WO2000046405A3 - Methods for identifying drug targets based on genomic sequence data - Google Patents

Methods for identifying drug targets based on genomic sequence data Download PDF

Info

Publication number
WO2000046405A3
WO2000046405A3 PCT/US2000/002882 US0002882W WO0046405A3 WO 2000046405 A3 WO2000046405 A3 WO 2000046405A3 US 0002882 W US0002882 W US 0002882W WO 0046405 A3 WO0046405 A3 WO 0046405A3
Authority
WO
WIPO (PCT)
Prior art keywords
drug targets
targets based
methods
sequence data
genomic sequence
Prior art date
Application number
PCT/US2000/002882
Other languages
French (fr)
Other versions
WO2000046405A2 (en
WO2000046405A9 (en
Inventor
Bernhard Palsson
Original Assignee
Bernhard Palsson
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Bernhard Palsson filed Critical Bernhard Palsson
Priority to AU34822/00A priority Critical patent/AU3482200A/en
Priority to EP00913358A priority patent/EP1147229A2/en
Publication of WO2000046405A2 publication Critical patent/WO2000046405A2/en
Publication of WO2000046405A3 publication Critical patent/WO2000046405A3/en
Publication of WO2000046405A9 publication Critical patent/WO2000046405A9/en

Links

Classifications

    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • 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
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/20—Screening of libraries
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry

Abstract

This invention provides a computational approach to identifying potential antibacterial drug targets based on a genome sequence and its annotation. Starting from a fully sequenced genome, open reading frame assignments are made which determine the metabolic genotype for the organism. The metabolic genotype, and more specifically its stoichiometric matrix, are analyzed using flux balance analysis to assess the effects of genetic deletions on the fitness of the organism and its ability to produce essential biomolecules required for growth.
PCT/US2000/002882 1999-02-02 2000-02-02 Methods for identifying drug targets based on genomic sequence data WO2000046405A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU34822/00A AU3482200A (en) 1999-02-02 2000-02-02 Methods for identifying drug targets based on genomic sequence data
EP00913358A EP1147229A2 (en) 1999-02-02 2000-02-02 Methods for identifying drug targets based on genomic sequence data

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US24302299A 1999-02-02 1999-02-02
US09/243,022 1999-02-02

Publications (3)

Publication Number Publication Date
WO2000046405A2 WO2000046405A2 (en) 2000-08-10
WO2000046405A3 true WO2000046405A3 (en) 2001-05-10
WO2000046405A9 WO2000046405A9 (en) 2001-09-07

Family

ID=22917056

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/002882 WO2000046405A2 (en) 1999-02-02 2000-02-02 Methods for identifying drug targets based on genomic sequence data

Country Status (4)

Country Link
US (4) US8606553B2 (en)
EP (1) EP1147229A2 (en)
AU (1) AU3482200A (en)
WO (1) WO2000046405A2 (en)

