TY - JOUR
T1 - Pathway logic
T2 - symbolic analysis of biological signaling.
AU - Eker, Steven
AU - Knapp, Merrill
AU - Laderoute, Keith
AU - Lincoln, Patrick
AU - Meseguer, Jose
AU - Sonmez, Kemal
PY - 2002
Y1 - 2002
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=0036364829&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036364829&partnerID=8YFLogxK
M3 - Article
C2 - 11928493
AN - SCOPUS:0036364829
SN - 2335-6936
SP - 400
EP - 412
JO - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
JF - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
ER -