Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2006-11-22
2011-11-22
Zhou, Shubo (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S006120, C702S020000, C703S002000, C703S011000
Reexamination Certificate
active
08065089
ABSTRACT:
Disclosed is a hierarchical computational method to predict the expression value of genes in time-series microarray data. The method may include the step of first applying a nonlinear independent component analysis (NICA) algorithm that extracts the major components covering all considered genes. An autoregressive exogenous (ARX) model may subsequently be used to quantitatively express the dynamic interactions of all components with each other. Then, using the predicted values for the components, and the nonlinear independent component analysis in the inverse form, the data may be used to predict the expression parameters for individual genes. The method may be used for the analysis of a eukaryotic gene expression throughout the cell cycle.
REFERENCES:
patent: 6090555 (2000-07-01), Fiekowsky et al.
patent: 6144388 (2000-11-01), Bornstein
patent: 6222093 (2001-04-01), Marton et al.
patent: 6263287 (2001-07-01), Zheng et al.
patent: 6303301 (2001-10-01), Mack
patent: 6453241 (2002-09-01), Bassett, Jr. et al.
patent: 6544170 (2003-04-01), Kajihara et al.
patent: 6642887 (2003-11-01), Owechko
patent: 6996476 (2006-02-01), Najarian
patent: 2006/0074566 (2006-04-01), Najarian
patent: 2008/0294613 (2008-11-01), Iyer et al.
Kauffman, “The Origins of Order: Self Organization and Selection in Evolution,” Oxford University Press, New York: 1993.
Martoglio et al., “A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer,” Bioinformatics, 2002, 18: 1617-1624.
Notice of Allowance and Fees Due mailed Jul. 15, 2005 for U.S. Appl. No. 10/812,726.
Office Communication mailed Dec. 9, 2005 for U.S. Appl. No. 10/812,726.
Ex Parte QuayleOffice Action mailed Feb. 9, 2005 for U.S. Appl. No. 10/812,726.
Office Action mailed Sep. 9, 2004 for U.S. Appl. No. 10/812,726.
Amendment and Response UnderEx Parte Quaylefor U.S. Appl. No. 10/812,726 sent to USPTO on Apr. 6, 2005.
Request for Certificate of Correction of Patent for Applicant's Mistake (37 C.F.R. § 1.323) and For PTO Mistakes (37 C.F.R. § 1.322(a)) for U.S. Appl. No. 10/812,726 sent to USPTO on Oct. 3, 2006.
Communication to USPTO for U.S. Appl. No. 10/812,726 faxed to USPTO on Oct. 7, 2005.
Notice of Non-Compliant Amendment (37 CFR 1.121) mailed Jul. 25, 2007 for U.S. Appl. No. 11/273,687.
Office Action Summary mailed Sep. 7, 2006 for U.S. Appl. No. 11/273,687.
Office Action Summary mailed Jun. 15, 2006 for U.S. Appl. No. 11/273,687.
Amendment and Response Under 37 C.F.R. § 1.111 mailed to USPTO on Aug. 10, 2007 for U.S. Appl. No. 11/273,687.
Amendment and Response Under 37 C.F.R. § 1.111 mailed to USPTO on Dec. 7, 2006 for U.S. Appl. No. 11/273,687.
Election and Response mailed to USPTO on Jul. 11, 2006 for U.S. Appl. No. 11/273,687.
Preliminary Amendment mailed to USPTO on Nov. 14, 2005 for U.S. Appl. No. 11/273,687.
Office Action mailed Feb. 18, 2009 for U.S. Appl. No. 11/273,687.
United States Patent and Trademark Office, Office Action, U.S. Appl. No. 11/273,687, mailed Feb. 7, 2008.
United States Patent and Trademark Office, Office Action, U.S. Appl. No. 11/273,687, mailed Sep. 4, 2008.
Amendment and Response to Office Action under 37 CFR § 1.111, filed Jun. 6, 2008.
Amendment and Response to Final Office Action under 37 CFR § 1.116, filed Nov. 20, 2008.
United States Patent and Trademark Office, Office Action, U.S. Appl. No. 11/273,687, mailed Oct. 14, 2009.
United States Patent and Trademark Office, Office Action, U.S. Appl. No. 11/273,687, mailed May 25, 2010.
Affymetrix webpage at http://www.biospace.com/company—profile.cfm?CompanyID=1271 as available via the internet and printed on Feb. 23, 2004.
