Innovations in Bioinformatics: Emerging tools for drug discovery and development

Table of Contents

Executive Summary

• Bioinformatics in the omics era
• Genomics and related ‘omics
• Proteomics
• Metabolomics and systems biology
• Knowledge management solutions
• Profiles of selected companies
• Trends and opportunities

Chapter 1 Bioinformatics in the omics era

• What is bioinformatics?
• End-users of bioinformatics tools and services
• Life sciences in the omics era
• Overview of omics
  • Genomics
  • Pharmacogenomics
  • Transcriptomics
  • Proteomics
  • Metabolomics
  • Other omics
• Background on drug discovery and development
• Types of drugs under development
  • Small molecules
  • Protein-based biotherapies
  • Nucleic acid-based biotherapies
• The drug discovery and development process
  • Stages (US)
  • Role of biomarkers
• Bioinformatics in drug discovery and development
• From biological data to drug knowledge

Chapter 2 Genomics and related omics

• Summary
• Background
• Categories of genomic analysis
• Sequencing
  • Next-generation sequencing
• Genotyping and gene expression
  • DNA microarrays
• Value of genomic analysis to the drug industry
• Bioinformatics solutions
• Analysis of sequencing data
  • Sequence databases
  • Sequence search tools
  • Multiple sequence alignment tools
  • Focus on RNAs
  • Genome finishing and annotating
  • Microarray platforms
  • Affymetrix
  • Illumina
  • Agilent Technologies
  • Applied Biosystems
• Genome-wide association studies
• Other advances

Chapter 3 Proteomics

• Summary
• Background
• Categories of proteomic analysis
• Protein separation
• Protein identification
  • Mass spectrometry
  • Protein microarrays
• Structure determination
• Value of proteomic analysis to the drug industry
• Bioinformatics solutions
• Analysis of sequencing data
  • Sequence databases
  • Sequence search tools
  • Multiple sequence alignment tools
• In silico drug discovery
• Data analysis and integration
  • Agilent Technologies
  • Applied Biosystems
  • BioWisdom
  • Bruker Daltonics
  • Geneva Bioinformatics
  • GeneLogics
  • Health Discovery Corporation
  • Nonlinear Dynamics
  • Sage-N Research
  • Thermo Scientific
  • Vermillion

Chapter 4 Metabolomics and Systems Biology

• Summary
• Background
• Metabolomics
• Introduction
• Value to the drug industry
• Commercial bioinformatics solutions
• Systems biology
• Introduction
• Value to the drug industry
  • Initiatives at Big Pharma
• Approaches
• In silico mathematical models
  • The Systems Biology Markup Language
• Publicly available modeling software
• Commercial pathway analysis tools
  • Ariadne Genomics
  • GeneGo
  • Ingenuity Systems
• Commercial modeling technologies
  • BG Medicine
  • Cellnomica
  • Compugen
  • CuraGen
  • Entelos
  • Genstruct
  • Genomatix
  • Genomatica
  • Gene Network Sciences
  • Health Discovery Corporation
  • Merrimack Pharmaceuticals

Chapter 5 Knowledge Management Solutions

• Summary
• Introduction
• Providers of high-performance computing
• Providers of storage systems
• Web-based solutions
• Ontologies
• Knowledge sharing
• The Semantic Web
• Software to support R&D labs
• Abrevity
• Accelrys
• Agilent Technologies
• BioWisdom
• CambridgeSoft
• Elsevier MDL
• Geospiza
• GeneLogics
• IO Informatics
• KOOPrime
• LabVantage
• MathWorks
• NextBio
• Oracle
• SAS
• Symyx
• Teranode
• Thermo Fisher Scientific
• Text searching and mining
• QUOSA
• Linguamatics
• Inforsense
• Insightful
• Nervana
• Velocity
• Clinical trials solutions
• Adobe Systems
• Infosys
• Oracle
• Pharsight

