WO2000070528A3 - Method and apparatus for predictive cellular bioinformatics - Google Patents

Method and apparatus for predictive cellular bioinformatics Download PDF

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Publication number
WO2000070528A3
WO2000070528A3 PCT/US2000/013154 US0013154W WO0070528A3 WO 2000070528 A3 WO2000070528 A3 WO 2000070528A3 US 0013154 W US0013154 W US 0013154W WO 0070528 A3 WO0070528 A3 WO 0070528A3
Authority
WO
WIPO (PCT)
Prior art keywords
database
dbms
descriptor
information
features
Prior art date
Application number
PCT/US2000/013154
Other languages
French (fr)
Other versions
WO2000070528A2 (en
WO2000070528A9 (en
Inventor
James H Sabry
Cynthia L Adams
Eugeni A Vaisberg
Anne M Crompton
Robert I Blum
Donald R Oestreicher
Nolan H Sigal
Original Assignee
Cytokinetics 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 US09/311,890 external-priority patent/US6743576B1/en
Application filed by Cytokinetics Inc filed Critical Cytokinetics Inc
Priority to AU48471/00A priority Critical patent/AU4847100A/en
Priority to EP00930696A priority patent/EP1188139A2/en
Publication of WO2000070528A2 publication Critical patent/WO2000070528A2/en
Publication of WO2000070528A3 publication Critical patent/WO2000070528A3/en
Publication of WO2000070528A9 publication Critical patent/WO2000070528A9/en

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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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V20/00—Scenes; Scene-specific elements
    • G06V20/60—Type of objects
    • G06V20/69—Microscopic objects, e.g. biological cells or cellular parts
    • G06V20/695—Preprocessing, e.g. image segmentation
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics

Abstract

Techniques for using information technology in therapeutics or drug discovery. In an exemplary embodiment, techniques for determining information about the properties of substances based upon information about structure of living or non-living cells exposed to substances are provided. A method according to the present invention enables researchers and/or scientists to identify promising candidates in the search for new and better medicines or treatments using, for example, a cellular informatics database. The present invention further teaches a system for acquiring knowledge from cellular information. The system has a database 1012 comprising a database management module ('DBMS'). The system also has a variety of modules, including a population module coupled to the DBMS for categorizing and storing a plurality of features (e.g., cell size, distance between cells, cell population, cell type) from an image acquisition device into the database. The system has a translation module coupled to the DBMS for defining a descriptor from a set of selected features from the plurality of features. In a specific embodiment, the descriptor is for a known or unknown compound, e.g., drug. A prediction module is coupled to the DBMS for selecting one of a plurality of descriptors from known and unknown compounds from the database based upon a selected descriptor from a selected compound. The selected compound may be one that is useful for treatment of human beings or the like.
PCT/US2000/013154 1999-05-14 2000-05-12 Method and apparatus for predictive cellular bioinformatics WO2000070528A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU48471/00A AU4847100A (en) 1999-05-14 2000-05-12 Method and apparatus for predictive cellular bioinformatics
EP00930696A EP1188139A2 (en) 1999-05-14 2000-05-12 Method and apparatus for predictive cellular bioinformatics

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US31199699A 1999-05-14 1999-05-14
US13410499P 1999-05-14 1999-05-14
US31087999A 1999-05-14 1999-05-14
US09/311,890 1999-05-14
US09/311,996 1999-05-14
US09/310,879 1999-05-14
US09/311,890 US6743576B1 (en) 1999-05-14 1999-05-14 Database system for predictive cellular bioinformatics
US60/134,104 1999-05-14

Publications (3)

Publication Number Publication Date
WO2000070528A2 WO2000070528A2 (en) 2000-11-23
WO2000070528A3 true WO2000070528A3 (en) 2001-03-08
WO2000070528A9 WO2000070528A9 (en) 2001-11-29

Family

ID=27495080

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/013154 WO2000070528A2 (en) 1999-05-14 2000-05-12 Method and apparatus for predictive cellular bioinformatics

Country Status (2)

Country Link
AU (1) AU4847100A (en)
WO (1) WO2000070528A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8114615B2 (en) 2006-05-17 2012-02-14 Cernostics, Inc. Method for automated tissue analysis