Akutsu et al., Proc. of the 1999 Pacific Symposium in Biocomputing, 4:17-28, 1999.
An IMS Mini-Meeting on Imaging, Classification, and Clustering, Department of Statistics, University of Florida, Jan. 11-12, 2002.
Arkin et al., “Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-InfectedEscherichia coliCells,” Genetics, 149:1633-1648, 1998.
Back, A.D. et al. “A First Application of Independent Component Analysis to Extracting Structure from Stock Returns,” Int. J. Neural Syst., vol. 8, No. 5, 1-16, 473-484, 1997.
Bar-Joseph, Z. et al., “Comparing the Continuous Representation of Time-Series Expression Profiles to Identify Differentially Expressed Genes,” Proc. Natl. Acad. Sci. USA, 100(18):10146-10151, 2003.
Bassett, D.E. Jr. et al., “Gene Expression Informatics—It's All in Your Mine,” Nat. Genet. Supp. , vol. 21:51-55, 1999.
Bioconductor, webpage at http://www.bioconductor.org/top.html as available via the internet and printed on Nov. 2, 2003.
Bioinformatics Graz-MPI Swarm Description http://genome.tugraz.at/Software/PathwayEditor/Description.html as available via the internet and printed on Nov. 2, 2003.
BioSieve Products—Microarray Data Analysis Software at http://www.biosieve.com/product.html as available via the internet and printed on Nov. 2, 2003.
Blohm, D.H. et al., “New Developments in Microarray Technology,” Curr. Opin. Biotechnol., 12:41-47, 2001.
Bowtell, D.D.L., “Options Available—From Start to Finish—for Obtaining Expression Data by Microarray,” Nat. Genet., vol. 21, Supp. 1:25-32, 1999.
Brazma, A. et al., “Gene Expression Data Analysis,” FEBS Lett., 480(1):17-24, 2000.
Cheung, V.G. et al., “Making and Reading Microarrays,” Nat. Genet., vol. 21, Supp. 1:15-19, 1999.
Cho, R.J., et al., “A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle,” Molecular Cell, 2:65-73, 1998.
Cluster Analysis on Microarray Data at webpage http://www.cs.bufalo.edu/˜djiang3/cluster.html as available via the internet and printed on Nov. 10, 2003.
Clustering Software webpage at http://genetics.stanford.edu/˜sherlock/cluster.html as available via the internet and printed on Nov. 2, 2003.
Cytoscape web page at http://www.cytoscape.org/ as available via the internet and printed on Nov. 2, 2003.
Darvish, A. et al., “A Hierarchical System Identification Technique for Modeling and Analysis of Dynamic Pathways,” Bioinformatics, 2004.
Darvish, A. et al., “Discovering Dynamic Regulatory Pathway by Applying an Auto Regressive Model to Time Series DNA Microarray Data,” IEEE Engineering in Medicine and Biology Society (IEEE/EMBS), Sep. 1-5, 2004.
Darvish, A. et al., “A New Hierarchical Method for Identification of Dynamic Regulatory Pathways from Time-Series DNA Microarray Data,” Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, CA, 2004.
Darvish, A. et al., “System Identification and Independent Factor Analysis for Estimation of Dynamic Gene Regulatory Networks,” Oxford University Press 2005.
Darvish, A. et al., “System Identification and Nonlinear Factor Analysis for Discovery and Visualization of Dynamic Gene Regulatory Pathways,” Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, CA, 2005.
Devaux, F. et al., “Transcriptomes, Transcription Activators and Microarrays,” FEBS Lett., 498(2-3):140-144, 2001.
Dudoit, S., “Statistical Methods and Software for the Analysis of DNA Microarray Experiments,” Bioinformatics and Computational Biology Workshop, Foundation BBVA, Madrid, Apr. 25-26, 2002.
Duggan, D.J. et al., “Expression Profiling using cDNA Microarrays,” Nat. Genet., Supp. 1:10-14, 1999.
Eisen et al., “Cluster Analysis and Display of Genome-Wide Expression Patterns,” Proc. Natl. Acad. Sci., USA., 95:14863-14868, 1998.
Engene Gene-Expression Data Processing and Exploratory Data Analysis webpage at http://www.engene.cnb.uam.es/ as available via the internet and printed on Nov. 2, 2003.
Expression Profiler web page at http://ep.ebi.ac.uk/EP/ as available via the
Kilpatrick Townsend & Stockton LLP
University of North Carolina at Charlotte
Zhou Shubo
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