Families Citing this family (99)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1147229A2 (en) 1999-02-02 2001-10-24 Bernhard O. Palsson Methods for identifying drug targets based on genomic sequence data
GB0225109D0 (en) * 2002-10-29 2002-12-11 Univ Newcastle Method of and apparatus for identifying components of a network having high importance for network integrity
EP1362319A2 (en) * 2001-01-10 2003-11-19 The Penn State Research Foundation Method and system for modeling cellular metabolism
US7127379B2 (en) 2001-01-31 2006-10-24 The Regents Of The University Of California Method for the evolutionary design of biochemical reaction networks
CA2439260C (en) * 2001-03-01 2012-10-23 The Regents Of The University Of California Models and methods for determining systemic properties of regulated reaction networks
AU2012203405B2 (en) * 2001-03-01 2015-02-12 Genomatica, Inc. Models and methods for determining systemic properties of regulated reaction networks
AU2001289843A1 (en) * 2001-08-28 2002-02-13 Bayer Cropscience Ag Polypeptides for identifying herbicidally active compounds
US7751981B2 (en) 2001-10-26 2010-07-06 The Regents Of The University Of California Articles of manufacture and methods for modeling Saccharomyces cerevisiae metabolism
JP2003180400A (en) * 2001-12-20 2003-07-02 Japan Science & Technology Corp Method for processing metabolic circuit information, apparatus for processing metabolic circuit information, program, and recording medium
US20030224363A1 (en) * 2002-03-19 2003-12-04 Park Sung M. Compositions and methods for modeling bacillus subtilis metabolism
US8949032B2 (en) 2002-03-29 2015-02-03 Genomatica, Inc. Multicellular metabolic models and methods
AU2003222128A1 (en) * 2002-03-29 2003-10-13 Genomatica, Inc. Human metabolic models and methods
AU2003239736A1 (en) * 2002-05-24 2003-12-12 Global Genomics Ab Methods for profiling molecules with an objective function
US7856317B2 (en) * 2002-06-14 2010-12-21 Genomatica, Inc. Systems and methods for constructing genomic-based phenotypic models
AU2003256480B2 (en) * 2002-07-10 2008-03-06 The Penn State Research Foundation Method for determining gene knockout strategies
US7826975B2 (en) * 2002-07-10 2010-11-02 The Penn State Research Foundation Method for redesign of microbial production systems
US7869957B2 (en) 2002-10-15 2011-01-11 The Regents Of The University Of California Methods and systems to identify operational reaction pathways
CA2500761C (en) * 2002-10-15 2012-11-20 Bernhard O. Palsson Methods and systems to identify operational reaction pathways
JP4894134B2 (en) 2003-07-29 2012-03-14 味の素株式会社 Methods for determining metabolic fluxes that affect substance production
JP4654592B2 (en) 2004-04-02 2011-03-23 味の素株式会社 Determination of metabolic flux
JP5331476B2 (en) 2005-06-15 2013-10-30 カリダ・ジェノミックス・インコーポレイテッド Single molecule array for genetic and chemical analysis
US20080065411A1 (en) * 2006-09-08 2008-03-13 Diaceutics Method and system for developing a personalized medicine business plan
US8673601B2 (en) * 2007-01-22 2014-03-18 Genomatica, Inc. Methods and organisms for growth-coupled production of 3-hydroxypropionic acid
LT2821494T (en) 2007-03-16 2017-04-25 Genomatica, Inc. Compositions and methods for the biosynthesis of 1,4-butanediol and its precursors
US20090023182A1 (en) * 2007-07-18 2009-01-22 Schilling Christophe H Complementary metabolizing organisms and methods of making same
