Modeling of Biological Networks

Biological networks, including gene regulatory networks, protein-protein interaction networks, and metabolic networks, play crucial roles in determining the behavior and functions of living organisms. Modeling these networks is essential for understanding their structure, dynamics, and emergent properties. Various mathematical and computational models have been developed to study biological networks, each with its strengths and limitations.

Mathematical Models:

  • Differential Equations: Used to describe the dynamics of biological networks by representing changes in concentrations or activities of network components over time.
  • Boolean Networks: A simplified model where network components are either active (1) or inactive (0), based on logical rules governing their interactions.
  • Graph Theory: Utilized to represent biological networks as graphs, with nodes representing components and edges representing interactions.

Computational Models:

  • Agent-Based Models: Simulate the behavior of individual components in a network, allowing for the study of complex, emergent behaviors.
  • Constraint-Based Models: Use optimization techniques to predict network behavior based on constraints such as mass balance and stoichiometry.
  • Machine Learning Models: Employed to predict interactions within biological networks based on large-scale data sets.

Applications:

  • Drug Discovery: Modeling biological networks can help identify potential drug targets and predict the effects of drugs on network behavior.
  • Disease Modeling: Understanding how biological networks are altered in disease states can lead to the development of new diagnostic tools and therapies.
  • Synthetic Biology: Modeling biological networks is crucial for designing and engineering synthetic biological systems with specific functions.

Challenges:

  • Data Quality: Biological network models are only as good as the data used to construct them, highlighting the importance of high-quality, comprehensive data.
  • Model Complexity: Biological networks are inherently complex, making it challenging to develop accurate models that capture all relevant interactions.
  • Model Validation: Validating biological network models requires experimental validation, which can be time-consuming and resource-intensive.

In conclusion, modeling biological networks is a powerful approach for gaining insights into the complexity of living systems. By combining mathematical modeling, computational simulations, and experimental validation, researchers can uncover the underlying principles governing biological networks and advance our understanding of living organisms.

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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (PE)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (AP)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (AP)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (APC)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (APC)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (HRP)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (HRP)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (FITC)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (FITC)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (Biotin)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (Biotin)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 405)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 405)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 490)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 490)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 550)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 550)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 750)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 750)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 650)
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USH1C (Usher Syndrome 1C (Autosomal Recessive, severe), AIE-75, DFNB18, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, ush1cpst) (MaxLight 650)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (AP)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (APC)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (APC)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (Biotin)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (Biotin)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (FITC)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (FITC)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (HRP)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (HRP)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (PE)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (PE)
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(untagged)-Human cDNA FLJ31250 fis, clone KIDNE2005336, weakly similar to Human antigen NY-CO-31 (NY-CO-31) mRNA
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (MaxLight 405)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (MaxLight 405)
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USH1C (Usher Syndrome Type-1C Protein, PDZ73, Autoimmune Enteropathy-related Antigen AIE-75, AIE-75, DFNB18, PDZ-45, PDZ-73, PDZD7C, DFNB18A, NY-CO-37, NY-CO-38, Ush1cpst, PDZ-73/NY-CO-38) (MaxLight 490)
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