EP1454282A4 - Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents - Google Patents

Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents

Info

Publication number
EP1454282A4
EP1454282A4 EP02773968A EP02773968A EP1454282A4 EP 1454282 A4 EP1454282 A4 EP 1454282A4 EP 02773968 A EP02773968 A EP 02773968A EP 02773968 A EP02773968 A EP 02773968A EP 1454282 A4 EP1454282 A4 EP 1454282A4
Authority
EP
European Patent Office
Prior art keywords
targets
identification
systems
methods
components
Prior art date
Legal status (The legal status 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 status listed.)
Withdrawn
Application number
EP02773968A
Other languages
German (de)
French (fr)
Other versions
EP1454282A1 (en
Inventor
Colin Hill
Iya Khalil
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Gene Network Sciences Inc
Original Assignee
Gene Network Sciences Inc
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
Priority claimed from US10/286,372 external-priority patent/US20030144823A1/en
Application filed by Gene Network Sciences Inc filed Critical Gene Network Sciences Inc
Publication of EP1454282A1 publication Critical patent/EP1454282A1/en
Publication of EP1454282A4 publication Critical patent/EP1454282A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5091—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing the pathological state of an organism
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/30—Dynamic-time models
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701—Details
    • G01N2333/4739—Cyclin; Prad 1
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • 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
    • G16B5/10—Boolean models
    • 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
    • G16B5/20—Probabilistic models

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Physiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Microbiology (AREA)
  • Cell Biology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
EP02773968A 2001-11-02 2002-11-04 Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents Withdrawn EP1454282A4 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US33599901P 2001-11-02 2001-11-02
US335999P 2001-11-02
US40676402P 2002-08-29 2002-08-29
US406764P 2002-08-29
US10/286,372 US20030144823A1 (en) 2001-11-01 2002-11-01 Scale-free network inference methods
US286372 2002-11-01
PCT/US2002/035301 WO2003040992A1 (en) 2001-11-02 2002-11-04 Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents

Publications (2)

Publication Number Publication Date
EP1454282A1 EP1454282A1 (en) 2004-09-08
EP1454282A4 true EP1454282A4 (en) 2005-04-06

Family

ID=27403609

Family Applications (1)

Application Number Title Priority Date Filing Date
EP02773968A Withdrawn EP1454282A4 (en) 2001-11-02 2002-11-04 Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents

Country Status (3)

Country Link
EP (1) EP1454282A4 (en)
CA (1) CA2501111A1 (en)
WO (1) WO2003040992A1 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7069534B2 (en) 2003-12-17 2006-06-27 Sahouria Emile Y Mask creation with hierarchy management using cover cells
US8554486B2 (en) 2004-02-20 2013-10-08 The Mathworks, Inc. Method, computer program product, and apparatus for selective memory restoration of a simulation
US7844431B2 (en) 2004-02-20 2010-11-30 The Mathworks, Inc. Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions
US20110289042A1 (en) * 2005-06-29 2011-11-24 Board Of Trustees Of Michagn State University Integrative Framework for Three-Stage Integrative Pathway Search

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002065119A1 (en) * 2001-02-09 2002-08-22 The Trustees Of Columbia University In The City Of New York A method for the prediction of molecular interaction networks

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
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
US6165709A (en) * 1997-02-28 2000-12-26 Fred Hutchinson Cancer Research Center Methods for drug target screening
US5965352A (en) * 1998-05-08 1999-10-12 Rosetta Inpharmatics, Inc. Methods for identifying pathways of drug action
US6132969A (en) * 1998-06-19 2000-10-17 Rosetta Inpharmatics, Inc. Methods for testing biological network models
WO2000023933A1 (en) * 1998-10-21 2000-04-27 Bios Group Lp Systems and methods for analysis of genetic networks
US6203987B1 (en) * 1998-10-27 2001-03-20 Rosetta Inpharmatics, Inc. Methods for using co-regulated genesets to enhance detection and classification of gene expression patterns
US20020068269A1 (en) * 2000-03-10 2002-06-06 Allen Eric B. System and method for simulating cellular biochemical pathways
WO2001080151A2 (en) * 2000-04-14 2001-10-25 Hybrigenics S.A. Method for constructing, representing or displaying protein interaction maps

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002065119A1 (en) * 2001-02-09 2002-08-22 The Trustees Of Columbia University In The City Of New York A method for the prediction of molecular interaction networks

Non-Patent Citations (9)

* Cited by examiner, † Cited by third party
Title
HASTY JEFF ET AL: "Computational studies of gene regulatory networks: In numero molecular biology", NATURE REVIEWS GENETICS, vol. 2, no. 4, April 2001 (2001-04-01), pages 268 - 279, XP002316687, ISSN: 1471-0056 *
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, June 1999 (1999-06-01), pages 469 - 480, XP002205218, ISSN: 0946-2716 *
IDEKER T ET AL: "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, US, vol. 292, 4 May 2001 (2001-05-04), pages 929 - 934, XP002963505, ISSN: 0036-8075 *
SCHERF U ET AL: "A gene expression database for the molecular pharmacology of cancer", NATURE GENETICS, NATURE AMERICA, NEW YORK, US, vol. 24, no. 3, March 2000 (2000-03-01), pages 236 - 244, XP002224798, ISSN: 1061-4036 *
SCHUSTER STEFAN ET AL: "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks", NATURE BIOTECHNOLOGY, vol. 18, no. 3, March 2000 (2000-03-01), pages 326 - 332, XP002316686, ISSN: 1087-0156 *
See also references of WO03040992A1 *
SHMULEVICH ILYA ET AL: "Gene perturbation and intervention in Probabilistic Boolean Networks.", BIOINFORMATICS (OXFORD), vol. 18, no. 10, October 2002 (2002-10-01), pages 1319 - 1331, XP002316689, ISSN: 1367-4803 *
SOMOGYI ROLAND ET AL: "The dynamics of molecular networks: Applications to therapeutic discovery.", DRUG DISCOVERY TODAY, vol. 6, no. 24, 2001, pages 1267 - 1277, XP002316688, ISSN: 1359-6446 *
WAGNER A: "How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps", BIOINFORMATICS, OXFORD UNIVERSITY PRESS, OXFORD,, GB, vol. 17, no. 12, 2001, pages 1183 - 1197, XP002973480, ISSN: 1367-4803 *

Also Published As

Publication number Publication date
WO2003040992A1 (en) 2003-05-15
EP1454282A1 (en) 2004-09-08
CA2501111A1 (en) 2003-05-15

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