Mining and communicating biomedical knowledge

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Mining and communicating biomedical knowledge

  1. 1. Mining and communicating biomedical knowledge Lars Juhl Jensen
  2. 2. Part 1 complex regulation
  3. 3. cell-cycle regulation
  4. 5. microarrays
  5. 7. time courses
  6. 8. Gauthier et al., Nucleic Acids Research , 2007
  7. 9. protein interactions
  8. 10. Jensen & Bork, Science , 2008
  9. 11. temporal network
  10. 12. de Lichtenberg, Jensen et al., Science , 2005
  11. 13. just-in-time assembly
  12. 14. de Lichtenberg, Jensen et al., Cell Cycle , 2007
  13. 15. evolutionary flexibility
  14. 16. individual genes
  15. 17. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  16. 18. protein complexes
  17. 19. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  18. 20. just-in-time assembly
  19. 21. Part 2 buried knowledge
  20. 22. exponential growth
  21. 25. some things are constant
  22. 27. ~45 seconds per paper
  23. 28. computer
  24. 29. as smart as a dog
  25. 30. teach it specific tricks
  26. 33. named entity recognition
  27. 34. new uses for old drugs
  28. 35. Campillos & Kuhn et al., Science , 2008
  29. 36. augmented browsing
  30. 37. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  31. 38. semantic indexing
  32. 39. >10 km <10 hours
  33. 41. Part 3 science communication
  34. 42. ~150 years ago
  35. 44. today
  36. 46. incremental evolution
  37. 47. historical baggage
  38. 51. subscription charges
  39. 52. space restrictions
  40. 53. issues
  41. 54. editorial filtering
  42. 55. pre-publication peer review
  43. 56. the world has changed
  44. 58. internet economy
  45. 60. publishing is changing
  46. 61. open access
  47. 62. free to download
  48. 63. free to reuse
  49. 64. same publication process
  50. 66. publish first
  51. 68. filter later
  52. 70. post-publication peer review
  53. 71. conference reporting
  54. 72. Brumfiel, Nature , 2009
  55. 73. Saunders et al., PLoS Computational Biology , 2009
  56. 75. Thanks <ul><li>Past and present colleagues at </li></ul><ul><ul><li>Center for Biological Sequence Analysis </li></ul></ul><ul><ul><li>European Molecular Biology Laboratory </li></ul></ul><ul><ul><li>Novo Nordisk Foundation Center for Protein Research </li></ul></ul><ul><li>The bloggers who made it happen at ISMB </li></ul><ul><li>The Lundbeck Foundation </li></ul><ul><li>All of you who are here today! </li></ul>

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