Abstract
R&D laboratories are co-ordinating the analysis of increasing volumes of disparate biological data, largely comprised of gene and protein sequences. Bioinformatics-enabled data management has enabled companies to improve productivity within their R&D programmes by identifying new drug targets, diagnostic biomarkers and biomarkers of drug efficacy and toxicity. From a systems biology approach, bioinformatics combine data into interactive models to highlight disease pathways and aid the discovery of on off-target effects of compounds. Knowledge management solutions are crucial in both instances, enabling project teams to make informed decisions about potential new drugs. ‘Innovations in Bioinformatics’ is a new report published by Business Insights that provides a detailed analysis of bioinformatic developments and applications. This report examines the bioinformatic tools used to manage high-throughput data from omic technologies, systems biology modelling and biomarker discovery. Knowledge management solutions are reviewed and the provisions of major bioinformatics contributors are highlighted. This report also provides forecasts for bioinformatic tools and services to 2011. Use this new report to identify the latest developments in bioinformatics, assess the tools and platforms that can improve drug developments and benchmark effective implementation strategies.
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
