WO2002061115A3 - Method for the evolutionary design of biochemical reaction networks - Google Patents

Method for the evolutionary design of biochemical reaction networks Download PDF

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Publication number
WO2002061115A3
WO2002061115A3 PCT/US2002/002939 US0202939W WO02061115A3 WO 2002061115 A3 WO2002061115 A3 WO 2002061115A3 US 0202939 W US0202939 W US 0202939W WO 02061115 A3 WO02061115 A3 WO 02061115A3
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Prior art keywords
methods
biochemical reaction
silico
reaction network
reaction networks
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PCT/US2002/002939
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French (fr)
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WO2002061115A2 (en
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Bernhard O Palsson
Jeremy S Edwards
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Univ California
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Priority to EP02709271A priority Critical patent/EP1377901A4/en
Priority to CA2434968A priority patent/CA2434968C/en
Priority to JP2002561050A priority patent/JP2004520829A/en
Publication of WO2002061115A2 publication Critical patent/WO2002061115A2/en
Publication of WO2002061115A3 publication Critical patent/WO2002061115A3/en

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

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  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Physiology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

The present invention relates to methods for achieving an optimal function of a biochemical reaction network. The methods can be performed in silico using a reconstruction of a biochemical reaction network of a cell an iterative optimization procedures. The methods can further include laboratory culturing steps to confirm and possibly expand the determinations made using the in silico methods, and to produce a cultured cell, or population of cells, with optimal functions. The current invention includes computer systems and computer products including computer-readable program code for performing the in silico steps of the invention.
PCT/US2002/002939 2001-01-31 2002-01-31 Method for the evolutionary design of biochemical reaction networks WO2002061115A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP02709271A EP1377901A4 (en) 2001-01-31 2002-01-31 Method for the evolutionary design of biochemical reaction networks
CA2434968A CA2434968C (en) 2001-01-31 2002-01-31 Method for the evolutionary design of biochemical reaction networks
JP2002561050A JP2004520829A (en) 2001-01-31 2002-01-31 Evolutionary design method of biochemical reaction network

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US26555401P 2001-01-31 2001-01-31
US60/265,554 2001-01-31
US09/940,686 2001-08-27
US09/940,686 US7127379B2 (en) 2001-01-31 2001-08-27 Method for the evolutionary design of biochemical reaction networks

Publications (2)

Publication Number Publication Date
WO2002061115A2 WO2002061115A2 (en) 2002-08-08
WO2002061115A3 true WO2002061115A3 (en) 2003-11-06

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PCT/US2002/002939 WO2002061115A2 (en) 2001-01-31 2002-01-31 Method for the evolutionary design of biochemical reaction networks

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US (5) US7127379B2 (en)
EP (2) EP2226739A1 (en)
JP (3) JP2004520829A (en)
CA (1) CA2434968C (en)
WO (1) WO2002061115A2 (en)

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US9434964B2 (en) 2009-06-04 2016-09-06 Genomatica, Inc. Microorganisms for the production of 1,4-butanediol and related methods

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