Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2002-06-14
2010-12-21
Lin, Jerry (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
Reexamination Certificate
active
07856317
ABSTRACT:
The invention provides a computer implemented process for constructing a scalable output network model of a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.
REFERENCES:
patent: 5273038 (1993-12-01), Beavin et al.
patent: 5556762 (1996-09-01), Pinilla et al.
patent: 5639949 (1997-06-01), Ligon et al.
patent: 5689633 (1997-11-01), Cotner et al.
patent: 5914891 (1999-06-01), Arkin et al.
patent: 5930154 (1999-07-01), Thalhammer-Reyero
patent: 5947899 (1999-09-01), Scollan et al.
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6165709 (2000-12-01), Friend et al.
patent: 6200803 (2001-03-01), Roberts
patent: 6221597 (2001-04-01), Roberts
patent: 6302302 (2001-10-01), Albisetti
patent: 6326140 (2001-12-01), Rine et al.
patent: 6329139 (2001-12-01), Nova et al.
patent: 6351712 (2002-02-01), Stoughton et al.
patent: 6370478 (2002-04-01), Stoughton et al.
patent: 6379964 (2002-04-01), Del Cardayre
patent: 6500710 (2005-01-01), Thalhammer-Reyero
patent: 6983227 (2006-01-01), Thalhammer-Reyero
patent: 6902692 (2006-10-01), Palsson et al.
patent: 7127379 (2006-10-01), Palsson et al.
patent: 2002/0012939 (2002-01-01), Palsson et al.
patent: 2002/0051998 (2002-05-01), Schmidt et al.
patent: 2002/0168654 (2002-11-01), Maranas et al.
patent: 2003/0059792 (2003-03-01), Palsson et al.
patent: 2003/0113761 (2003-06-01), Tan et al.
patent: 2003/0233218 (2003-12-01), Schilling
patent: 2008/0176327 (2008-07-01), Palsson et al.
patent: WO 92/09300 (1992-06-01), None
patent: WO 00/46405 (2000-08-01), None
patent: WO 01/36658 (2001-05-01), None
patent: WO 01/57775 (2001-08-01), None
patent: WO 02/055995 (2002-07-01), None
patent: WO 2002/061115 (2002-08-01), None
patent: WO 03/106998 (2003-12-01), None
Ogata et al., Nucleic Acids Research, vol. 27, pp. 29-34, 1999.
Goto et al., Bioinformatics, vol. 14, pp. 591-599, 1998.
Goto et al., Nucleic Acids Research, vol. 27, pp. 377-379, 1999.
Karp, P., Bioinformatics, vol. 16, pp. 269-285, 2000.
Matrix, Dictionary.com, pp. 1-2, 2004.
Schuster et al., Bioinformatics, vol. 18, No. 2, pp. 351-361, Feb. 1, 2002.
Voet & Voet, Biochemstry, John Wiley & Sons, Inc., pp. 335-338, and 409-410, 1990.
Dandekar et al. Biochem. J., vol. 343, pp. 115-124, 1999.
Bansal, A. K., Bioinformatics and Bioengineering Conference, 2001, pp. 209-216, 2001.
Covert et al., “Regulation of Gene Expression in Flux Balance Models of Metabolism,”J. Theor. Biol., 213:73-88 (2001).
Covert et al., “Metabolic modeling of microbial strains in silico,”Trends in Biochemical Sciences, 26:179-186 (2001).
Dauner and Sauer, “Stoichiometric Growth Model for Riboflavin-ProducingBacillus subtilis,” Biotechnol. Bioeng., 76:132-143 (2001).
Dauner et al., “Metabolic Flux Analysis with a Comprehensive Isotopomer Model inBacillus subtilis,” Biotechnol. Bioeng., 76:144-156 (2001).
Dauner et al., “Bacillus subtilisMetabolism and Energetics in Carbon-Limited and Excess-Carbon Chemostat Culture,”J. Bact., 183:7308-7317 (2001).
Edwards et al., “In silico predictions ofEscherichia colimetabolic capabilities are consistent with experimental data,”Nature Biotech., 19:125-130 (2001).
