Bioinformatics of cellular processes

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EMBO Practical Course on Methods in Cell Biology: Exploring the Dynamics of Cellular Organization, European Molecular Biology Laboratory, Heidelberg, Germany, August 23-31, 2007

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Bioinformatics of cellular processes

  1. 1. Bioinformatics of cellular processes Protein networks, signaling and regulation Lars Juhl Jensen EMBL Heidelberg
  2. 2. functional networks
  3. 3. data integration
  4. 4. protein interactions
  5. 6. genetic interactions
  6. 8. gene coexpression
  7. 10. genomic context methods
  8. 11. gene neighborhood
  9. 13. gene fusion
  10. 15. phylogenetic profiles
  11. 17. literature mining
  12. 19. curated knowledge
  13. 21. variable quality
  14. 22. benchmarking
  15. 24. probabilistic network
  16. 26. signaling networks
  17. 27. phosphoproteomics
  18. 29. in vivo phosphosites
  19. 30. kinases are unknown
  20. 31. computational methods
  21. 33. overprediction
  22. 34. context
  23. 35. scaffolders
  24. 36. interaction networks
  25. 38. NetworKIN
  26. 41. benchmarking
  27. 43. DNA damage response
  28. 45. experimental validation
  29. 46. dynamic networks
  30. 47. the cell cycle
  31. 49. microarrays
  32. 51. expression profiles
  33. 53. cell-cycle-regulated genes
  34. 54. protein interactions
  35. 56. temporal network
  36. 58. global observations
  37. 59. dynamic and static subunits
  38. 61. consistent timing
  39. 63. phosphorylation by CDK
  40. 64. 27% of dynamic proteins
  41. 65. 8% of static proteins
  42. 66. targeted degradation
  43. 67. 44% of dynamic proteins
  44. 68. 29% of static proteins
  45. 69. just-in-time assembly
  46. 71. summary
  47. 72. networks
  48. 73. data integration
  49. 74. highly specific predictions
  50. 75. new biological principles
  51. 76. Acknowledgments <ul><li>The STRING database </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Sean Hooper </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Julien Lagarde </li></ul></ul><ul><ul><li>Mathilde Foglierini </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Cell-cycle regulation </li></ul><ul><ul><li>Ulrik de Lichtenberg </li></ul></ul><ul><ul><li>Thomas Skøt Jensen </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>The NetworKIN method </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Gerard Ostheimer </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>

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