Modern Genome Annotation

The BioSapiens Network

  • Dmitrij Frishman
  • Alfonso Valencia

Table of contents

  1. Front Matter
    Pages I-XVIII
  2. Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources

  3. Gene definition

    1. Front Matter
      Pages 5-5
    2. T. Alioto, R. Guigó
      Pages 7-39
    3. A. Nagy, H. Hegyi, K. Farkas, H. Tordai, E. Kozma, L. Bányai et al.
      Pages 41-52
  4. Gene regulation and expression

    1. Front Matter
      Pages 53-53
    2. O. Sand, J.-V. Turatsinze, J. van Helden
      Pages 55-89
    3. T. Manke, H. Roider, M. Vingron
      Pages 91-103
    4. R. Coulson, T. Manke, K. Palin, H. Roider, O. Sand, J. van Helden et al.
      Pages 105-119
  5. Annotation and genetics

    1. Front Matter
      Pages 121-121
  6. Functional annotation of proteins

    1. Front Matter
      Pages 137-137
    2. A. J. Bridge, A.-Lise Veuthey, N. J. Mulder
      Pages 139-164
    3. C. Médigue, A. Danchin
      Pages 165-190
    4. I. Artamonova, S. Kramer, D. Frishman
      Pages 191-212
    5. C. Yeats, Ch. Orengo, A. Lise Veuthey, B. Boeckmann, L. Juhl Jensen, A. Valencia et al.
      Pages 213-238
    6. J. D. Watson, J. M. Thornton, M. L. Tress, G. Lopez, A. Valencia, O. Redfern et al.
      Pages 239-262
    7. B. Vroling, G. Vriend
      Pages 263-279
  7. Protein structure prediction

    1. Front Matter
      Pages 281-281
    2. A. Tramontano, D. Jones, L. Rychlewski, R. Casadio, P. Martelli, D. Raimondo et al.
      Pages 283-307
    3. R. Casadio, P. Fariselli, P. L. Martelli, A. Pierleoni, I. Rossi, G. von Heijne
      Pages 309-326
  8. Protein-protein complexes, pathways and networks

    1. Front Matter
      Pages 327-327
    2. P.-Y. Bourguignon, J. van Helden, C. Ouzounis, V. Schächter
      Pages 329-351
    3. D. Frishman, M. Albrecht, H. Blankenburg, P. Bork, E. D. Harrington, H. Hermjakob et al.
      Pages 353-410
  9. Infrastructure for distributed protein annotation

    1. Front Matter
      Pages 411-411
    2. G. A. Reeves, A. Prlic, R. C. Jimenez, E. Kulesha, H. Hermjakob
      Pages 413-426
  10. Applications

    1. Front Matter
      Pages 427-427
    2. B. Adams, A. Carolyn McHardy, C. Lundegaard, T. Lengauer
      Pages 429-452
    3. M. L. Tress, R. Casadio, A. Giorgetti, P. F. Hallin, A. S. Juncker, E. Kulberkyte et al.
      Pages 453-484
  11. Back Matter
    Pages 485-490

About this book


An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry.

Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.


Annotation ENCODE biochemistry bioinformatics biology data mining development genes genetics genome molecular biology protein protein complexes protein structure protein structure prediction

Editors and affiliations

  • Dmitrij Frishman
    • 1
  • Alfonso Valencia
    • 2
  1. 1.Wissenschaftszentrum WeihenstephanTU MünchenFreisingGermany
  2. 2.Structural and Computational ProgrammeSpanish National Cancer Research CentreMadridSpain

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