Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2002-11-04
2008-08-19
Zeman, Mary K (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C703S011000, C707S793000
Reexamination Certificate
active
07415359
ABSTRACT:
Systems and methods are presented for cell simulation and cell state prediction. For example, a cellular biochemical network intrinsic to a phenotype of a cell can be simulated by specifying its components and their interrelationships. The various interrelationships can be represented with one or more mathematical equations which can be solved to simulate a first state of the cell. The simulated network can then be perturbed, and the equations representing the perturbed network can be solved to simulate a second state of the cell which can then be compared to the first state, identifying the effect of such perturbation on the network, and thereby identifying one or more components as targets. Alternatively, components of a cell can be identified as targets for interaction with therapeutic agents based upon an analytical approach, in which a stable phenotype of a cell is specified and correlated to the state of the cell and the role of that cellular state to its operation. A cellular biochemical network believed intrinsic to that phenotype can then be specified, mathematically represented, and perturbed, and the equations representing the perturbed network solved, thereby identifying one or more components as targets.
REFERENCES:
patent: 5047969 (1991-09-01), Sloane
patent: 5914891 (1999-06-01), McAdams et al.
patent: 5930154 (1999-07-01), Thalhammer-Reyero
patent: 5947899 (1999-09-01), Winslow et al.
patent: 5965352 (1999-10-01), Stoughton et al.
patent: 5991525 (1999-11-01), Shah et al.
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6165709 (2000-12-01), Friend et al.
patent: 6203987 (2001-03-01), Friend et al.
patent: 6983227 (2006-01-01), Thalhammer-Reyero
patent: 7076472 (2006-07-01), Addison
patent: 2002/0019705 (2002-02-01), Kauffman et al.
patent: 2002/0068269 (2002-06-01), Allen et al.
patent: 2002/0155422 (2002-10-01), Ingber et al.
patent: 2003/0130798 (2003-07-01), Hood et al.
patent: 2005/0273305 (2005-12-01), Thalhammer-Reyero
patent: WO 96/22575 (1996-07-01), None
patent: WO01/80151 (2001-10-01), None
patent: WO02/065119 (2002-08-01), None
Kohn, K. Molecular Biology of the Cell, 1999 vol. 10: 2703.
Glass et al., Ordered and disordered dynamics in random networks.Europhysics Letters, vol. 41, No. 6, 1998, pp. 599-604.
Tomita et al, E-CELL; Software environment for whole-cell simulation.Bioinformatics. vol. 15, No. 1, 1999 pp. 72-84.
Goryanin et al. Mathematical simulation and analysis of cellular metabolism and regulation.Bioinformatics, 1999, vol. 15, No. 9, pp. 749-758.
Huang Sui, Gene expression profiling, genetic networks, and cellular states; An integrating concept for tumorigenesis and drug discovery.Journal of Molecular Medicine, Springer Verlag, DE, vol. 77, No. 6, Jun. 1999, pp. 469-480.
Schuster Stefan et al., A general definition of metabolic pathways for systemic organization and analysis of complex metabolic networks.Nature Biotechnology(Nature America), vol. 18, No. 3, Mar. 2000, pp. 326-333.
Scherf U. et al., A gene expression database for the molecular pharmacology of cancer.Nature Genetics(Nature America), New York, vol. 24 No. 3, Mar. 2000, pp. 236-244.
Voit et al. Biochemical systems analysis of genome wide expression data.Bioinformatics, vol. 16, No. 11, (2000) pp. 1023-1037.
Marhl et al, Complex calcium oscillations and the role of mitochondria and cytosolic proteins.BioSystems, vol. 57 (2000), pp. 75-86.
Haberichter et al., Birhyhmicity, trihythmicity and chaos in bursting calcium oscillations,Biophysical Chemistryvol. 90, (2001), pp. 17-30.
Bader et al., BIND- The biomolecular interaction network database.Nucleic Acids Research, vol. 29, No. 1 (2001), pp. 242-245.
Hasty Jeff et al., Computational studies of gene regulatory networks: In numero molecular biology.Nature Reviews/Genetics. vol. 2, No. 4, Apr. 2001, pp. 268-279.
Ideker et al., Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.Science, American Association for the Advancement of Science; vol. 292, No. 4, May 2001, pp. 929-934.
Somogyi Roland et al., The dynamics of molecular networks: applications to therapeutic discovery.Drug Discovery Today, vol. 6, No. 24, 2001, pp. 1267-1277.
Wagner A: How to reconstruct a large genetic network from n gene perturbations in fewer than n2 east steps.Bioinformatics, Oxford University Press, vol. 17, No. 12, 2001, pp. 1183-1197.
Browning et al., Towards the Development of a Minimal Cell Model by Generalization of a Model ofEsherichia coli: Use of Dimensionless Rate Parameters,Biotechnology and Bioengineering, vol. 76, No. 3, Nov. 2001, pp. 187-192.
Fox et al., From topology to dynamics in biochemical networks.Chaos, vol. 2, No. 4, Dec. 2001, pp. 809-815.
Kierzek, A. STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.Bioinformatics, vol. 18, No. 3, (Mar. 2002) pp. 470-481.
Shmulevich Ilya et al., Gene perturbation and intervention in Probabilistic Boolean Networks,Bioinformatics, vol. 18, No. 10 (Oct. 2002), pp. 1319-1331.
Maimon et al., Diagrammatic Notation and Computational Structure of Gene Networks, Gene Network Sciences;Proceedings of the Second International Conference on Systems Biology, Pasadena, CA, 311-317 (2001) pp. 1-7.
Hill Colin
Khalil Iya
Cornell Research Foundation Inc.
Evans, Esq. Barry
Gene Network Sciences, Inc.
Haleva, Esq. Aaron
Kramer Levin Naftalis & Frankel LLP
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