Pathway logic

symbolic analysis of biological signaling.

Steven Eker, Merrill Knapp, Keith Laderoute, Patrick Lincoln, Jose Meseguer, Mustafa (Kemal) Sonmez

Research output: Chapter in Book/Report/Conference proceedingChapter

98 Citations (Scopus)

Abstract

The genomic sequencing of hundreds of organisms including homo sapiens, and the exponential growth in gene expression and proteomic data for many species has revolutionized research in biology. However, the computational analysis of these burgeoning datasets has been hampered by the sparse successes in combinations of data sources, representations, and algorithms. Here we propose the application of symbolic toolsets from the formal methods community to problems of biological interest, particularly signaling pathways, and more specifically mammalian mitogenic and stress responsive pathways. The results of formal symbolic analysis with extremely efficient representations of biological networks provide insights with potential biological impact. In particular, novel hypotheses may be generated which could lead to wet lab validation of new signaling possibilities. We demonstrate the graphic representation of the results of formal analysis of pathways, including navigational abilities, and describe the logical underpinnings of the approach. In summary, we propose and provide an initial description of an algebra and logic of signaling pathways and biologically plausible abstractions that provide the foundation for the application of high-powered tools such as model checkers to problems of biological interest.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Pages400-412
Number of pages13
StatePublished - 2002
Externally publishedYes

Fingerprint

Information Storage and Retrieval
Proteomics
Gene Expression
Growth
Research
Datasets

Cite this

Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., & Sonmez, M. K. (2002). Pathway logic: symbolic analysis of biological signaling. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (pp. 400-412)

Pathway logic : symbolic analysis of biological signaling. / Eker, Steven; Knapp, Merrill; Laderoute, Keith; Lincoln, Patrick; Meseguer, Jose; Sonmez, Mustafa (Kemal).

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2002. p. 400-412.

Research output: Chapter in Book/Report/Conference proceedingChapter

Eker, S, Knapp, M, Laderoute, K, Lincoln, P, Meseguer, J & Sonmez, MK 2002, Pathway logic: symbolic analysis of biological signaling. in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. pp. 400-412.
Eker S, Knapp M, Laderoute K, Lincoln P, Meseguer J, Sonmez MK. Pathway logic: symbolic analysis of biological signaling. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2002. p. 400-412
Eker, Steven ; Knapp, Merrill ; Laderoute, Keith ; Lincoln, Patrick ; Meseguer, Jose ; Sonmez, Mustafa (Kemal). / Pathway logic : symbolic analysis of biological signaling. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2002. pp. 400-412
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