Heuristics for dependency conjectures in proteomic signaling pathways

ABSTRACT

A key issue in the study of protein signaling networks is understanding the relationships among proteins in the network. Understanding these relationships in the context of a network is one of the major challenges for modern biology [2, 6]. In the laboratory a time series of protein modification measurements is taken in order that relationships among the activations can be conjectured. Laubenbacher and Stigler [5] have developed an algorithm to make conjectures concerning gene expression. Their algorithm analyses the relations as variables in polynomials, using techniques based in computational algebra. This paper focuses on heuristics for applying their method to conjecture dependencies between proteins in signal transduction networks.

REFERENCES

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INDEX TERMS

Primary Classification:
  I. Computing Methodologies
  I.1 SYMBOLIC AND ALGEBRAIC MANIPULATION
      I.1.2 Algorithms

Additional Classification:
  I. Computing Methodologies
  I.2 ARTIFICIAL INTELLIGENCE
      I.2.8 Problem Solving, Control Methods, and Search

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES

Keywords:
computational biology, glycolysis regulation, heuristics, proteomics, signal transduction