US7947483B2 (en) 2007-08-10 2011-05-24 Genomatica, Inc. Methods and organisms for the growth-coupled production of 1,4-butanediol
AU2008307381B2 (en) 2007-08-10 2014-02-20 Genomatica, Inc. Methods for the synthesis of acrylic acid and derivatives from fumaric acid
US8592150B2 (en) 2007-12-05 2013-11-26 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing
CA2712779C (en) * 2008-01-22 2021-03-16 Genomatica, Inc. Methods and organisms for utilizing synthesis gas or other gaseous carbon sources and methanol
WO2009105591A2 (en) * 2008-02-19 2009-08-27 The Regents Of The University Of California Methods and systems for genome-scale kinetic modeling
SI2262901T1 (en) 2008-03-05 2019-02-28 Genomatica, Inc. Primary alcohol producing organisms
CN103555643B (en) 2008-03-27 2016-08-10 基因组股份公司 For producing the microorganism of adipic acid and other compounds
CA2722680A1 (en) 2008-05-01 2009-11-05 Genomatica, Inc. Microorganisms for the production of methacrylic acid
WO2009155382A1 (en) 2008-06-17 2009-12-23 Genomatica, Inc. Microorganisms and methods for the biosynthesis of fumarate, malate, and acrylate
US20100021978A1 (en) * 2008-07-23 2010-01-28 Genomatica, Inc. Methods and organisms for production of 3-hydroxypropionic acid
EP3514242A3 (en) 2008-09-10 2019-08-28 Genomatica, Inc. Microrganisms for the production of 1,4-butanediol
US8647642B2 (en) 2008-09-18 2014-02-11 Aviex Technologies, Llc Live bacterial vaccines resistant to carbon dioxide (CO2), acidic PH and/or osmolarity for viral infection prophylaxis or treatment
US20100184173A1 (en) * 2008-11-14 2010-07-22 Genomatica, Inc. Microorganisms for the production of methyl ethyl ketone and 2-butanol
AU2009327490A1 (en) * 2008-12-16 2011-07-28 Genomatica, Inc. Microorganisms and methods for conversion of syngas and other carbon sources to useful products
EP2401696B1 (en) 2009-02-26 2017-06-21 Intrexon CEU, Inc. Mammalian cell line models and related methods
CN106119113A (en) 2009-04-30 2016-11-16 基因组股份公司 For producing the biology of 1,3 butanediols
WO2010127303A1 (en) 2009-04-30 2010-11-04 Genomatica, Inc. Organisms for the production of isopropanol, n-butanol, and isobutanol
EP2427544B1 (en) 2009-05-07 2019-07-17 Genomatica, Inc. Microorganisms and methods for the biosynthesis of adipate, hexamethylenediamine and 6-aminocaproic acid
JP2012526561A (en) * 2009-05-15 2012-11-01 ゲノマチカ， インク． Organisms for the production of cyclohexanone
CN113528417A (en) 2009-06-04 2021-10-22 基因组股份公司 Microorganisms for producing 1, 4-butanediol and related methods
JP6133599B2 (en) * 2009-06-04 2017-05-24 ゲノマチカ， インク． Method for separating components of fermentation broth
WO2010144746A2 (en) * 2009-06-10 2010-12-16 Genomatica, Inc. Microorganisms and methods for carbon-efficient biosynthesis of mek and 2-butanol
EP3190174A1 (en) 2009-08-05 2017-07-12 Genomatica, Inc. Semi-synthetic terephthalic acid via microorganisms that produce muconic acid
BR112012005296A2 (en) 2009-09-09 2019-01-15 Genomatica Inc microorganisms and methods for the co-production of isopropanol with primary alcohols, dios and acids.
JP2013507145A (en) 2009-10-13 2013-03-04 ゲノマチカ， インク． Microorganisms and related methods for the production of 1,4-butanediol, 4-hydroxybutanal, 4-hydroxybutyryl-CoA, putrescine and related compounds
KR20120088753A (en) * 2009-10-23 2012-08-08 게노마티카 인코포레이티드 Microorganisms for the production of aniline
US8530210B2 (en) 2009-11-25 2013-09-10 Genomatica, Inc. Microorganisms and methods for the coproduction 1,4-butanediol and gamma-butyrolactone
