Contents:

Innovations in Bioinformatics: Emerging tools for drug discovery and development 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) 68 Figure 2.5: miRBase Targets database, a new resource for predicting miRNA targets in animals 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

Companies Mentioned

- Accelrys Inc - Affymetrix Inc - Agilent Technologies Inc - Avalon Pharmaceuticals Inc - BG Medicine Incs - BioWisdom Ltd - Caliper Life Sciences Inc - Compugen Ltd - CuraGen Corporation - Entelos Inc - Genstruct Inc - Gene Network Scien ces Inc - GeneGo Inc - Health Discovery Corporation - Illumina Inc - Ingenuity Systems Incs - Insightful Corp - NextBio - SAS Institute Inc - Vermillion Inc