Methods and systems to identify operational reaction pathways

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C703S002000, C703S011000

Reexamination Certificate

active

07734420

ABSTRACT:
The present invention provides a method for identifying an operational reaction pathway of a biosystem. The method includes (a) providing a set of systemic reaction pathways through a reaction network representing said biosystem; (b) providing a set of phenomenological reaction pathways of said biosystem, and (c) comparing said set of systemic reaction pathways with said set of phenomenological reaction pathways, wherein a pathway common to said sets is an perational reaction pathway of said biosystem. Also described is a method of refining a biosystem reaction network; a method of reconciling biosystem data sets; a method of determining the effect of a genetic polymorphism on whole cell function; and a method of diagnosing a genetic polymorphism-mediated pathology.

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: 5980096 (1999-11-01), Thalhammer-Reyero
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: 6983227 (2006-01-01), Thalhammer-Reyero
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: 2003/0224363 (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 01/36658 (2001-05-01), 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 02/061115 (2002-08-01), None
patent: WO 03/106998 (2003-12-01), None
Covert et al. (Journal of Theor. Biol. (2001) vol. 213, pp. 73-88).
Covert et al., Metabolic Modeling of Microbial Strainsin silico, TIBSMar. 2001. vol. 26, No. 3, pp. 179-186.
Schilling et al., Assessment of the Metabolic Capabilities ofHeamophilis influenzaRd through a Genome-scale Pathway Analysis,J. Theoretical Biology, 2000, vol. 203, pp. 249-273.
Schilling et al., The underlying pathway structure of biochemical reaction networks,PNAS, Apr. 1998, vol. 95, pp. 4193-4198.
Mendes et al., Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation,Bioinformatics, 1998, vol. 14, No. 10, pp. 869-883.
Edwards et al.,In silicopredictions ofEscherichia colimetabolic capabilities are consistent with experimental data.,Nature Biotechnology, Feb. 2001, vol. 19, pp. 125-130.
Bialy, H., Living on the Edges,Nature Biotechnology, Feb. 2001, vol. 19, pp. 111-112.
Varner et al., Mathematical models of metabolic pathways,Current Opinion in Biotechnology, 1999, vol. 10, pp. 146-150.
Jamshidi et al., In silico model-driven assessment of the effects of single nucleotide polymorphisms (SMPs) on human red blood cell-metabolism,Genome Research, Nov. 2002, vol. 12, No. 11, pp. 1687-1692.
Edwards et al., TheEscherichia coliMG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities.PNAS, May 2000, vol. 97, No. 10, pp. 5528-5533.
Beard et al., “Energy Balance for Analysis of Complex Metabolic Networks”,Biophysical Journal, 83:79-86 (2002).
Delgado & Liao, “Identifying Rate-Controlling Enzymes in Metabolic Pathways without Kinetic Parameters”,Biotechnology Progress, 7:15-20 (1991).
Forst C.V., “Network genomics—A novel approach for the analysis of biological systems in the post-genomic era”,Molecular Biology Reports, 29:265-280 (2002).
Price et al., “Network-based analysis of metabolic regulation in the human red blood cell”,Journal of Theoretical Biology, 225:185-194 (2003).
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).
Alberty, “Calculation of Biochemical Net Reactions and Pathways by Using Matrix Operations,”Biophys J, 71(1):507-515 (1996).
Alm, et al., “Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter 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, “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).
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, “Complex Biology With No Parameters,”Nat Biotechnol, 19(6):503-504 (2001).
Bailey, TL and Elkan, C, “Fitting a mixture model by expectation maximization to discover motifs in biopolymers,”Proc Int Conf Intell Syst Mol Biol, 2:28-36 (1994).
Bailey, TL and Gribskov, M, “Combining evidence using p-values: application to sequence homology searches,”Bioinformatics, 14(1):48-54 (1998).
Bairoch, A, and Apweiler, R, “The SWISS-PROT Protein Sequence database and its supplement TrEMBL in 2000,”Nucleic Acids Res, 28(1):45-48 (2000).
Ball, et al., “Integrating functional genomic information into theSaccharomycesgenome database,”Nucleic Acids Res, 28(1):77-80 (2000).
Baltz, et al., “DNA Sequence Sampling of theStreptococcusPneumonia Genome to Identify Novel Targets for Antibiotic Development,”Microbial Drug Resistance, 4(1):1-9 (1998).
Ban, et al., “Thymine and uracil catabolism inEscherichia coli,” J Gen Microbiol, 73(2):267-272 (1972).
Bansal, “Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways,”Bioinformatics and Bioengineering Conference, 209-216 (2001).
Bard, et al., “Sterol mutants ofSaccharomyces cerevisiae: chromatographic analyses,”Lipids, 12(8):6

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Methods and systems to identify operational reaction pathways does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Methods and systems to identify operational reaction pathways, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods and systems to identify operational reaction pathways will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-4236525

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.