Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-09-27
2005-09-27
Marschel, Ardin H. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S006120, C435S069100, C703S011000
Reexamination Certificate
active
06950752
ABSTRACT:
The invention provides methods for removing unwanted response components (i.e., “artifacts”) from a measured biological profile comprising measurements of a plurality of cellular constituents of a cell or organism in response to a perturbation. The methods involve subtracting from the measured biological profile one or more artifact patterns, each of which comprises measurements of changes in cellular constituents as a result of deviation of one or more experimental variables, such as cell culture density and temperature, hybridization temperature, as well as concentrations of total RNA and/or hybridization reagents, from desired values.
REFERENCES:
patent: 4946778 (1990-08-01), Ladner et al.
patent: 5445934 (1995-08-01), Fodor et al.
patent: 5510270 (1996-04-01), Fodor et al.
patent: 5539083 (1996-07-01), Cook et al.
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 5569588 (1996-10-01), Ashby et al.
patent: 5578832 (1996-11-01), Trulson et al.
patent: 5645988 (1997-07-01), Vande Woude et al.
patent: 5744305 (1998-04-01), Fodor et al.
patent: 5777888 (1998-07-01), Rine et al.
patent: 5798262 (1998-08-01), Garini et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5811231 (1998-09-01), Farr et al.
patent: 5866331 (1999-02-01), Singer et al.
patent: 5965352 (1999-10-01), Stoughton et al.
patent: 6132969 (2000-10-01), Stoughton
patent: 6165709 (2000-12-01), Friend et al.
patent: 6232066 (2001-05-01), Felder et al.
patent: 0 534 858 (1992-09-01), None
patent: 0 816 511 (1996-01-01), None
patent: WO 88/09810 (1988-12-01), None
patent: WO 90/11364 (1990-10-01), None
patent: WO 94/17208 (1994-08-01), None
patent: WO 97/10365 (1997-03-01), None
patent: WO 97/27317 (1997-07-01), None
patent: WO 98/06874 (1998-02-01), None
patent: WO 98/38329 (1998-09-01), None
patent: WO 98/41531 (1998-09-01), None
patent: WO 99/58720 (1999-11-01), None
Anderson et al., 1994, “Involvement of the protein tyrosine kinase p56lck in T cell signaling and thymocyte development”, Adv Immunol 56:151-178.
Anderson, 1995, “Mutagenesis”, Methods Cell Biol 48:31.
Amone and Davidson, 1997, “The hardwiring of development: organization and function of genomic regulatory systems”, Development 124:1851-1864.
Baudin et al., 1993, “A simple and efficient method for direct gene deletion inSaccharomyces cerevisiae,” Nucl Acids Res 21:3329-3330.
Belshaw et al., 1996, “Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins”, Proc Natl Acad Sci USA 93:4604-4607.
Benoist and Chambon, 1981, “In vivo sequence requirements of the SV40 early promotor region”, Nature 290:304-310.
Biocca and Cattaneo, 1995, “Intracellular immunization: antibody targeting to subcellular compartments”, Trends Cell Biology 5:248-252.
Blanchard and Hood, 1996, “Sequence to array: probing the genome's secrets”, Nat Biotechnol 14:1649.
Blanchard and Hood, 1996, “High-density oligonucleotide arrays”, Biosensors and Bioelectronics 11:687-690.
Bradbury et al., 1995, “The cloning of Hybridoma V regions for their ectopic expression in intracellular and intercellular immunization” inAntibody Engineering,vol. 2, Borrebaeck (ed.) Oxford University Press, pp. 295-361.
Brinster et al., 1982, “Regulation of metallothionein—thymidine kinase fusion plasmids injected into mouse eggs”, Nature 296:39-42.
Brown and Hartwell, 1998, “Genomics and human disease-variations on variation”, Nature Genetics 18:91-93.
Bryant et al., (1998), “Gene Expression and Genetic Networks,”Pacific Symposium on Biocomputing 3:3-5.
Burke and Warren, 1984, “Microinjection of mRNA coding for an anti-Golgi antibody inhibits intracellular transport of a viral membrane protein”, Cell 36:847-858.