WO2011071682A1 (en) 2009-12-10 2011-06-16 Genomatica, Inc. Methods and organisms for converting synthesis gas or other gaseous carbon sources and methanol to 1,3-butanediol
SG182686A1 (en) 2010-01-29 2012-08-30 Genomatica Inc Microorganisms and methods for the biosynthesis of p-toluate and terephthalate
US8048661B2 (en) * 2010-02-23 2011-11-01 Genomatica, Inc. Microbial organisms comprising exogenous nucleic acids encoding reductive TCA pathway enzymes
US8637286B2 (en) * 2010-02-23 2014-01-28 Genomatica, Inc. Methods for increasing product yields
US9023636B2 (en) 2010-04-30 2015-05-05 Genomatica, Inc. Microorganisms and methods for the biosynthesis of propylene
KR20180005263A (en) 2010-05-05 2018-01-15 게노마티카 인코포레이티드 Microorganisms and methods for the biosynthsis of butadiene
CA2806230A1 (en) 2010-07-26 2012-02-09 Genomatica, Inc. Microorganisms and methods for the biosynthesis of aromatics, 2,4-pentadienoate and 1,3-butadiene
AU2012212118B2 (en) 2011-02-02 2015-11-12 Genomatica, Inc. Microorganisms and methods for the biosynthesis of butadiene
WO2012118933A1 (en) * 2011-03-01 2012-09-07 Rutgers, The State University Of New Jersey Genetically engineered microbes and uses thereof
US9169486B2 (en) 2011-06-22 2015-10-27 Genomatica, Inc. Microorganisms for producing butadiene and methods related thereto
US8617862B2 (en) 2011-06-22 2013-12-31 Genomatica, Inc. Microorganisms for producing propylene and methods related thereto
WO2013028519A1 (en) 2011-08-19 2013-02-28 Genomatica, Inc. Microorganisms and methods for producing 2,4-pentadienoate, butadiene, propylene, 1,3-butanediol and related alcohols
KR20140070605A (en) 2011-09-16 2014-06-10 게노마티카 인코포레이티드 Microorganisms and methods for producing alkenes
MY197970A (en) 2011-11-02 2023-07-25 Genomatica Inc Microorganisms and methods for the production of caprolactone
WO2013109865A2 (en) 2012-01-20 2013-07-25 Genomatica, Inc. Microorganisms and processes for producing terephthalic acid and its salts
CN111705028A (en) 2012-06-04 2020-09-25 基因组股份公司 Microorganisms and methods for making 4-hydroxybutyrate, 1, 4-butanediol, and related compounds
US9842198B2 (en) * 2012-06-05 2017-12-12 Mcmaster University Screening method and systems utilizing mass spectral fragmentation patterns
US9657316B2 (en) 2012-08-27 2017-05-23 Genomatica, Inc. Microorganisms and methods for enhancing the availability of reducing equivalents in the presence of methanol, and for producing 1,4-butanediol related thereto
EP2909325A4 (en) 2012-10-22 2016-05-25 Genomatica Inc Microorganisms and methods for enhancing the availability of reducing equivalents in the presence of methanol, and for producing succinate related thereto
WO2014071286A1 (en) 2012-11-05 2014-05-08 Genomatica, Inc. Microorganisms for enhancing the availability of reducing equivalents in the presence of methanol, and for producing 1,2-propanediol
WO2014071289A1 (en) 2012-11-05 2014-05-08 Genomatica, Inc. Microorganisms for enhancing the availability of reducing equivalents in the presence of methanol, and for producing 3-hydroxyisobutyrate
WO2014076232A2 (en) 2012-11-19 2014-05-22 Novozymes A/S Isopropanol production by recombinant hosts using an hmg-coa intermediate
JP2015536669A (en) 2012-11-30 2015-12-24 ノボザイムス，インコーポレイティド Production of 3-hydroxypropionic acid by recombinant yeast
TWI716752B (en) 2012-12-17 2021-01-21 美商奇諾麥提卡公司 Microorganisms and methods for enhancing the availability of reducing equivalents in the presence of methanol, and for producing adipate, 6-aminocaproate, hexamethylenediamine or caprolactam related thereto
EP2971021A4 (en) 2013-03-15 2016-12-21 Genomatica Inc Microorganisms and methods for producing butadiene and related compounds by formate assimilation
MY187966A (en) 2013-04-26 2021-11-02 Genomatica Inc Microorganisms and methods for production of 4-hydroxybutyrate, 1,4-butanediol and related compounds
US11814664B2 (en) 2013-05-24 2023-11-14 Genomatica, Inc. Microorganisms and methods for producing (3R)-hydroxybutyl (3R)-hydroxybutyrate
DK3027733T3 (en) 2013-07-31 2018-12-10 Novozymes As Preparation of 3-Hydroxypropionic Acid in Recombinant Yeast Expressing an Insect Aspartate-1 Decarboxylase
WO2015077752A1 (en) 2013-11-25 2015-05-28 Genomatica, Inc. Methods for enhancing microbial production of specific length fatty alcohols in the presence of methanol
PL3077501T3 (en) 2013-12-03 2022-01-31 Genomatica, Inc. Microorganisms and methods for improving product yields on methanol using acetyl-coa synthesis
WO2016007365A1 (en) 2014-07-11 2016-01-14 Genomatica, Inc. Microorganisms and methods for the production of butadiene using acetyl-coa
US10480375B2 (en) 2014-10-28 2019-11-19 Cummins Emission Solutions Inc. SCR conversion efficiency diagnostics
WO2016100910A1 (en) 2014-12-19 2016-06-23 Novozymes A/S Recombinant host cells for the production of 3-hydroxypropionic acid
DK3262161T3 (en) 2015-02-27 2021-09-13 Novozymes As Recombinant host cells for the production of 3-hydroxypropionic acid
EP3341475A1 (en) 2015-08-24 2018-07-04 Novozymes A/S Beta-alanine aminotransferases for the production of 3-hydroxypropionic acid
US11129906B1 (en) 2016-12-07 2021-09-28 David Gordon Bermudes Chimeric protein toxins for expression by therapeutic bacteria
US11180535B1 (en) 2016-12-07 2021-11-23 David Gordon Bermudes Saccharide binding, tumor penetration, and cytotoxic antitumor chimeric peptides from therapeutic bacteria
BR112019013005A2 (en) 2016-12-21 2019-10-08 Creatus Biosciences Inc metschnikowia species isolated, method for producing xylitol, bioderivated xylitol and composition
BR112019013007A2 (en) 2016-12-21 2019-10-08 Creatus Biosciences Inc unnatural microbial organism, method of producing a bioderivated compound, bioderivated compound and composition
EP3601546A1 (en) 2017-03-31 2020-02-05 Genomatica, Inc. Aldehyde dehydrogenase variants and methods of use
CN110691847A (en) 2017-03-31 2020-01-14 基因组股份公司 3-hydroxybutyryl-CoA dehydrogenase variants and methods of use
US20210079334A1 (en) 2018-01-30 2021-03-18 Genomatica, Inc. Fermentation systems and methods with substantially uniform volumetric uptake rate of a reactive gaseous component
KR20210068489A (en) 2018-09-26 2021-06-09 게노마티카 인코포레이티드 Aldehyde dehydrogenase variants and methods of use thereof
CN109439606B (en) * 2018-11-14 2022-06-28 中国科学院青岛生物能源与过程研究所 Genetically engineered bacterium for increasing phloroglucinol yield and construction method and application thereof
CN110923289B (en) * 2019-12-10 2023-01-10 北京联合大学 Screening method of drug for treating citrus greening disease
CN111019877B (en) * 2019-12-31 2022-04-19 浙江工业大学 Genetically engineered bacterium for producing L-cysteine, construction method and application
CN114369562B (en) * 2022-03-21 2022-05-31 中国农业科学院北京畜牧兽医研究所 Method for improving expression quantity of 5-aminolevulinic acid

Family Cites Families (38)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5273038A (en) 1990-07-09 1993-12-28 Beavin William C Computer simulation of live organ
US5639949A (en) 1990-08-20 1997-06-17 Ciba-Geigy Corporation Genes for the synthesis of antipathogenic substances
WO1992009300A1 (en) 1990-11-21 1992-06-11 Iterex Pharmaceuticals Ltd. Partnership Synthesis of equimolar multiple oligomer mixtures, especially of oligopeptide mixtures
US5553234A (en) 1994-09-23 1996-09-03 International Business Machines Corporation System and method for including stored procedures, user-defined functions, and trigger processing in an existing unit of work
US5980096A (en) 1995-01-17 1999-11-09 Intertech Ventures, Ltd. Computer-based system, methods and graphical interface for information storage, modeling and stimulation of complex systems
US5930154A (en) 1995-01-17 1999-07-27 Intertech Ventures, Ltd. Computer-based system and methods for information storage, modeling and simulation of complex systems organized in discrete compartments in time and space
US6983227B1 (en) 1995-01-17 2006-01-03 Intertech Ventures, Ltd. Virtual models of complex systems
US5914891A (en) 1995-01-20 1999-06-22 Board Of Trustees, The Leland Stanford Junior University System and method for simulating operation of biochemical systems
US6329139B1 (en) 1995-04-25 2001-12-11 Discovery Partners International Automated sorting system for matrices with memory
US6326140B1 (en) 1995-08-09 2001-12-04 Regents Of The University Of California Systems for generating and analyzing stimulus-response output signal matrices
US5947899A (en) 1996-08-23 1999-09-07 Physiome Sciences Computational system and method for modeling the heart
US5817475A (en) * 1996-11-15 1998-10-06 Giles Scientific, Inc. Automatic microbiological testing apparatus and method
CA2276064C (en) 1997-01-17 2013-12-17 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
US6165709A (en) 1997-02-28 2000-12-26 Fred Hutchinson Cancer Research Center Methods for drug target screening
US6132969A (en) 1998-06-19 2000-10-17 Rosetta Inpharmatics, Inc. Methods for testing biological network models
US6351712B1 (en) 1998-12-28 2002-02-26 Rosetta Inpharmatics, Inc. Statistical combining of cell expression profiles
US6370478B1 (en) 1998-12-28 2002-04-09 Rosetta Inpharmatics, Inc. Methods for drug interaction prediction using biological response profiles
EP1147229A2 (en) 1999-02-02 2001-10-24 Bernhard O. Palsson Methods for identifying drug targets based on genomic sequence data
FR2789981B1 (en) 1999-02-19 2001-05-04 Oreal LOCKABLE DISTRIBUTION HEAD AND DISTRIBUTOR THUS EQUIPPED
US6221597B1 (en) 1999-05-21 2001-04-24 Rosetta Inpharmatics, Inc. Essential genes of yeast as targets for antifungal agents, herbicides, insecticides and anti-proliferative drugs
US6200803B1 (en) 1999-05-21 2001-03-13 Rosetta Inpharmatics, Inc. Essential genes of yeast as targets for antifungal agents, herbicides, insecticides and anti-proliferative drugs
JP3464414B2 (en) 1999-06-15 2003-11-10 富士通株式会社 Nonvolatile semiconductor memory device and method of manufacturing the same
EP1158447A1 (en) 2000-05-26 2001-11-28 GMD- Forschungszentrum Informationstechnik GmbH Method for evaluating states of biological systems
AU2257401A (en) 1999-12-08 2001-06-18 California Institute Of Technology Directed evolution of biosynthetic and biodegration pathways
IL151070A0 (en) 2000-02-07 2003-04-10 Physiome Sciences Inc System and method for modeling genetic, biochemical, biophysical and anatomical information: in silico cell
DE10190511D2 (en) 2000-02-19 2003-02-20 Hossein Hosseini Tudeshki Method and device for the compression of cohesive and non-cohesive material by pulsating displacement
US6986940B1 (en) 2000-07-27 2006-01-17 General Electric Company Fiber reinforced composite article, fiber member, and method for making
EP1362319A2 (en) 2001-01-10 2003-11-19 The Penn State Research Foundation Method and system for modeling cellular metabolism
US7127379B2 (en) 2001-01-31 2006-10-24 The Regents Of The University Of California Method for the evolutionary design of biochemical reaction networks
CA2439260C (en) 2001-03-01 2012-10-23 The Regents Of The University Of California Models and methods for determining systemic properties of regulated reaction networks
AU2002355996A1 (en) 2001-08-16 2003-03-03 Biotech Research Venture Pte Limited Method for modelling biochemical pathways
US20030224363A1 (en) 2002-03-19 2003-12-04 Park Sung M. Compositions and methods for modeling bacillus subtilis metabolism
US8949032B2 (en) 2002-03-29 2015-02-03 Genomatica, Inc. Multicellular metabolic models and methods
AU2003222128A1 (en) 2002-03-29 2003-10-13 Genomatica, Inc. Human metabolic models and methods
US7856317B2 (en) 2002-06-14 2010-12-21 Genomatica, Inc. Systems and methods for constructing genomic-based phenotypic models
AU2003256480B2 (en) 2002-07-10 2008-03-06 The Penn State Research Foundation Method for determining gene knockout strategies
CA2500761C (en) 2002-10-15 2012-11-20 Bernhard O. Palsson Methods and systems to identify operational reaction pathways
US20070111294A1 (en) 2005-09-09 2007-05-17 Genomatica, Inc. Methods and organisms for the growth-coupled production of succinate

Non-Patent Citations (14)

* Cited by examiner, † Cited by third party
Title
ARIGONI ET AL: "A GENOME-BASED APPROACH FOR THE IDENTIFICATION OF ESSENTIAL BACTERIAL GENES", NATURE BIOTECHNOLOGY,US,NATURE PUBLISHING, vol. 16, no. 9, September 1998 (1998-09-01), pages 851 - 856, XP002119419, ISSN: 1087-0156 *
BALTZ ET AL: "DNA sequence sampling of the Streptococcus pneumoniae genome to identify novel targets for antibiotic development", MICROBIAL DRUG RESISTANCE,US,LIEBERT, vol. 4, no. 1, 21 March 1998 (1998-03-21), pages 1 - 9, XP002112153, ISSN: 1076-6294 *
BONARIUS H P J ET AL: "Flux analysis of underdetermined metabolic networks: the quest for the missing constraints", TRENDS IN BIOTECHNOLOGY,GB,ELSEVIER PUBLICATIONS, CAMBRIDGE, vol. 15, no. 8, 1 August 1997 (1997-08-01), pages 308 - 314, XP004083358, ISSN: 0167-7799 *
EDWARDS JEREMY S ET AL: "How will bioinformatics influence metabolic engineering?", BIOTECHNOLOGY AND BIOENGINEERING, vol. 58, no. 2-3, 20 April 1998 (1998-04-20), pages 162 - 169, XP002153942, ISSN: 0006-3592 *
GALPERIN M Y ET AL: "Using metabolic pathway databases for functional annotation", TRENDS IN GENETICS,NL,ELSEVIER SCIENCE PUBLISHERS B.V. AMSTERDAM, vol. 14, no. 8, 1 December 1998 (1998-12-01), pages 332 - 333, XP004131498, ISSN: 0168-9525 *
KARP P D: "Metabolic databases", TIBS TRENDS IN BIOCHEMICAL SCIENCES,EN,ELSEVIER PUBLICATION, CAMBRIDGE, vol. 23, no. 3, 1 March 1998 (1998-03-01), pages 114 - 116, XP004111317, ISSN: 0968-0004 *
KARP PETER D ET AL: "EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.", NUCLEIC ACIDS RESEARCH, vol. 25, no. 1, 1997, pages 43 - 50, XP002153948, ISSN: 0305-1048 *
PALSSON: "What lies beyond bioinformatics?", NATURE BIOTECHNOLOGY, vol. 15, January 1997 (1997-01-01), pages 3 - 4, XP002153943 *
PRAMANIK J ET AL: "Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements.", BIOTECHNOLOGY AND BIOENGINEERING, vol. 56, no. 4, 1997, pages 398 - 421, XP002153946, ISSN: 0006-3592 *
SAUER UWE ET AL: "Metabolic capacity of Bacillus subtilis for the production of purine nucleosides, riboflavin, and folic acid.", BIOTECHNOLOGY AND BIOENGINEERING, vol. 59, no. 2, 20 July 1998 (1998-07-20), pages 227 - 238, XP002153947, ISSN: 0006-3592 *
SCHILLING CHRISTOPHE H ET AL: "The underlying pathway structure of biochemical reaction networks.", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES, vol. 95, no. 8, 14 April 1998 (1998-04-14), April 14, 1998, pages 4193 - 4198, XP002153944, ISSN: 0027-8424 *
SCHILLING CHRISTOPHE H ET AL: "Toward metabolic phenomics: Analysis of genomic data using flux balances.", BIOTECHNOLOGY PROGRESS, vol. 15, no. 3, May 1999 (1999-05-01), pages 288 - 295, XP000961124, ISSN: 8756-7938 *
TOMITA MASARU ET AL: "E-CELL: Software environment for whole-cell simulation.", BIOINFORMATICS (OXFORD), vol. 15, no. 1, January 1999 (1999-01-01), pages 72 - 84, XP000961128, ISSN: 1367-4803 *
XIE L ET AL: "Integrated approaches to the design of media and feeding strategies for fed-batch cultures of animal cells", TRENDS IN BIOTECHNOLOGY,GB,ELSEVIER PUBLICATIONS, CAMBRIDGE, vol. 15, no. 3, 1 March 1997 (1997-03-01), pages 109 - 113, XP004054783, ISSN: 0167-7799 *

