| Preface | 7 |
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| Acknowledgements | 11 |
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| Contents | 13 |
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| Introduction | 27 |
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| Introduction | 27 |
| Bioinformatics | 28 |
| Systems Biology | 33 |
| Research Areas for Analysis | 39 |
| Collaborative Research | 40 |
| European Commission Research Projects | 43 |
| A Practical Guide to Project Websites, Participants, Coordinators, Publications | 44 |
| Key Sources | 47 |
| Part I Fundamental Collaborative Research and Computational Biology | 49 |
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| Bioinformatics | 51 |
| Introduction | 51 |
| Genome Annotation | 52 |
| Bioinformatics Tools For Annotation | 58 |
| Gene Definition/Alternative Transcripts and Splicing | 63 |
| Gene Regulation and Expression | 65 |
| Functional Annotation of Proteins | 68 |
| Post-translation Modification, Membrane and Localisation Prediction | 70 |
| Protein Complexes, Networks and Pathways | 73 |
| Encyclopaedia of DNA Elements | 75 |
| Systems Biology | 79 |
| Introduction | 79 |
| Cell Cycle | 80 |
| P53 | 84 |
| Spindle Formation and Imaging | 86 |
| Signalling and Control | 88 |
| Metabolic Regulation | 93 |
| Circadian Clock | 96 |
| Multiple Pathway Integration | 97 |
| Cellular Systems Biology | 100 |
| Local and Worldwide Scientific Collaboration | 101 |
| A Major FP7 Initiative in Systems Biology | 104 |
| Developmental Biology and Ageing | 111 |
| Introduction | 111 |
| Plant Development | 112 |
| Stem Cells and Development | 116 |
| Mitochondria and Ageing | 117 |
| Nuclear Receptors and Ageing | 119 |
| Implementation in the Seventh Framework Programme | 120 |
| Part II Resources Supporting Bioinformatics and Systems Biology Research | 123 |
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| Databases, Computational Tools and Services | 125 |
| Introduction | 125 |
| Major Gateway to Collaborative Research | 126 |
| Distributed Development of Resources | 129 |
| Distributed Annotation System | 131 |
| Database Grid Integration | 132 |
| Ontologies | 139 |
| Text Mining | 140 |
| Systems Biology Toolboxes | 141 |
| Supporting Infrastructures | 149 |
| Introduction | 149 |
| Wet-Laboratory Research Infrastructures | 150 |
| Research Infrastructures: Future Priorities | 155 |
| Medical Information Systems | 158 |
| Knowledge Management Systems | 158 |
| Education | 160 |
| Part III Disease-Related Collaborative Research and Computational Biology | 163 |
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| Infectious and Major Diseases | 165 |
| Introduction | 165 |
| Viral Pathogens | 168 |
| Bacterial Pathogens | 170 |
| Cardiovascular–Pulmonary Diseases and Diabetes | 173 |
| Neurological Diseases | 176 |
| Immunology | 179 |
| Drug Development | 179 |
| Implementation in the Seventh Framework Programme | 188 |
| Cancer | 191 |
| Introduction | 191 |
| Nature of Cancer and Biology and Genetics of Cells and Organisms | 194 |
| Tumour Viruses | 195 |
| Cellular Oncogenes | 196 |
| Growth Factors and Their Receptors | 199 |
| Cytoplasmic Signalling Circuitry | 199 |
| Cell Cycle | 200 |
| Tumour Suppressor Genes | 201 |
| p53 and Apoptosis | 202 |
| Cell Immortalisation, Tumourigenesis and Senescence | 205 |
| Multistep Tumourigenesis | 206 |
| Genomic Integrity and the Development of Cancer | 207 |
| Angiogenesis and Lymphangiogenesis | 207 |
| Metastasis | 209 |
| Tumour Immunology and Immunotherapy | 210 |
| Implementation in the Seventh Framework Programme | 210 |
| Genetic Variation and Diseases | 213 |
| Introduction | 213 |
| Genetic Variation Workshop | 214 |
| Status of Genetic Variation Research | 215 |
| Genotype to Phenotype | 217 |
| Data and Analysis Challenges | 218 |
| Databases | 221 |
| Data Generation | 225 |
| The Way Forward | 227 |
| Research in the Fifth Framework Programme and the Sixth Framework Programme | 229 |
| A Major Seventh Framework Programme Initiative in Genetic Variation | 233 |
| Part IV Science Management, Perspectives and Conclusions | 239 |
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| Science Management | 241 |
| Introduction | 241 |
| How To Participate and Develop Proposals | 246 |
| Evaluation of Proposals | 254 |
| Project Negotiation | 257 |
| Operating Project Attributes and its Management | 261 |
| Contractual and Financial Obligations | 264 |
| Information Dissemination | 265 |
| IPR and Exploitation | 266 |
| Perspectives | 271 |
| Introduction | 271 |
| Bioinformatics | 272 |
| Systems Biology | 274 |
| Disease | 277 |
| Seventh Framework Programme | 279 |
| Longer Term | 280 |
| Outstanding Results and Conclusions | 281 |
| Introduction | 281 |
| Outstanding Resources Created | 282 |
| Outstanding Scientific Results | 284 |
| Overall Conclusions | 287 |
| References | 289 |
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| Index | 307 |