Chapter 6 Profiles of selected companies

• Summary
• Accelrys Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Affymetrix Inc
• Company overview
• Bioinformatics tools and services
• Agilent Technologies Inc
• Company overview
• Bioinformatics tools and services
• Avalon Pharmaceuticals Inc
• Company overview
• Bioinformatics-related collaborations
• BG Medicine Inc
• Company overview
• Bioinformatics tools and services
• BioWisdom Ltd
• Company overview
• Bioinformatics tools and services
• Caliper Life Sciences Inc
• Company overview
• Bioinformatics tools and services
• Compugen Ltd
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• CuraGen Corporation
• Company overview
• Bioinformatics tools and services
• Entelos Inc
• Company overview
• Bioinformatics tools and services
• Genstruct Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Gene Network Sciences Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• GeneGo Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Health Discovery Corporation
• Company overview
• Bioinformatics tools and services
• Illumina Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Ingenuity Systems Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Insightful Corp
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• NextBio
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• SAS Institute Inc
• Company overview
• Bioinformatics tools and services
• Bioinformatics-related collaborations
• Vermillion Inc
• Company overview
• Bioinformatics tools and services

Chapter 7 Trends and opportunities

• Summary
• End-user needs and sentiment
• Emerging trends in market evolution
• Bioinformatics-enabled biomarker discovery
• The promise of Semantic Web technology
• Facilitating implementation of IT systems
• Market snapshot and forecasts
• Genomics and related omics
• Proteomics
• Systems biology
• Life science enterprise knowledge management
• Market estimates

Chapter 8 Appendix

• Research methodology
• Index

List of Figures

• Figure 2.1: An entry from Entrez GENE, the US NCBI' s web-based interface to GENBANK
• Figure 2.2: Genomic context of the myostatin gene (GDF8) using the NCBI Map Viewer
• Figure 2.3: Search page of microInspector
• Figure 2.4: Search page of the miRNA database (miRBase)
• Figure 2.5: miRBase Targets database, a new resource for predicting miRNA targets in animals69
• Figure 2.6: Predicted Human Genomic Targets for the hsa-let-7g* miRNA
• Figure 2.7: Dharmacon siRNA Designer Search Page
• Figure 3.8: Advanced Search page of the Protein Data Bank (PDB), the central repository for 3D protein structure information
• Figure 3.9: PDB Entry for the complex of the acetylcholine receptor with carbamylcholine (1UV6)
• Figure 3.10: Results of a search in the UniProt KnowledgeBase (Swiss-PROT and TrEMBL) for MAP kinase phosphatases
• Figure 3.11: Partial UniProt record for Dual Specificity Protein Phosphatase 4 (DUSP4) / MAP Kinase Phosphatase 2
• Figure 3.12: UniProt Feature Aligner for Dual Specificity Protein Phosphatase 4 (DUSP4)
• Figure 3.13: UniProt sequences at least 90% similar to Dual Specificity Protein Phosphatase 4 (DUSP4)
• Figure 3.14: Front page of the Protein Kinase Resource, University of California at San Diego
• Figure 3.15: UniProt sequences at least 90% similar to Dual Specificity Protein Phosphatase 4 (DUSP4)
• Figure 4.16: Genomatica' s SimPheny™ Systems Biology Model Development Process

List of Tables

• Table 2.1: Bioinformatic Analyses of DNA/RNA Sequences
• Table 2.2: Contribution of Bioinformatics to Genomics-Based Drug Discovery
• Table 2.3: Databases and On-line Tools for Analyzing DNA Sequences and Signals
• Table 2.4: Leading Sequence Comparison Servers
• Table 2.5: BLAST Applications and Flavors
• Table 2.6: Online Pairwise Alignment Programs
• Table 2.7: Multiple Sequence Alignment Tools
• Table 2.8: RNA Secondary Structure Prediction
• Table 2.9: miRNA and siRNA Resources
• Table 2.10: Selected genome-sequencing packages
• Table 2.11: Phylogeny and Orthology
• Table 2.12: Summary of patent-related genes in the major organisms
• Table 3.13: Role of Bioinformatics in Protein Diagnostics and Therapeutics
• Table 3.14: Selected Protein Databases
• Table 3.15: On-line tools to test for protein transmembrane segments
• Table 3.16: Principal Protein Domain Recognition Resources
• Table 3.17: Protein Structure Prediction
• Table 4.18: Software for Systems Biology
• Table 7.19: World Bioinformatics Market, 2006-2011