Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2011-04-05
2011-04-05
Clow, Lori A (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C703S011000, C435S455000, C435S468000, C435S471000, C702S019000
Reexamination Certificate
active
07920994
ABSTRACT:
The present invention relates to methods for achieving an optimal function of a biochemical reaction network. The methods can be performed in silico using a reconstruction of a biochemical reaction network of a cell and iterative optimization procedures. The methods can further include laboratory culturing steps to confirm and possibly expand the determinations made using the in silico methods, and to produce a cultured cell, or population of cells, with optimal functions. The current invention includes computer systems and computer products including computer-readable program code for performing the in silico steps of the invention.
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
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
patent: 2003/0224363 (2003-12-01), Park et al.
patent: 2003/0233218 (2003-12-01), Schilling
patent: 2004/0009466 (2004-01-01), Maranas et al.
patent: 2004/0029149 (2004-02-01), Palsson et al.
patent: 2004/0072723 (2004-04-01), Palsson et al.
patent: 2006/0147899 (2006-07-01), Famili et al.
patent: 2007/0111294 (2007-05-01), Burgard et al.
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 01/57775 (2001-08-01), None
patent: WO 02/055995 (2002-07-01), None
patent: WO 02/061115 (2002-08-01), None
patent: WO 03/106998 (2003-12-01), None
Baily, “Complex Biology with No Parameters,”Nature Biotechnology, 19:503-504, Nature Publishing Group (2001).
Berry, “Improving Production of Aromatic Compounds inEscherichia coliby Metabolic Engineering,”TIBTECH, 14:250-256, Elsevier Science Ltd. (1996).
Bialy, “Living on the Edges,”Nature Biotechnology, 19:111-112, Nature Publishing Group (2001).
Burgard and Maranas, “Probing the Performance Limits of theEscherichia coliMetabolic Network Subject to Gene Additions or Deletions,”Biotechnology and Bioengineering, 74(5):364-375, John Wiley & Sons, Inc. (2001).
Edwards and Palsson, “Robustness Analysis ofEscherichia coliMetabolic Network,”Biotechnol. Prog. 2000, 16:927-939, American Chemical Society and American Institute of Chemical Engineers (2000).
Edwards and Palsson, “Systems Properties of theHaemophilus influenzaeRd Metabolic Genotype,”The Journal of Biological Chemistry, 274(25):17410-17416, The American Society for Biochemistry and Molecular Biology, Inc. (1999).
Edwards et al., “In silicoPredictions ofEscherichia coliMetabolic Capabilities are Consistent with Experimental Data,”Nature Biotechnology, 19:125-130, Nature Publishing Group (2001).
Hasty et al., “Computational Studies of Gene Regulatory Networks:In NumeroMolecular Biology,”Nat. Rev. Genet., 2:268-279, Macmillan Magazines Ltd (2001).
Heinrich and Rapoport, “Metabolic Regulation and Mathematical Models,”Prog. Biophys. Molec. Biol., 32:1-82, Pergamon Press (1977).
Heinrich et al., “Stoichiometric Analysis,”The Regulation of Cellular Systems, xix:75-111, Chapman & Hall, New York (1996).
Sauer, “Evolutionary Engineering of Industrially Important Microbial Phenotypes,”Advances in Biochemical Engineering/Biotechnology, 73:129-169, Springer-Verlag (2001).
Savageau, “Biochemical Systems Analysis,”J. Theoret. Biol., 25:365-369, (1969).
Stephanopoulos, “Metabolic Engineering,”Current Opinion in Biotechnology, 5:196-200, Current Biology (1994).
Varner and Ramkrishna, “Mathematical Models of Metabolic Pathways,”Current Opinion in Biotechnology, 10:146-150, Elsevier Science Ltd (1999).
Edwards & Palsson, “How Will Bioinformatics Influence Metabolic Engineering?”,Biotechnol. Bioeng., John Wiley & Sons, Inc., 58:162-169 (1998).
Edwards & Palsson, “Metabolic flux balance analysis and the in silico analysis ofEscherichia coliK-12 gene deletions”,BMC Bioinformatics, Oxford University Press, 1(1):1-10 (2000).
Edwards & Palsson, “TheEscherichia coliMG1655in silicometabolic genotype: Its definition, characteristics, and capabilities”,Poceedings of the National Academy of Sciences of USA, 97(10):5528-5533 (2000).
Hatzimanikatis et al., “Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization”,AIChE Journal, 42(5):1277-1292 (1996).
Adamowicz et al., “Nutritional complementation of oxidative glucose metabolism inEscherichia colivia pyrroloquinoline quinone-dependent glucose dehydrogenase and the Entner-Doudoroff pathway,”Appl Environ Microbiol, 57(7):2012-2015 (1991).
Akutsu, “Estimation Algorithm of Genetic Network,” Mathmatical Science (Suri-Kagaku) Science 37(6)40-46 (19991.
Alberty, “Calculation of Biochemical Net Reactions and Pathways by Using Matrix Operations,”Biophys J, 71(1):507-515 (1996).
Alm “Genomic-sequence comparison of two unrelated isolates of the human gastric pathogenHelicobacter pylori,” Nature, 397(6715):176-80 (1999).
Alon et al., “Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays,”Proc Natl Acad Sci U.S.A., 96(12):6745-6750 (1999).
Alter, et al., “Singular value decomposition for genome-wide expression data processing and modeling,”Proc Natl Acad Sci U.S.A., 97(18):10101-10106 (2000).
Altschul ,et al., “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,”Nucl Acids Res, 25(17):3389-3402 (1997).
Alves, et al., “Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways,”Bioinformatics, 16(6):534-547 (2000).
Andre, B, “An overview of membrane transport proteins inSaccharomyces cerevisiae,” Yeast, 11(16):1575-1611 (1995).
Anonymous, “The yeast genome directory”Nature, 387(6632 Suppl):5 (1997).
Appel, et al., “A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server,”Trends Biochem Sci, 19(6):258-260 (1994).
Arigoni, et al., “A Genome-Based Approach for the Identification of Essential Bacterial Genes,”Nature Biotechnology, 16(9):851-856 (1998).
Aristidou and Penttila, “Metabolic engineering applications to renewable resource utilization.” Curr Opin in Biotech 11 (2)187-198 (2000).
Attanoos, et al., “Ileostomy polyps, adenomas, and adenocarcinomas,”Gut, 37(6):840-844 (1995).
Baba, et al., “Construction ofEscherichia coliK-12 in-frame, single-gene knockout mutants: the Keio collection,”Mol Syst Biol, 2:2006-2008 (2006).
Bailey, J“Complex Biology With No Parameters,”Nat Biotechnol, 19(6):503-504 (2001).
Bailey, T and Elkan, , “Fitting a mixture model by expectation maximization to discover motifs in biopolymers,”Proc Int Conf Intell Syst Mol Biol, 2:28-3
Edwards Jeremy S.
Palsson Bernhard O.
Clow Lori A
DLA Piper (LLP) US
The Regents of the University of California
LandOfFree
Method for the evolutionary design of biochemical reaction... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method for the evolutionary design of biochemical reaction..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for the evolutionary design of biochemical reaction... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2623456