Analyzing and Synthesizing Genomic Logic Functions

  • Nicola Paoletti
  • Boyan Yordanov
  • Youssef Hamadi
  • Christoph M. Wintersteiger
  • Hillel Kugler
Conference paper

DOI: 10.1007/978-3-319-08867-9_23

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8559)
Cite this paper as:
Paoletti N., Yordanov B., Hamadi Y., Wintersteiger C.M., Kugler H. (2014) Analyzing and Synthesizing Genomic Logic Functions. In: Biere A., Bloem R. (eds) Computer Aided Verification. CAV 2014. Lecture Notes in Computer Science, vol 8559. Springer, Cham

Abstract

Deciphering the developmental program of an embryo is a fundamental question in biology. Landmark papers [9,10] have recently shown how computational models of gene regulatory networks provide system-level causal understanding of the developmental processes of the sea urchin, and enable powerful predictive capabilities. A crucial aspect of the work is empirically deriving plausible models that explain all the known experimental data, a task that becomes infeasible in practice due to the inherent complexity of the biological systems. We present a generic Satisfiability Modulo Theories based approach to analyze and synthesize data constrained models. We apply our approach to the sea urchin embryo, and successfully improve the state-of-the-art by synthesizing, for the first time, models that explain all the experimental observations in [10]. A strength of the proposed approach is the combination of accurate synthesis procedures for deriving biologically plausible models with the ability to prove inconsistency results, showing that for a given set of experiments and possible class of models no solution exists, and thus enabling practical refutation of biological models.

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Nicola Paoletti
    • 1
    • 2
  • Boyan Yordanov
    • 1
  • Youssef Hamadi
    • 1
  • Christoph M. Wintersteiger
    • 1
  • Hillel Kugler
    • 1
  1. 1.Microsoft ResearchCambridgeUK
  2. 2.Department of Computer ScienceUniversity of OxfordUK

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