Market Report Source

Overview

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.

Key findings from this report:

• The bioinformatics market is forecast to grow at a CAGR of 23% to $4.5bn by 2011, from a value of $1.6bn in 2006. The US led the geographical market with a share of 45% in 2006, but Europe’s CAGR of 24.6% will narrow the gap over the forecast period.
• Bioinformatics-enabled protein biomarker discovery will enable the development of safer and more effective drugs, targeted therapies and molecular diagnostics.
• Systems biology modelling is forecast to grow at a rate of 35% over the next five years, the highest growth of any bioinformatics sector. The potential for widespread integration throughout all stages of drug discovery will act as a catalyst for this expansion.
• Knowledge management is currently the leading bioinformatics market segment. This lead will be strengthened by mass adoption of Semantic Web technology and the increasing availability of software through the internet.
• Software for next-generation sequencing has vastly reduced time and cost constraints of DNA-sequencing. The miniaturization of reactions has increased their quality and density, subsequently lowering per-reaction costs.

Key issues examined by this report:

• R&D improvements. Emerging bioinformatics tools that promise to improve productivity in drug R&D are creating new opportunities for pharma companies, as pressure from declining pipelines and patent protection expiries continues to mount.
• Data efficiencies. Bioinformatics solutions enable users to manage and interpret research data far more effectively than by attempting to traverse the deluge of heterogeneous data provided by omics technologies.
• Compound failures. The use of bioinformatics tools can help to detect potential toxicity earlier in the drug discovery and development process, drastically reducing toxicity and safety related compound failures during full clinical development.
• Impact of biomarkers. The utility of bioinformatics in biomarker discovery and validation has made them integral to the new, cost effective model of drug discovery and development which emphasises the use of biomarkers throughout the process.
• Internet dominance. As growing numbers of knowledge management solutions leverage open web standards, the internet is set to become the dominant bioinformatics platform and broad adoption of Semantic Web technology is anticipated.

Key questions answered:

• What are the major segments of the bioinformatics market?
• How can bioinformatics tools be used in genomics/proteomics?
• How is enterprise knowledge managed and how are the contributions of modelling providers changing?
• What are the services and strategies of key companies in the fields of knowledge management, systems biology and high-throughput genotyping?
• Which segments are forecast to dominate the bioinformatics market in 2011?
• How are these dominant segments likely to evolve?

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
Physiomics

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 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) 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 (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 (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