inhibit chemical elimination pathways and cause synergistic mixture effects. We have created a mathematical bottom-up model for a synergistic ... -
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz; Yadetie, Fekadu; Zielinski, Daniel Craig; Goksøyr, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-11)The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ...