Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2008-08-28
2011-12-20
Tsai, Carol (Department: 2857)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S006120, C436S131000, C436S501000, C514S789000
Reexamination Certificate
active
08082109
ABSTRACT:
The invention relates to computational methods, systems and apparatus useful in the analysis of sets of biomolecules in an accessible body fluid or tissue sample from a patient, which biomolecules collectively or individually are candidates to serve as biomarkers, i.e., biomolecules which together or individually upon detection or change are indicative that the patient is in some biological state, such as a diseased state. The methods permit one to examine such potential biological markers to determine whether each one is indeed present as a consequence of the biological state, or as an artifact of the biomarker search protocol.
REFERENCES:
patent: 4385125 (1983-05-01), Preti et al.
patent: 4935877 (1990-06-01), Koza
patent: 5136686 (1992-08-01), Koza
patent: 5148513 (1992-09-01), Koza et al.
patent: 5343554 (1994-08-01), Koza et al.
patent: 5390282 (1995-02-01), Koza et al.
patent: 5742738 (1998-04-01), Koza et al.
patent: 5867397 (1999-02-01), Koza et al.
patent: 5914891 (1999-06-01), McAdams et al.
patent: 6058385 (2000-05-01), Koza et al.
patent: 6360191 (2002-03-01), Koza et al.
patent: 6424959 (2002-07-01), Bennett, III et al.
patent: 6532453 (2003-03-01), Koza et al.
patent: 6537744 (2003-03-01), Al-Bayati
patent: 6564194 (2003-05-01), Koza et al.
patent: 6594587 (2003-07-01), Askenazi
patent: 6665669 (2003-12-01), Han et al.
patent: 6741986 (2004-05-01), Cho et al.
patent: 6772160 (2004-08-01), Cho et al.
patent: 2001/0016822 (2001-08-01), Bessette
patent: 2001/0047353 (2001-11-01), Talib et al.
patent: 2002/0002559 (2002-01-01), Busa
patent: 2002/0049782 (2002-04-01), Herzenberg et al.
patent: 2002/0123847 (2002-09-01), Askenazi
patent: 2002/0198858 (2002-12-01), Stanley et al.
patent: 2003/0074516 (2003-04-01), Cho et al.
patent: 2004/0249620 (2004-12-01), Chandra et al.
patent: 2005/0165594 (2005-07-01), Chandra et al.
patent: 2006/0166242 (2006-07-01), Pennell et al.
patent: 2008/0009552 (2008-01-01), Pennell et al.
patent: 2009/0298053 (2009-12-01), Almstrup et al.
patent: 1248231 (2002-10-01), None
patent: WO-02/11048 (2002-02-01), None
patent: WO-02/093409 (2002-11-01), None
patent: WO-03067504 (2003-08-01), None
patent: WO-03/082214 (2003-10-01), None
patent: WO-2005055113 (2005-06-01), None
International Search Report for PCT/US2007/006877 dated Sep. 25, 2007 (8 pages).
Written Opinion of the International Searching Authority for PCT/US2007/006877 dated Sep. 25, 2007 (12 pages).
Pollard, Jr., Ph.D. et al., “A Computational Model to Define the Molecular Causes of Type 2 Diabetes Mellitus,” Diabetes Technology and Therapeutics, Vol. 7, No. 2, 2005 (14 pages).
Hartemink et al., “Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks,” (12 pages).
Pe'er et al., “Minreg: Inferring an active regulator set,” Bioinformatics, vol. 18, Suppl. 1 2002 (pp. S258-S267).
International Search Report and Written Opinion of PCT/US2008/074620, completed Nov. 20, 2008 (11 pages).
Center for Development of Advanced Computing, “Workshop on Genetic Algorithms in Bioinformatics,”http://www.cdacindia.com/html/ecents/bioinfo/genetic/genidx.asp, pp. 1-6 (printed Oct. 22, 2002).
Jansen, Ronald, “A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data,” Science, vol. 302, pp. 449-453 (Oct. 17, 2003).
Karp, Peter D., “The EcoCyc Database,” pp. 1-6 (Jan. 25, 2002).
Karp, Peter D., “Integrated Access to Metabolic and Genomic Data,” pp. 1-32 (Apr. 1, 1996).
Karp, Peter D., “The MetaCyc Database,” pp. 1-7 (Jan. 25, 2002).
Karp, Peter D., “Pathway Databases: A Case Study in Computational Symbolic Theories,” Science, vol. 293, pp. 2040-2044 (Sep. 14, 2001).
Karp, Peter D., “The Pathway Tools Software,” Bioinformatics, vol. 18 Suppl. 1 2002, pp. S1-S8 (2002).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” pp. 1-53 (2000).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” Symposium on Computational Discovery of Communicatable Knowledge, pp. 1-63 (Mar. 25, 2001).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” Biomedical Informatics, pp. 1-12.
Rindfleisch, Thomas C., “Extracting Molecular Binding Relationships from Biomedical Text,” pp. 188-195.
Stevens, Robert “Building a Reason-able Bioinformatics Ontology Using OIL,” Department of Computer Science, University of Manchester, p. 1-11.
Yen, John, “A Hybrid Approach to Modeling Metabolic Systems Using Genetic Algorithm and Siomplex Method,” pp. 1-42.
Yen, John, “Using Fuzzy Logic and a Hybrid Genetic Algorithm for Metabolic Modeling,” pp. 1-6.
International Search Report for PCT/US2003/030653, mailed Feb. 3, 2004.
Goldberg, David E., “Genetic and Evolutionary Algorithms Come of Age,” Communications of the ACM, vol. 37, No. 3, Mar. 1994, pp. 113-119.
Van Helden, Jacques, et al., “Representing and Analyzing Molecular and Cellular Function Using the Computer,” Biol. Chem., vol. 381, pp. 921-935, Sep.-Oct. 2000.
Uetz P., et al. “Visualization and integration of protein-protein interactions.” Retrieved from the Internet: URL:http://itgmv1.fzk.de/www/itg/uetz/publications/Visualization.pdf.
International Search Report for International Application No. PCT/US/2005/00202 mailed from the International Searching Authority on Nov. 24, 2005.
Written Opinion of the International Searching Authority for International Application No. PCT/US/2005/00202 mailed from the International Searching Authority on Nov. 24, 2005.
International Preliminary Report on Patentability for PCT/US2004/039159 dated May 29, 2006.
Written Opinion of the International Searching Authority for PCT/US2004/039159 dated May 29, 2006.
International Search Report for PCT/US03/36857, mailed Mar. 9, 2005.
International Search Report for International Application No. PCT/US/2004/039159 mailed from the International Searching Authority on Aug. 31, 2005.
International Preliminary Report on Patentability for PCT/US2004/039159 dated May 29, 2006.
Written Opinion of the International Searching Authority for PCT/US2004/039159 dated May 29, 2006.
Written Opinion of the International Searching Authority for International Application No. PCT/US/2004/039159 mailed from the International Searching Authority on Aug. 31, 2005.
Elliston Keith O.
Ladd William M.
Loureiro Joseph J.
Judson David H.
Selventa, Inc.
Tsai Carol
LandOfFree
Computer-aided discovery of biomarker profiles in complex... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Computer-aided discovery of biomarker profiles in complex..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Computer-aided discovery of biomarker profiles in complex... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4314401