Families Citing this family (22)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030228565A1 (en) * 2000-04-26 2003-12-11 Cytokinetics, Inc. Method and apparatus for predictive cellular bioinformatics
US6876760B1 (en) 2000-12-04 2005-04-05 Cytokinetics, Inc. Classifying cells based on information contained in cell images
US6651008B1 (en) 1999-05-14 2003-11-18 Cytokinetics, Inc. Database system including computer code for predictive cellular bioinformatics
US6743576B1 (en) 1999-05-14 2004-06-01 Cytokinetics, Inc. Database system for predictive cellular bioinformatics
US7151847B2 (en) 2001-02-20 2006-12-19 Cytokinetics, Inc. Image analysis of the golgi complex
AU2002232892B2 (en) 2000-10-24 2008-06-26 Intrexon Corporation Method and device for selectively targeting cells within a three -dimensional specimen
US7218764B2 (en) 2000-12-04 2007-05-15 Cytokinetics, Inc. Ploidy classification method
WO2002066961A1 (en) 2001-02-20 2002-08-29 Cytokinetics, Inc. Method and apparatus for automated cellular bioinformatics
US6956961B2 (en) 2001-02-20 2005-10-18 Cytokinetics, Inc. Extracting shape information contained in cell images
US7016787B2 (en) * 2001-02-20 2006-03-21 Cytokinetics, Inc. Characterizing biological stimuli by response curves
US7778782B1 (en) 2002-12-17 2010-08-17 Entelos, Inc. Peroxisome proliferation activated receptor alpha (PPARα) signatures
US7396645B1 (en) 2002-12-17 2008-07-08 Entelos, Inc. Cholestasis signature
US7519519B1 (en) 2002-12-20 2009-04-14 Entelos, Inc. Signature projection score
US7422854B1 (en) 2002-12-20 2008-09-09 Entelos, Inc. Cholesterol reduction signature
US20050014217A1 (en) 2003-07-18 2005-01-20 Cytokinetics, Inc. Predicting hepatotoxicity using cell based assays
EP1646926A2 (en) 2003-07-18 2006-04-19 Cytokinetics, Inc. Characterizing biological stimuli by response curves
US7235353B2 (en) 2003-07-18 2007-06-26 Cytokinetics, Inc. Predicting hepatotoxicity using cell based assays
US7323318B2 (en) 2004-07-15 2008-01-29 Cytokinetics, Inc. Assay for distinguishing live and dead cells
CA3212002A1 (en) 2011-03-17 2012-09-20 Cernostics, Inc. Systems and compositions for diagnosing barrett's esophagus and methods of using the same
GB2527755B (en) * 2014-06-28 2019-03-27 Siemens Medical Solutions Usa Inc System and method for retrieval of similar findings from a hybrid image dataset
US10962544B2 (en) 2015-11-25 2021-03-30 Cernostics, Inc. Methods of predicting progression of Barrett's esophagus
WO2024006308A1 (en) * 2022-06-27 2024-01-04 Viqi, Inc. Auto high content screening using artificial intelligence for drug compound development

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997040055A1 (en) * 1996-04-19 1997-10-30 The Dow Chemical Company Fluorescent chelates as visual tissue specific imaging agents
WO1998038490A1 (en) * 1997-02-27 1998-09-03 Cellomics, Inc. A system for cell-based screening
WO1998045704A2 (en) * 1997-04-07 1998-10-15 Bioimage A/S A method for extracting quantitative information relating to an influence on a cellular response
WO1999039184A1 (en) * 1998-01-29 1999-08-05 Ribozyme Pharmaceuticals, Inc. Image acquisition and image analysis of biological material
WO2000017643A2 (en) * 1998-09-18 2000-03-30 Cellomics, Inc. A system for cell-based screening
WO2000050872A2 (en) * 1999-02-26 2000-08-31 Cellomics, Inc. A system for cell-based screening

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997040055A1 (en) * 1996-04-19 1997-10-30 The Dow Chemical Company Fluorescent chelates as visual tissue specific imaging agents
WO1998038490A1 (en) * 1997-02-27 1998-09-03 Cellomics, Inc. A system for cell-based screening
WO1998045704A2 (en) * 1997-04-07 1998-10-15 Bioimage A/S A method for extracting quantitative information relating to an influence on a cellular response
WO1999039184A1 (en) * 1998-01-29 1999-08-05 Ribozyme Pharmaceuticals, Inc. Image acquisition and image analysis of biological material
WO2000017643A2 (en) * 1998-09-18 2000-03-30 Cellomics, Inc. A system for cell-based screening
WO2000050872A2 (en) * 1999-02-26 2000-08-31 Cellomics, Inc. A system for cell-based screening

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
GIULIANO K A ET AL: "Fluorescent-protein biosensors: new tools for drug discovery", TRENDS IN BIOTECHNOLOGY,GB,ELSEVIER PUBLICATIONS, CAMBRIDGE, vol. 16, no. 3, 1 March 1998 (1998-03-01), pages 135 - 140, XP004108592, ISSN: 0167-7799 *
MONTIRONI R ET AL: "COMPUTED CELL CYCLE AND DNA HISTOGRAM ANALYSES IN IMAGE CYTOMETRY IN BREAST CANCER", JOURNAL OF CLINICAL PATHOLOGY,GB,LONDON, vol. 46, no. 9, 1 September 1993 (1993-09-01), pages 795 - 800, XP000644549, ISSN: 0021-9746 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8114615B2 (en) 2006-05-17 2012-02-14 Cernostics, Inc. Method for automated tissue analysis
US8597899B2 (en) 2006-05-17 2013-12-03 Cernostics, Inc. Method for automated tissue analysis

Also Published As

Publication number Publication date
WO2000070528A2 (en) 2000-11-23
AU4847100A (en) 2000-12-05
WO2000070528A9 (en) 2001-11-29

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