Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-05-10
2005-05-10
Fredman, Jeffrey (Department: 1637)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C435S006120
Reexamination Certificate
active
06892139
ABSTRACT:
The invention provides novel methods for characterizing the function of nucleic acids and polypeptides. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The characterization is based on use of methods of the invention comprising algorithms that can identify functional relationships between diverse sets of non-homologous nucleic acid and polypeptide sequences. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The invention provides a computer system, comprising a processor and a computer program product of the invention.
REFERENCES:
patent: 6466874 (2002-10-01), Eisenberg et al.
patent: 6564151 (2003-05-01), Pellegrini et al.
patent: WO 0045322 (2000-08-01), None
Tatusov, R. L. et al., “Metabolism and evolution ofHaemophilus influenzaededuced from a whole-genome comparison withEscherichia coli”, Curr. Biol., vol. 6, pp. 279-291 (1996).*
Philipp, W. J. et al., “An integrated map of the genome of the tubercle bacillus,Mycobacterium tuberculosisH37Rv, and comparison withMycobacterium leprae”, PNAS, vol. 93, pp. 3132-3137 (1996).*
Koonin, E.V. et al., “Sequence similarity analysis ofEscherichia coliproteins: Functional and evolutionary implications”, PNAS, vol. 92, pp. 11921-11925 (1995).*
Dandekar et al., “Conservation of gene order: a fingerprint of proteins that physically interact”, TIBS, vol. 23, pp. 364-328 (Sep. 1998).*
Marcotte, E.M., et al., “A combined algorithm for genome-wide prediction of protein function,” NATURE GB, vol. 402, No. 6757 (1999), pp. 83-86.
Pellegrini, M., et al., “Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles,” Proc. Natl. Acad. Sci. USA, vol. 96 (1999) pp. 4285-4288.
Enright, A.J., et al., “Protein Interaction maps for complete genomes based on gene fusion events,” NATURE, vol. 402 (1999), pp. 86-90.
Tatusov, R.L., et al., “A Genomic Perspective on Protein Families,” SCIENCE, vol. 278 (1997), pp. 631-637.
Marcotte, E.M., et al., “Detecting Protein Function and Protein-Protein Interactions from Genome Sequences,” SCIENCE, vol. 285 (1999), pp. 751-753.
Eisen, M.B., et al., “Cluster analysis and display of genome-wide expression patterns,” Proc. Natl. Acad. Sci. USA, vol. 95 (1998), pp. 14863-14868.
Bork et al., “Predicting Function: From Genes to Genomes and Back”,J. Mol. Biol.,(1998) 283, 707-725.
Mark A. Ragan et al., “Microbial Genescapes: A Prokarotic View of the Yeast Genome”,Microbial&Comparative Genomics,vol. 3, No. 4, 1998.
Roman L. Tatusov et al., “Metabolism and evolution ofHaemophilus influenzaededuced from a whole-genome comparison withEscherichia coli, ” Current Biology,1996, vol. 6, No. 3, pp. 279-291.
Stanley Fields et al., “A novel genetic system to detect protein-protein interactions”,Nature,vol. 340, Jul. 20, 1989, pp. 245-246.
Frederick R. Blattner et al., “The Complete Genome Sequence ofEscherichia coliK-12,”Science,vol. 277, Sep. 5, 1997, pp. 1453-1462.
Peter D. Karp et al., “EcoCyc: Encyclopedia ofEscherichia coligenes and metabolism”,Nucleic Acids Research,1998, vol. 26, No. 1, pp. 50-53.
Pazos, et al., “Comparative analysis of different method for the detection of specificity regions in protein families,” Biocomputing and Emergent Computation, Online, pp. 1-13, 1997, Retrieved from the Internet on Jun. 22, 2000 <URL:http://www.cnb.uam.es/{cnbprot/conf/TD.html.
Corpet et al., “The ProDom database of protein domain families”,Nucleic Acids Research,1998, vol. 26, No. 1, pp. 323-326.
Lynn et al., Science (1986) 233(4764):647-649.
Eisenberg David
Marcotte Edward M.
Rotstein Sergio H.
Morrison & Foerster / LLP
Strzelecka Teresa
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