Also Published As

Publication number Publication date
US20080270096A1 (en) 2008-10-30
US8606553B2 (en) 2013-12-10
US8635031B2 (en) 2014-01-21
US20170053059A1 (en) 2017-02-23
EP1147229A2 (en) 2001-10-24
AU3482200A (en) 2000-08-25
WO2000046405A2 (en) 2000-08-10
WO2000046405A9 (en) 2001-09-07
US20020012939A1 (en) 2002-01-31
US20150112652A1 (en) 2015-04-23

Similar Documents

Publication Publication Date Title
WO2000046405A3 (en) Methods for identifying drug targets based on genomic sequence data
WO2004076612A3 (en) Genetic diagnosis using multiple sequence variant analysis combined with mass spectrometry
WO2003012046A3 (en) Stk15 (stk6) gene polymorphism and methods of determining cancer risk
WO2002055995A3 (en) Method and system for modeling cellular metabolism
AU2008304205A8 (en) Methods and systems for genomic analysis using ancestral data
EP1633884A4 (en) Identification of clonal cells by repeats in (eg.) t-cell receptor v/d/j genes
WO2006048291A3 (en) Transcriptome microarray technology and methods of using the same
Aguirre et al. Optimizing ddRADseq in non-model species: A case study in Eucalyptus dunnii Maiden
WO2007000663A3 (en) Genetic diagnosis using multiple sequence variant analysis
WO2004113570A3 (en) Genotype test for dogs
NO20070757L (en) New sequence for enhancing expression of nucleic acid (s)
WO2005067648A3 (en) Multiplex spatial profiling of gene expression
WO2005033982A3 (en) Method for simulating the interaction of chemical substances and living organisms
AU2003265768A8 (en) Automated framework for the analysis of biological data
Hall et al. Potential applications of nanopore sequencing for forensic analysis
WO2003046203A3 (en) Genetic markers associated with desirable and undesirable traits in horses, methods of identifying and using such markers
Hashmi et al. Plant exomics: concepts, applications and methodologies in crop improvement
WO2004035741A3 (en) Susceptibility gene for myocardial infarction; methods of treatment
Kaundun et al. Derived polymorphic amplified cleaved sequence (dPACS): A novel PCR-RFLP procedure for detecting known single nucleotide and deletion–insertion polymorphisms
GB0310880D0 (en) Resistance dilution
AU2003211867A1 (en) Novel method of highly sensitive nucleic acid analysis
Trněný et al. Allelic variants for candidate nitrogen fixation genes revealed by sequencing in red clover (Trifolium pratense L.)
WO2008065544A3 (en) Genetic predictors of risk for type 2 diabetes mellitus
AU2003284127A1 (en) Nucleic acid supported protein complementation
WO2006058395A3 (en) Tools and methods for the quantification of dna repeats

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AL AM AT AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ CZ DE DE DK DK DM EE EE ES FI FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AL AM AT AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ CZ DE DE DK DK DM EE EE ES FI FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

WWE Wipo information: entry into national phase

Ref document number: 2000913358

Country of ref document: EP

AK Designated states

Kind code of ref document: C2

Designated state(s): AE AL AM AT AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ CZ DE DE DK DK DM EE EE ES FI FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: C2

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

COP Corrected version of pamphlet

Free format text: PAGES 1/3-3/3, DRAWINGS, REPLACED BY NEW PAGES 1/4-4/4; DUE TO LATE TRANSMITTAL BY THE RECEIVING OFFICE

WWP Wipo information: published in national office

Ref document number: 2000913358

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642