Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2011-06-14
2011-06-14
Smith, Carolyn L. (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C702S019000, C703S011000, C707S723000, C707S748000, C536S023100
Reexamination Certificate
active
07962316
ABSTRACT:
The present invention provides a method for identifying siRNA target motifs in a transcript using a position-specific score matrix approach. The invention also provides a method for identifying off-target genes of an siRNA using a position-specific score matrix approach. The invention further provides a method for designing siRNAs with higher silencing efficacy and specificity. The invention also provides a library of siRNAs comprising siRNAs with high silencing efficacy and specificity.
REFERENCES:
patent: 6506559 (2003-01-01), Fire et al.
patent: 2002/0086356 (2002-07-01), Tuschl et al.
patent: 2002/0162126 (2002-10-01), Beach et al.
patent: 2003/0143597 (2003-07-01), Finney et al.
patent: 2003/0166282 (2003-09-01), Brown et al.
patent: 2003/0175950 (2003-09-01), McSwiggen
patent: 2003/0194725 (2003-10-01), Greener et al.
patent: WO 02/44321 (2002-06-01), None
patent: WO 03/006477 (2003-01-01), None
patent: 03/070193 (2003-08-01), None
patent: WO 03/065281 (2003-08-01), None
Levenkova et al. “Gene Specific siRNA Selector”, 2004, Bioinformatics, vol. 20, No. 3, pp. 430-432.
Aza-Blanc et al. (2003). “Identification of Modulators of TRAIL-Induced Apoptosis via RNAi-Based Phenotypic Screening”. Mol. Cell 12(3):627-637.
Bass (2000). “Double-Stranded RNA as a Template for Gene Silencing”. Cell 101(3):235-238.
Boden et al. (2003). “Promoter Choice Affects the Potency of HIV-1 Specific RNA Interference”. Nucleic Acids Res. 31(17):5033-5038.
Brummelkamp et al. (2002). “A System for Stable Expression of Short Interfering RNAs in Mammalian Cells”. Science 296(5567):550-553.
Campbell (1994). “Advances in Statistical Methodology for the Evaluation of Diagnostic and Laboratory Tests”. Stat. Med. 13(May 7):499-508.
Couzin (2002). “Breakthrough of the Year. Small RNAs Make Big Splash”. Science 298(5602):2296-2297.
Elbashir et al. (2001). “Duplexes of 21-Nucleotide RNAs Mediate RNA Interference in Cultured Mammalian Cells”. Nature 411(6836):494-498.
Elbashir et al. (2001). “Functional Anatomy of siRNAs for Mediating Efficient RNAi inDrosophila melanogasterEmbryo Lysate”. EMBO J 20(23):6877-6888.
Elbashir et al. (2001). “RNA Interference Is Mediated By 21- and 22-Nucleotide RNAs”. Genes Dev. 15(2):188-200.
Fire et al. (1998). “Potent and Specific Genetic Interference by Double-Stranded RNA inCaenorhabditis elegans”. Nature 391(6669):806-811.
Grant (1999). “Dissecting The Mechanisms Of Posttranscriptional Gene Silencing: Divide And Conquer”. Cell 96(3):303-306.
Gribskov et al. (1987). “Profile Analysis: Detection Of Distantly Related Proteins”. Proc. Natl. Acad. Sci. U S A 84(13):4355-4358.
Gribskov et al. (1990). “Profile Analysis”. Methods Enzymol. 183:146-159.
Gribskov et al. (1996). “Use Of Receiver Operating Characteristic (ROC) Analysis To Evaluate Sequence Matching”. Comput. Chem. 20(1):25-33.
Grishok et al. (2001). “Genes And Mechanisms Related To RNA Interference Regulate Expression Of The Small Temporal RNAs That ControlC. elegansDevelopmental Timing”. Cell 106(I):23-34.
Guo et al. (1995). “par-1, A Gene Required for Establishing Polarity inC. elegansEmbryos, Encodes A Putative Ser/Thr Kinase That is Asymmetrically Distributed”. Cell 81(4):611-620.
Hammond et al. (2001). “Argonaute2, A Link Between Genetic and Biochemical Analyses of RNAi”. Science 293(5532):1146-1150.
Hannon (2002). “RNA Interference”. Nature 418(6894):244-251.
Henikoff et al. (1994). “Position-Based Sequence Weights”. J. Mol. Biol. 243(4):574-578.
Hutvagner et al. (2001). “A Cellular Function for the RNA-Interference Enzyme Dicer In The Maturation Of The let-7 Small Temporal RNA”. Science 293(5531):834-838.
Hutvagner et al. (2002). “A microRNA in a Multiple-Turnover RNAi Enzyme Complex”. Science 297(5589):2056-2060.
Kawasaki et al. (2003). “Short Hairpin Type of dsRNAs that are Controlled by tRNA(Val) Promoter Significantly induce RNAi-mediated Gene Silencing in the Cytoplasm of Human Cells”. Nucleic Acids Res. 31(2):700-707.