Edwards et al., “Characterizing the Metabolic Phenotype: A Phenotype Phase Plane Analysis,”Biotech. Bioeng., 77:27-36 (2002).
Edwards and Palsson, “TheEscherichia coliMG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities,”Proc. Natl. Acad. Sci. USA, 97:5528-5533 (2000).
Edwards and Palsson, “Systems Properties of theHaemophilus influenzaeRd Metabolic Genotype,”J. Biol. Chem., 274:17410-17416 (1999).
Fell and Small, “Fat synthesis in adipose tissue An examination of stoichiometric constraints,”Biochem. J., 238:781-786 (1986).
Kunst et al., “The complete genome sequence of the Gram-positive bacteriumBacillus subtilis,” Nature, 390:249-256 (1997).
Majewski and Domach, “Simple Constrained-Optimization View of Acetate Overflow inE. coli,” Biotech. Bioeng., 35:732-738 (1990).
Palsson, B., “The challenges of in silico biology,”Nat. Biotech, 18:1147-1150 (2000).
Sauer and Bailey, “Estimation of P-to-O Ratio inBacillus subtilisand Its Influence on Maximum Riboflavin Yield,”Biotechnol. Bioeng., 64:750-754 (1999).
Schilling et al., “Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective,”J. Theor. Biol., 203:229-248 (2000).
Schilling and Palsson, “Assessment of the Metabolic CapabilitiesHaemophilus influenzaeRd through a Genome-scale Pathway Analysis,”J. Theor. Biol., 203:249-283 (2000).
Schilling et al., “Combining Pathway Analysis with Flux Balance Analysis for the Comprehensive Study of Metabolic Systems,”Biotech. Bioeng., 71:286-306 (2000).
Schilling et al., “Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances,”Biotech. Prog., 15:288-295 (1999).
Schilling et al, “Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era,”Biotech. Prog., 15:296-303 (1999).
Schilling and Palsson, “The underlying pathway structure of biochemical reaction networks,”Proc. Natl. Acad. Sci. USA, 95:4193-4198 (1998).
Thomas, R., “Logical Analysis of Systems Comprising Feedback Loops,”J. Theor. Biol., 73:631-656 (1978).
Thomas, R., “Boolean Formalization of Genetic Control Circuits,”J. Theor. Biol., 42:563-585 (1973).
Vanrolleghem et al., “Validation of a Metabolic Network forSaccharomyces cerevisiaeUsing Mixed Substrate Studies,”Biotech. Prog., 12:434-448 (1996).
Varma and Palsson,“Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use,”Biotech., 12:994-998 (1994).
Beckers et al., “Large-scare mutational analysis for the annotation of the mouse genome,”Curr. Opin. Chem. Biol., 6:17-23 (2001).
Hardison et al., “Globin gene server: a prototype e-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis,”Genomics, 21:344-353 (1994).
Jenssen et al., “A literature network of human genes for high-throughput analysis of gene expression,”Nat. Genetics, 28:21-28 (2001).
Juty et al., “Simultaneous modeling of metabolic, genetic and product-interaction networks,”Briefings in Bioinformatics, 2(3):223-232 (2001).
Moszer, I., “The complete genome ofBacillus subtilis: from sequence annotation to data management and analysis,”FEBS Letters, 430:28-36 (1998).
Romero et al., “Nutrient-related analysis of pathway/genome databases”Pacific Symposium on Biocomputing, pp. 471-482 (2001).
Covert et al., “Metabolic modeling of microbial strains in silico,”TRENDS in Biochem. Sci. 26(3):179-186 (2001).
Schilling et al., “Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems,”Biotech Bioeng71(4):286-306 (2000).
Schilling et al., “Toward metabolic phenomics: analysis of genomic data using flux balances,”Biotechnol. Prog. 15:288-295 (1999).
Adamowicz, et al., “Nutritional complementation of oxidative glucose metabolism inEscherichia colivia pyrroloquinoline quinone-dependent glucose dehydrogenase and the Entner-Doudor
Genomatica, Inc.
Lin Jerry
McDermott Will & Emery LLP
LandOfFree
Systems and methods for constructing genomic-based... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Systems and methods for constructing genomic-based..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Systems and methods for constructing genomic-based... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4218857