Protein networks: A basis for large-scale data mining

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MiTiN Consortium Meeting, Institute for Research in Biomedicine, Barcelona, Spain, March 9, 2010.

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  • Integration Automation Collaboration
  • Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome
  • Protein networks: A basis for large-scale data mining

    1. 1. Protein networks A basis for large-scale data mining Lars Juhl Jensen
    2. 6. Phase 1 association networks
    3. 7. who?
    4. 9. Frishman et al., Modern Genome Annotation , 2009
    5. 10. STRING
    6. 11. computational predictions
    7. 12. Korbel et al., Nature Biotechnology , 2004
    8. 13. experimental data
    9. 14. Jensen & Bork, Science , 2008
    10. 15. curated knowledge
    11. 16. Letunic & Bork, Trends in Biochemical Sciences , 2008
    12. 17. literature mining
    13. 19. confidence scores
    14. 20. cross-species transfer
    15. 21. Phase 2 signaling networks
    16. 22. what?
    17. 23. phosphoproteomics
    18. 25. signaling events
    19. 26. NetPhorest
    20. 27. automation
    21. 28. Miller, Jensen et al., Science Signaling , 2008
    22. 29. specificity atlas
    23. 31. NetworKIN
    24. 32. Linding, Jensen, Ostheimer et al., Cell , 2007
    25. 33. benchmarking
    26. 34. Linding, Jensen, Ostheimer et al., Cell , 2007
    27. 35. context is crucial
    28. 36. Phase 3 dynamic networks
    29. 37. when?
    30. 38. cell-cycle regulation
    31. 40. microarray time courses
    32. 41. Gauthier et al., Nucleic Acids Research , 2007
    33. 42. protein interactions
    34. 43. temporal network
    35. 44. de Lichtenberg, Jensen et al., Science , 2005
    36. 45. de Lichtenberg, Jensen et al., Science , 2005
    37. 46. just-in-time assembly
    38. 47. de Lichtenberg, Jensen et al., Cell Cycle , 2007
    39. 48. evolutionary flexibility
    40. 49. individual genes
    41. 50. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    42. 51. summary
    43. 52. networks
    44. 53. data integration
    45. 54. specific predictions
    46. 55. systems properties
    47. 57. Acknowledgments <ul><li>NetPhorest.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Martin Lee Miller </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Francesca Diella </li></ul></ul><ul><ul><li>Claus Jørgensen </li></ul></ul><ul><ul><li>Michele Tinti </li></ul></ul><ul><ul><li>Lei Li </li></ul></ul><ul><ul><li>Marilyn Hsiung </li></ul></ul><ul><ul><li>Sirlester A. Parker </li></ul></ul><ul><ul><li>Jennifer Bordeaux </li></ul></ul><ul><ul><li>Thomas Sicheritz-Pontén </li></ul></ul><ul><ul><li>Marina Olhovsky </li></ul></ul><ul><ul><li>Adrian Pasculescu </li></ul></ul><ul><ul><li>Jes Alexander </li></ul></ul><ul><ul><li>Stefan Knapp </li></ul></ul><ul><ul><li>Nikolaj Blom </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Shawn Li </li></ul></ul><ul><ul><li>Gianni Cesareni </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul><ul><ul><li>Benjamin E. Turk </li></ul></ul><ul><ul><li>Michael B. Yaffe </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><li>STRING-DB.org </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Chris Creevey </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Alexander Roth </li></ul></ul><ul><ul><li>Milan Simonovic </li></ul></ul><ul><ul><li>Jan Korbel </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Cyclebase.org </li></ul><ul><ul><li>Ulrik de Lichtenberg </li></ul></ul><ul><ul><li>Thomas Skøt Jensen </li></ul></ul><ul><ul><li>Nicholas Paul Gauthier </li></ul></ul><ul><ul><li>Rasmus Wernersson </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><li>NetworKIN.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Gerard Ostheimer </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Martin Lee Miller </li></ul></ul><ul><ul><li>Francesca Diella </li></ul></ul><ul><ul><li>Karen Colwill </li></ul></ul><ul><ul><li>Jing Jin </li></ul></ul><ul><ul><li>Pavel Metalnikov </li></ul></ul><ul><ul><li>Vivian Nguyen </li></ul></ul><ul><ul><li>Adrian Pasculescu </li></ul></ul><ul><ul><li>Jin Gyoon Park </li></ul></ul><ul><ul><li>Leona D. Samson </li></ul></ul><ul><ul><li>Rob Russell </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Michael Yaffe </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul>
    48. 58. larsjuhljensen

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