Ketting et al. (2001). “Dicer Functions in RNA Interference and in Synthesis of Small RNA Involved in Developmental Timing inC. Elegans”. Genes Dev. 15(20):2654-2659.
Krogh et al. (1994). “Hidden Markov Models in Computational Biology. Applications To Protein Modeling”. J. Mol. Biol. 235(5):1501-1531.
Kwak et al. (2003). “RNA Interference With Small Hairpin RNAs Transcribed From A Human U6 Promoter-Driven DNA Vector”. J. Pharmacol. Sci. 93(2):214-217.
Lau et al. (2001). “An Abundant Class Of Tiny RNAs With Probable Regulatory Roles inCaenorhabditis elegans”. Science 294(5543):858-862.
Lee et al. (1993). “TheC. elegansHeterochronic Gene lin-4 Encodes Small RNAs With Antisense Complementarity To lin-14”. Cell 75(5):843-854.
Lee et al. (2001). “An Extensive Class of Small RNAs inCaenorhabditis elegans”. Science 294(5543):862-864.
Lewis et al. (2002). “Efficient Delivery Of siRNA For Inhibition Of Gene Expression In Postnatal Mice”. Nat. Genet. 32(1):107-108.
Martinez et al. (2002). “Single-Stranded Antisense siRNAs Guide Target RNA Cleavage In RNAi”. Cell 110(5):563-574.
Martinez et al. (2002). “Synthetic Small Inhibiting RNAs: Efficient Tools To Inactivate Oncogenic Mutations And Restore p53 Pathways”. Proc. Natl. Acad. Sci. U S A 99(23):14849-14854.
McCaffrey et al. (2002). “RNA Interference in Adult Mice”. Nature 418(6893):38-39.
McManus et al. (2002). “Gene Silencing in Mammals by Small Interfering RNAs”. Nat. Rev. Genet. 3(10):737-747.
Metz (1986). “ROC Methodology In Radiologic Imaging”. Invest. Radiol. 21(9):720-733.
Miyagishi et al. (2002). “U6 Promoter-Driven siRNAs With Four Uridine 3' Overhangs Efficiently Suppress Targeted Gene Expression In Mammalian Cells”. Nat. Biotechno. 20(5):497-500.
Mourelatos et al. (2002). “miRNPs: A Novel Class Of Ribonucleoproteins Containing Numerous microRNAs”. Genes Dev. 16(6):720-728.
Paddison et al. (2002). “RNA Interference: The New Somatic Cell Genetics?”. Cancer Cell 2(I):17-23.
Paddison et al. (2002). “Short Hairpin RNAs (shRNAs) Induce Sequence-Specific Silencing In Mammalian Cells”. Genes Dev. 16(8):948-958.
Paddison et al. (2002). “Stable Suppression Of Gene Expression By RNAi in Mammalian Cells”. Proc. Natl. Acad. Sci. U S A 99(3):1443-1448.
Paul et al. (2002). “Effective Expression Of Small Interfering RNA In Human Cells”. Nat. Biotechnol. 20(5):505-508.
Petcherski et al. (2000). “LAG-3 Is A Putative Transcriptional Activator In TheC. elegansNotch Pathway”. Nature 405(6784):364-368.
Reinhart et al. (2000). “The 21-Nucleotide let-7 RNA Regulates Developmental Timing inCaenorhabditis elegans”. Nature 403(6772):901-906.
Rubinson et al. (2003). “A Lentivirus-Based System to Functionally Silence Genes in Primary Mammalian Cells, Stem Cells and Transgenic Mice by RNA Interference”. Nat. Genet. 33(3):401-406.
Salzberg et al. (1998). “Microbial Gene Identification Using Interpolated Markov Models”. Nucleic Acids Res. 26(2):544-548.
Song et al. (2003). “RNA Interference Targeting Fas Protects Mice From Fulminant Hepatitis”. Nat. Med. 9(3):347-351.
Sorensen et al. (2003). “Gene Silencing By Systemic Delivery Of Synthetic siRNAs In Adult Mice”. J. Mol. Biol. 327(4):761-766.
Sui et al. (2002). “A DNA Vector-Based RNAi Technology To Suppress Gene Expression In Mammalian Cells”. Proc. Natl. Acad. Sci. U S A 99(8):5515-5520.
Tabara et al. (1999). “The rde-1 Gene, RNA Interference, And Transposon Silencing inC. elegans”. Cell 99(2):I23-32.
Tiscornia et al. (2003). “A General Met
Bartz Steven R.
Burchard Julja
Cavet Guy L.
Ge Wei
Jackson Aimee L.
Christensen O'Connor Johnson & Kindness PLLC
Merck Sharp & Dohme Corp.
Smith Carolyn L.
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