Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2007-12-11
2007-12-11
Zhou, Shubo (Joe) (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C703S002000, C703S011000
Reexamination Certificate
active
10055775
ABSTRACT:
Biological and chemical systems are represented as a symbolic model. Minimal sets of elements of the system are identified from the model, for example, by automatic inference. The model can be constructed from Boolean propositions that are mapped to a binary decision diagram. The model can also be probed using a branch and bound algorithm.
REFERENCES:
patent: 5113342 (1992-05-01), Zamora
patent: 5621671 (1997-04-01), Bodnar
patent: 5805461 (1998-09-01), Fant et al.
patent: 5914891 (1999-06-01), McAdams et al.
patent: 5930154 (1999-07-01), Thalhammer-Reyero
patent: 5980096 (1999-11-01), Thalhammer-Reyero
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6438496 (2002-08-01), Yoshida et al.
patent: 2002/0068269 (2002-06-01), Allen et al.
patent: 2003/0033126 (2003-02-01), Lincoln et al.
patent: WO 99/66067 (1999-12-01), None
Akutsu et al., Bioinformatics, vol. 16, pp. 727-734, 2000.
Goto et al., Bioinformatics, vol. 14, pp. 591-599, 1998.
Darnell et al., Molecular Cell Biology, 1987, pp. 53-63, 106-124, and 192-200.
Akutsu et al., “Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model”,Bioinformatics17-28, 1999.
Akutsu et al., “Inferring qualitative relations in genetic networks and metabolic pathways”,Bioinformatics16(8):727-734 (2000).
Becskel et al., “Engineering stability in gene networks by autoregulation”,Nature405:590-593 (2000).
D'haeseleer et al., “Genetic network inference: from co-expression clustering to reverse engineering”,Bioinformatics16(8):707-726 (2000).
Endy and Brent, “Modelling cellular behaviour”,Nature409:391-395 (2001).
Gibbs, W.W., “Cybernetic Cells”,Scientific American53-57 (Aug. 2001).
Glass and Kauffman, “The Logical Analysis of Continuous, Non-linear Biochemical Control Networks”,J. Theor. Biol. 39:103-129 (1973).
Karp, P.D., “An ontology for biological function based on molecular interactions”,Bioinformatics16:269-285 (2000).
Kauffman, S.A., “Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets”,J. Theoret. Biol. 22:437-467 (1969).
Kohn, K.W., “Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems”,Molecular Biology of the Cell10:2703-2734 (1999).
Liang et al., “Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures”,Proc. Pacific Symp. On Biocomputing3:18-29, 1998.
McAdams and Arkin, “Simulation of Prokaryotic Genetic Circuits”,Annu. Rev. Biophys. Struct. 27:199-224 (1998).
Akutsu et al., “Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model”,Bioinformatics17-28 (1999).
Liang et al., “Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures”,Proc. Pacific Symp. On Biocomputing3:18-29 (1998).
McAdams and Shapiro, “Circuit Simulation of Genetic Networks”,Science269:650-656 (1995).
Mikulecky, D.C., “Modeling Intestinal Absorption and Other Nutrition-Related Processes Using PSPICE and STELLA”,Journal of Pediatric Gastroenterology and Nutrition11:7-20 (1990).
Novick and Weiner, “Enzyme Induction as an All-or-None Phenomenon*”,Proc. Nat. Acad. USA43:553-566 (1957).
Ogata et al., “Computation with the KEGG pathway database”,BioSystems47:119-128 (1998).
Ouzounis and Karp, “Global Properties of the Metabolic Map ofEscherichia coli”, Genomic Research10:568-576 (2000).
Owre et al., “PVS: A Prototype Verification System”,11thInternational Conference on Automated Deduction(CADE) 748-752 (1992).
Rosen, R., “Recent Developments in the Theory of Control and Regulation of Cellular Processes”,International Review of Cytology23:25-88 (1968).
Shea and Ackers,“The ORControl System of Bacteriophage Lambda A Physical-Chemical Model for Gene Regulation”,J. Mol. Biol181:211-230 (1985).
Snoussi and Thomas, “Logical Identification of All Steady States: The Concept of Feedback Loop Characteristic States”,Bulletin of Mathematical Biology55:973-991 (1993).
Somogyi and Sniegoski, “Modeling the Complexity of Genetic Networks: Understanding Multigenic and Pleiotropic Regulation”,Complexity1:45-64 (1996).
Stahl, W. R., “Algorithmically Unsolvable Problems for a Cell Automaton”,J. Theoret. Biol. 8:371-394 (1965).
Stahl, W. R., “Self-Reproducing Automata”,Perspectives in Biology and Medicine:373-393 (1965).
Stahl and Goheen, “Molecular Algorithms”,J Theoret. Biol. 5:266-287 (1963).
Sugita, M., “Functional Analysis of Chemical Systems in vivo using a Logical Circuit Equivalent. II. The Idea of a Molecular Automaton”,J. Theoret. Biol. 4:179-192 (1963).
Szallasi and Liang, “Modeling the Normal and Neoplastic Cell Cycle with “Realistic Boolean Genetic Networks”: Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies”,Proc. Pacific Symp. On Biocomputing3:66 (1998).
Thomas, R., “Boolean Formalization of Genetic Control Circuits”,J. Theor. Biol. 42:563-585 (1973).
Thomas, R., “Regulatory Networks Seen as Asynchronous Automata: A Logical Description”,J. Theor. Biol. 153:1-23 (1991).
Thomas et al., “A Complex Control Circuit: Regulation of Immunity in Temperature Bacteriophages”,Eur. J. Biochem. 71:211-227 (1976).
Thomas et al., “Dynamical Behaviour of Biological Regulatory Networks—I. Biological Role of Feedback Loops and Practical Use of the Concept of the Loop-Characteristic State”,Bulletin of Mathematical Biology57:247-276 (1995).
Weng et al., “Complexity in Biological Signaling Systems”,Science284:92-96 (1999).
Yuh et al., “Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene”,Science279:1896-1902 (1998).
Eker Steven Mark
Karp Peter D.
Lincoln Patrick Denis
Romero Pedro
Patterson & Sheridan LLP
SRI - International
Tong, Esq. Kin-Wah
Zhou Shubo (Joe)
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