TABLE OF CONTENTS
Chapter 1: Executive Summary
Chapter 2: Definitions and Models
- Metabolomics and Metabonomics
- Metabonome Provides Real-World Information about Drug Toxicity, Gene Function, and Homeostasis
- The Metabolome
- Utility of the Metabolome and Metabolic Toxicology in Drug Discovery
- Beyond the Genome and the Proteome
- Metabonomic Intervention in the Drug Development Pipeline
- Glucoronidation and Metabonates
- The Complexity of Metabolome
- Metabolomics and Plants
- Metabonomics Needs Biologists, Computer Scientists, Chemists, Engineers, Mathematicians, and Physicists
- Systems Biology
- Metabolic Control Analysis (MCA)
- Historical Genesis of MCA
- Biochemical Considerations
- Mammal-Microbe-Xenobiotic Systems Interactions
- Gut Metabolic System
- Pattern Recognition Methodologies
- Global Metabolomic Analysis-Metabolomic Vector Analysis
- Predictive and Preventive Medicine
- Related "Omic" Disciplines and Drug Discovery Platforms
- Genomics and Transcriptomics
- Lipomics and Glycomics .
- The Immunome
- References
Chapter 3: Bioinformatics-Databases and Software .
- Databases for Metabolic Pathway Analysis
- Introduction to Pathway Analysis
- Bibliome
- Data Mining
- Information Technology in Life Sciences
- Bioinformatics in Molecular R&D
- Predicting Gene Function and Structure
- DNA Technologies
- Intranet and Internet
- Gene Mapping and Genome Sequencing
- Automation and Computerization of Biotech Research
- Algorithms
- Chemometrics
- University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
- Leading Database Resources
- PathDB Depiction
- Selective Target Evaluation in Microbes (STEM.)
- PseudoCyc, a Pathway/Genome Database for Pseudomonas Aeruginosa
- and MetaCyc Database
- Biomolecular Interaction Network Database (BIND)
- 123genomics
- GGOBI
- Plant Systems
- Platform Plant Metabolomics (PPM)
- Arabidopsis
- Medicago Trunculata
- International Rice Research Institute (IRRI)
- Natural Product Analysis
- Max Planck Institute (MPI) for Molecular Plant Physiology
- Databases Associated with Genomics and Proteomics
- National Center for Biological Information (NCBI)
- Databases and Software
- NCBI s Nucleotide and Genomic Database
- European Bioinformatics Institute, and the Wellcome Trust Genome
- ExPASy Molecular Biology Server
- Boehringer Mannheim Biochemical Pathways
- Biocarta s Proteomic Pathway Project
- Structural Classification of Proteins (SCOP)
- Protein Function and Biochemical Pathways (PFBP) Project
- BRENDA
- Software for Metabolic Pathway Analysis .
- Computer Simulation of Metabolism
- Compound, Organism, Reaction and Enzyme (CORE)
- Artificial Neural Nets (ANN)
- Quantification of Biotechnological Systems
- The GO Consortium
- FlyBase
- CellML and E-Cell.
- E-Cell Project .
- References
- On the representation of gene function in genetic databases.
Chapter 4: Techniques in Metabolomics and Metabonomics
- Analytical Techniques
- Overview of Spectroscopic Techniques
- Mass Spectrometry (MS)
- FTIR Spectroscopy
- Diffuse Reflectance-Absorbance FT-IR
- Dispersive Raman Spectroscopy
- Atomic Absorption Spectrophotometry
- Pyrolysis Mass Spectrometry
- Combination Strategies Including: GC/MS, FTIR-MS, Liquid Chromatography (LC)/MS, and LC/MS/MS
- Evaluation of Glycosylation Sites by MS/MS
- MS/MS Analysis Used For Flavonoid Identification and Determination .
- High Throughput Screening (HTS) LC-MS
- Analysis of Fingerprinting Methods
- Use of NMR in Biomedicine
- LC/NMR
- Gas Chromatography (GC)
- High Performance Liquid Chromatography (HPLC) .
- Lab-on-a-Chip
- Capillary Electrophoresis (CE)/MS of Plants
- Recent Examples of Drug Enantioseparations by Chiral CE
- Conclusions Technological overview of Spectroscopic Methodologies
Chapter 5: Metabolomics and Metabonomics: Markets, Applications, and Current Research .
- Market Value
- Innovative Enhancements to the MS Technologies
- 2D Gels
- Mass Spectroscopy
- SWOT Analysis for Metabolomic Technologies
- Applications and Research
- Main Metabolomic and Metabonomic Application Categories
- Unifying Research in Genomics and Proteomics
- Drug Discovery and Development
- Genomics to Metabolomics
- Metabolite Profiling Defines Metabotypes
- Bioarray Innovations
- Integrated Genomics
- Third Generation Proteomics
- Target Identification and Diagnostic Biomarkers
- Clinical End Point and Presence of Biomarker
- Target Validation .
- Lead Prioritization
- Preclinical and Clinical Studies
- Metabolomic Analyses to Assist With Toxicity Profiles
- Personalized Medicine and Nutrition
- Current Research on Pathway Analysis .
- Future Directions.
Chapter 6: Company Profiles
- Taxicogenomics-Icora (formerly Paradigm Genetics), Morphochem Inc
- Chemogenomics-Acadia Pharmaceuticals, Amorpha Discovery Corp, Neogenesis Pharmaceuticals, Vertex Pharmaceuticals
- Ribonomics-Biolog, Intradigm Corp., Ribonomics Inc, Sequitur .
- Phenomics-Mitokor Inc, Cellular Genomics Inc, Phenomenome Discoveries Inc, Organon
- Target Identification-Metabolon Inc, High Chem Ltd., Metabometrix, GeneGo
- COMET Network, Vion Pharmaceuticals, Pfizer
- PhysioLab Entelos
- Acadia Pharmaceuticals
- Accelyrs Inc
- Agilent Technologies, Inc
- Bruker BioSciences Corp.
- Caliper Life Sciences
- Icoria, Inc. (Paradigm Genetics)
- Sequenom
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