Abstract: The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational skeletons for integrating various types of high-throughput data. The present invention provides the first metabolic reconstruction study of a eukaryotic organism based solely on expressed sequence tag (EST) data. System Reconstruction also provides a method for the identification of novel therapeutic targets and biomarkers using network analysis. The initial seed networks are built from the lists of novel targets for diseases with the high-throughput experimental data being superimposed on the seed networks to identify specific targets.
Type:
Application
Filed:
August 6, 2015
Publication date:
November 26, 2015
Applicant:
GENEGO, INC.
Inventors:
Tatiana NIKOLSKAYA, Andrej BUGRIM, Yuri NIKOLSKY
Abstract: A system is provided for the prediction of human drug metabolism and toxicity of novel compounds. The system enables the visualization of pre-clinical and clinical high-throughput data in the context of a complete biological organism. Substructure and similarity structure searches can be performed using the underlying databases of xenobiotics, active ligands, and endobiotics. The system also has an analytical component for the parsing, integration, and network analysis of genomics, proteomics, and metabolomics high-throughput data. From this information, the system further generates networks around proteins, genes and compounds to assess toxicity and drug-drug interactions.
Type:
Application
Filed:
March 28, 2011
Publication date:
February 2, 2012
Applicant:
GeneGo, Inc.
Inventors:
Sean Ekins, Andrej Bugrim, Tatiana Nikolskaya, Yuri Nikolsky
Abstract: The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational “skeletons” for integrating various types of “high throughput” data. The present invention provides the first metabolic reconstruction study of a eukaryotic organism based solely on expressed sequence tag (EST) data.
Type:
Grant
Filed:
June 18, 2002
Date of Patent:
August 30, 2011
Assignee:
Genego, Inc.
Inventors:
Tatiana Nikolskaya, Andrej Bugrim, Aleksander Markov, Evgeny Kirtlov, Igor Gariev
Abstract: The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational “skeletons” for integrating various types of “high throughput” data.
Type:
Grant
Filed:
June 18, 2003
Date of Patent:
August 16, 2011
Assignee:
Genego, Inc.
Inventors:
Andrej Bugrim, Tatiana Nikolskaya, Aleksander Markov
Abstract: The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational skeletons for integrating various types of high-throughput data. The present invention provides the first metabolic reconstruction study of a eukaryotic organism based solely on expressed sequence tag (EST) data. System Reconstruction also provides a method for the identification of novel therapeutic targets and biomarkers using network analysis. The initial seed networks are built from the lists of novel targets for diseases with the high-throughput experimental data being superimposed on the seed networks to identify specific targets.
Type:
Grant
Filed:
August 4, 2006
Date of Patent:
August 16, 2011
Assignee:
Genego, Inc.
Inventors:
Tatiana Nikolskaya, Andrej Bugrim, Yuri Nikolsky