Shirin Fallahi
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View article: Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod
Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod Open
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 these processes. At…
View article: Dynamic modelling of biochemical reaction networks and sampling methods for constraint-based models
Dynamic modelling of biochemical reaction networks and sampling methods for constraint-based models Open
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 dynamic Modelling o…
View article: ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species Open
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 bacteria, archaea, an…
View article: 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
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 Open
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 mixture effect where …
View article: A comparison of Monte Carlo sampling methods for metabolic network models
A comparison of Monte Carlo sampling methods for metabolic network models Open
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 has to be fulfi…
View article: ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species
ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species Open
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 bacteria, archaea, and…
View article: Evaluating model reduction under parameter uncertainty
Evaluating model reduction under parameter uncertainty Open
A method to compare different models under parameter uncertainty is developed. It can be applied to any model reduction method. We also showed that the amount of parameter uncertainty influences the choice of reduced models.
View article: Additional file 1 of Evaluating model reduction under parameter uncertainty
Additional file 1 of Evaluating model reduction under parameter uncertainty Open
Scripts. Archive file containing all the scripts needed to produce and analyse the data of this paper. These scripts also produce Figs. 3, 4, and 5. (ZIP 23.3 kb)
View article: Terminal Deoxynucleotidyl Transferase (TdT) Inhibition of Cord Blood Derived B and T Cells Expansion
Terminal Deoxynucleotidyl Transferase (TdT) Inhibition of Cord Blood Derived B and T Cells Expansion Open
Purpose: Terminal deoxynucleotidyl transferase(TdT) is a DNA polymerase that is present in immature pre-B and pre-T cells. TdT inserts N-nucleotides to the V (D) J gene segment during rearrangements of genes, therefore, it plays a vital ro…
View article: Impact of C-rel inhibition of cord blood-derived B-, T-, and NK cells
Impact of C-rel inhibition of cord blood-derived B-, T-, and NK cells Open
The c-Rel transcription factor is a unique member of the nuclear factor (NF)-κB family that has a role in curtailing the proliferation, differentiation, cytokine production, and overall activity of B- and T-cells. In addition, c-Rel is a k…