Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2006-10-03
2006-10-03
Zeman, Mary K. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C435S006120, C707S793000, C536S023100
Reexamination Certificate
active
07117095
ABSTRACT:
Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.
REFERENCES:
patent: 5571639 (1996-11-01), Hubbell et al.
patent: 5593839 (1997-01-01), Hubbell et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 5856101 (1999-01-01), Hubbell et al.
patent: 5862242 (1999-01-01), Takewa et al.
patent: 5871928 (1999-02-01), Fodor et al.
patent: 5959098 (1999-09-01), Goldberg et al.
patent: 6013449 (2000-01-01), Hacia et al.
patent: 6027880 (2000-02-01), Cronin et al.
patent: 6027884 (2000-02-01), Lane et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6040183 (2000-03-01), Ferrari et al.
patent: 6130046 (2000-10-01), Hubbell et al.
patent: 6153743 (2000-11-01), Hubbell et al.
patent: 6188783 (2001-02-01), Balaban et al.
patent: 6251588 (2001-06-01), Shannon et al.
patent: 6307042 (2001-10-01), Goldberg et al.
patent: 6309823 (2001-10-01), Cronin et al.
patent: 6340565 (2002-01-01), Oliner et al.
patent: 6458530 (2002-10-01), Morris et al.
patent: 6468744 (2002-10-01), Cronin et al.
patent: 6706875 (2004-03-01), Goldberg et al.
patent: 6746844 (2004-06-01), Oliner et al.
patent: 6826296 (2004-11-01), Balaban et al.
patent: 2002/0102564 (2002-08-01), Mittmann et al.
Mei, G. et al. Octamer-primed sequencing technology: development of primer identification software. Nucleic Acids Research (Apr. 1, 2000) vol. 28 No. 7 pp. e22 (i-ix).
Burke et al., “A Validated Method for Clustering EST and Full-Length cDNA Sequences”,Genome Research, vol. 9, 1999, pp. 1135-1142.
Chee et al., “Accessing Genetic Information with High-Density DNA Arrays”,Science, abstract, vol. 274, Jul. 1996, 14 pages.
Cronin et al., “Cystic Fibrosis Mutation Detection by Hybridization to Light-Generated DNA Probe Arrays”,Human Mutation, vol. 7, 1996, pp. 244-255.
de Saizieu et al., “Bacteria transcript imaging by hybridization of total RNA to oligonucleotide arrays”,Nature Biotechnology, vol. 16, No. 1, Jan. 1998, pp. 45-48.
Hacia et al., “Strategies of Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays”,Genome Research, vol. 8, Issue 12, Dec. 1998; pp. 1245-1258.
Hacia et al., “Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-color fluorescence analysis”,Nature Genetics, vol. 14, 1996, pp. 441-447.
Hacia et al., “New approaches to BRCA1 mutation detection”,Breast Disease, vol. 10, pp. 45-59.
Kozal et al., “Extensive polymorphisms observed in HIV-1 clade B protease gene using high density oligonucleotide arrays”,Nature Medicine, vol. 2, No. 7, Jul. 1996, pp. 753-759.
Lockhart et al., “Expression monitoring by hybridization to high-density oligonucleotide arrays”,Nature Biotechnology, vol. 14, Dec. 1996, pp. 1675-1680.
Lander “Array of Hope”,Nature-Geneticsvol. 21, 1999.
Searls, “Bioinformatics Tools for Whole Genomex”,Annu. Rev. Genom. Hum. Genetics, vol. 1, 2000, pp. 251-279.
Ramsay, “DNA chips: State-of-Art”,Nature Biotechnology, vol. 16, 1998, pp. 40-44.
Wodicka et al., “Genome-wide Expression Monitoring inSaccharomyces cerevisiae”, Nature Biotechnology, vol. 15, Dec. 1997, pp. 1359-1367.
U.S. Appl. No. 09/721,042, filed Nov. 21, 2000, Hunt.
U.S. Appl. No. 09/718,295, filed Nov. 21, 2000, Mei.
U.S. Appl. No. 08/767,892, filed Dec. 17, 1996, Hubbell, et al.
U.S. Appl. No. 09/567,548, filed May 5, 2000, Hubbel, et al.
U.S. Appl. No. 09/607,536, filed Jun. 29, 2000, Hubbell, et al.
U.S. Appl. No. 10/975,245, filed Oct. 27, 2004, Hubbell, et al.
U.S. Appl. No. 09/811,364, filed Mar. 16, 2001, Balaban, et al.
U.S. Appl. No. 10/925,393, filed Aug. 24, 2004, Balaban, et al.
U.S. Appl. No. 09/640,962, filed Aug. 16, 2000, Hubbell.
U.S. Appl. No. 10/627,271, filed Jul. 25, 2003, Hubbell.
U.S. Appl. No. 11/038,614, filed Jan. 18, 2005, Hubbell, et al.
U.S. Appl. No. 10/226,355, filed Aug. 23, 2002, Morris, et al.
U.S. Appl. No. 10/017,034, filed Dec. 14, 2001, Mei, et al.
U.S. Appl. No. 10/308,379, filed Dec. 2, 2002, Mei.
U.S. Appl. No. 10/914,937, filed Aug. 9, 2004, Mei, et al.
U.S. Appl. No. 10/782,614, filed Feb. 19, 2004, Bekiranov, et al.
Cheng, et al; NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis; Bioinformatics Applications note; vol. 20; No. 9, 2004; pp. 1462-1463.
Cho, et al; Genome-wide Mapping with Biallelic Markers in Arabidopsis Thaliana; Nature Genetics, vol. 23, Oct. 1999 pp. 203-207.
Di, et al; Dynamic Model Based Algorithms for Screening and Genotyping over 100K SNPs on Oligonucleotide Microarrays; Bioinformatics Advance Access; Jan. 18, 2005.
Hubbell, et al; Fidelity Probes for DNA Arrays; Proc Int Conf Intell Sys Biol. 1999 (abstract).
Liu, et al; Analysis of High Density Expression Microarrays with Signed-Rank Call Algorithms; Bioinformatics; vol. 18; No. 12; 2000; pp. 1593-1599.
Mei, et al; Probe Selection for High-Density Oligonucleotide Arrays; PNAS; Sep. 30, 2003; vol. 100; No. 20; pp. 11237-11242.
Wang: et al; Gene Structure-Based Splice Variant Deconvolution Using a Microarray Platform: Bioinformatics; vol. 19; Suppl. 1; 2003; pp. i315-i1322.
Wang, et al; Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome; Science; vol. 280; May 15, 1998; pp. 1077-1082.
Affymetrix Inc.
Zeman Mary K.
Zhou Wei
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