Large-scale data and text mining

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Hagedorn Research Institute, Gentofte, Denmark, October 8, 2009.

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Large-scale data and text mining

  1. 1. Large-scale data and text mining Lars Juhl Jensen
  2. 4. function prediction
  3. 5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
  4. 8. cell-cycle regulation
  5. 9. de Lichtenberg, Jensen et al., Science , 2005
  6. 10. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  7. 11. phosphorylation
  8. 13. signaling networks
  9. 14. upstream events
  10. 15. downstream events
  11. 16. NetworKIN
  12. 18. sequence motifs
  13. 19. NetPhorest
  14. 20. automated pipeline
  15. 21. Miller, Jensen et al., Science Signaling , 2008
  16. 22. data organization
  17. 23. Miller, Jensen et al., Science Signaling , 2008
  18. 24. compilation of datasets
  19. 25. redundancy reduction
  20. 26. training and evaluation
  21. 27. motif atlas
  22. 29. model organisms
  23. 30. other modifications
  24. 31. protein networks
  25. 32. functional associations
  26. 34. STRING
  27. 35. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  28. 36. 630 genomes
  29. 37. genomic context
  30. 38. Korbel et al., Nature Biotechnology , 2004
  31. 39. Korbel et al., Nature Biotechnology , 2004
  32. 40. Korbel et al., Nature Biotechnology , 2004
  33. 41. physical interactions
  34. 42. Jensen & Bork, Science , 2008
  35. 43. genetic interactions
  36. 44. Beyer et al., Nature Reviews Genetics , 2007
  37. 45. gene coexpression
  38. 47. curated knowledge
  39. 48. Letunic & Bork, Trends in Biochemical Sciences , 2008
  40. 49. literature mining
  41. 50. >10 km
  42. 52. confidence scores
  43. 53. cross-species integration
  44. 54. visualization
  45. 55. Frishman et al., Modern Genome Annotation , 2009
  46. 56. small molecules
  47. 57. STITCH
  48. 58. Kuhn et al., Nucleic Acids Research , 2008
  49. 59. kinase inhibitor screens
  50. 60. Fedorov et al., PNAS , 2007
  51. 61. new targets for old drugs
  52. 62. chemical similarity
  53. 63. Campillos & Kuhn et al., Science , 2008
  54. 64. side-effect similarity
  55. 65. information on side effects
  56. 66. package inserts
  57. 67. Campillos, Kuhn et al., Science , 2008
  58. 68. text mining
  59. 69. side-effect ontology
  60. 70. Campillos, Kuhn et al., Science , 2008
  61. 71. side-effect correlations
  62. 72. Campillos, Kuhn et al., Science , 2008
  63. 73. side-effect frequencies
  64. 74. Campillos & Kuhn et al., Science , 2008
  65. 75. combined similarity score
  66. 76. Campillos, Kuhn et al., Science , 2008
  67. 77. thousands of predictions
  68. 78. categorization
  69. 79. Campillos, Kuhn et al., Science , 2008
  70. 80. 20 drug–drug relations
  71. 81. Campillos, Kuhn et al., Science , 2008
  72. 82. in vitro binding assays
  73. 83. K i <10 µM for 11 of 20
  74. 84. cell assays
  75. 85. 9 of 9 showed activity
  76. 86. augmented browsing
  77. 87. Reflect
  78. 89. collaborate publishers
  79. 91. 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>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><ul><li>STITCH-DB.org </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Damian Szklarczyk </li></ul></ul><ul><ul><li>Andrea Franceschini </li></ul></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Lars Juhl Jensen </li></ul></ul><ul><ul><li>Andreas Beyer </li></ul></ul><ul><ul><li>Peer Bork </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><ul><ul><li>Reflect.ws </li></ul></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Nigel Brown </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul>
  80. 92. larsjuhljensen

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