Burnette, 1981, “Western blotting: electropheretic transfer of proteins from sodium dodecyl sulphate-polyacrylamide gels to unmodifed nitrocellulose and radiographic detection with antibody and radioiodinated protein A”,A. Anal. Biochem. 112:195-203.
Cannon-Albright and Skolnick, 1996, “The genetics of familial breast cancer”, Seminars in Oncology 23:1-5.
Cardenas et al., 1994, “Yeast as model T cells”, Perspectives in Drug Discovery and Design 2:103-126.
Carr et al., 1997, “Templates for Looking at Gene Expression Clustering,” Statistical Computing & Statistical Graphics Newsletter pp. 20-29.
Cech, 1987, “The chemistry of self-splicing RNA and RNA enzymes”, Science 236:1532-1539.
Chee et al., 1996, “Accessing genetic information with high-density DNA arrays”, Science 274:610-614.
Chirgwin et al., 1979, “Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease”, Biochemistry 18:5294-5299.
Chowdhury et al., 1997, “Lack of association of angiotensin II Type 1 receptor gene polymorphism with diabetic neuropathy in insulin-dependant Diabetes mellitus”, Diabet Med 14:837-840.
Cole et al., 1985, “The EBV-Hybridoma technique and its application to human lung cancer” inMonoclonal Antibodies and Cancer Therapy,Alan R. Liss, Inc., pp. 77-96.
Cote et al., 1983, “Generation of human monoclonal antibodies reactive with cellular antigens”, Proc Natl Acad Sci USA 80:2026-2030.
Cotten and Birnstiel, 1989, “Ribozyme mediated destruction of RNA in vivo”, EMBO J 8:3861-3866.
Cunningham and Dunlop, 1996, “Molecular genetic basis of colorectal cancer susceptibility”, British Journal of Surgery 83:321-329.
Cyert et al., 1992, “Regulatory subunit (CNB1 gene product) of yeast Ca2+/calmodulin-dependent phosphoprotein phosphatases is required for adaptation to pheromone”, Mol Cell Biol 12:3460-3469.
D'haeseleer et al., (1998), “Mining the Gene Expression Matrix: Inferring Gene Relationships From Large Scale Gene Expression Data” Available Web Site: www.cs.unm.edu/˜patrik
etworks/IPCAT/ipcat.html Accessed on: Nov. 18, 1998 6:16 p.m.
DeRisi et al., 1996, “Use of a cDNA microarray to analyze gene expression patterns in human cancer,” Nature Genetics 14:457-460.
DeRisi et al., 1997, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278:680-686.
Deshaies et al., 1988, “A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides”, Nature 332:800-805.
Dohmen et al., 1994, “Heat-inducible degron: a method for constructing temperature-sensitive mutants”, Science 263:1273-1276.
Dujon et al., 1994, “Complete DNA sequence of yeast chromosome XI”, Nature 369:371-378.
Egholm et al., 1993, “PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules”, Nature 365:566-568.
Feldmann et al., 1994, “Complete DNA sequence of yeast chromosome II”, EMBO J 13:5795-5809.
Ferguson et al., 1996, “A fiber-optic DNA biosensor microarray for the analysis of gene expression”, Nature Biotechnol 14:1681-1684.
Fodor et al., 1991, “Light-directed, spatially addressable parallel chemical synthesis”, Science 251:767-773.
Frebourg and Friend, 1992, “Cancer risks for germline p53 mutations”, J Clin Invest 90:1637-1641.
Friend, 1994, “p53: A glimpse at the puppet behind the shadow play”, Science 265:334-335.
Froehler et al., 1986, “Synthesis of DNA via deoxynucleoside H-phosphonate intermediates”, Nucleic Acids Res 14:5399-5407.
Fuhrman et al., (1997), “Genetic Network Inference,”Proceedings of the International Conference on Complex Systems,Nashua, NH, 21-26. Available Web Site: http://rsb.info.nih.gov/mol-physiol/ICCS/inference/ICCS.html Accessed on: Nov. 18, 1998 6:14 p.m.
Galibert et al., 1996, “Complete nucleotide sequenc
Friend Stephen H.
He Yudong
Stoughton Roland
Jones Day
Marschel Ardin H.
Rosetta Inpharmatics LLC
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