Network biology - A basis for large-scale biomedica data mining

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  • Integration Automation Collaboration
  • Network biology - A basis for large-scale biomedica data mining

    1. 1. Network biology A basis for large-scale biomedical data mining Lars Juhl Jensen
    2. 4. sequence analysis
    3. 5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
    4. 8. data mining
    5. 9. de Lichtenberg, Jensen et al., Science , 2005
    6. 13. data mining
    7. 14. text mining
    8. 15. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    9. 16. signaling networks
    10. 17. phosphoproteomics
    11. 18. Linding, Jensen, Ostheimer et al., Cell , 2007
    12. 19. in vivo phosphosites
    13. 20. kinases are unknown
    14. 21. sequence motifs
    15. 22. Miller, Jensen et al., Science Signaling , 2008
    16. 23. NetPhorest
    17. 24. data organization
    18. 25. Miller, Jensen et al., Science Signaling , 2008
    19. 26. automated pipeline
    20. 27. Miller, Jensen et al., Science Signaling , 2008
    21. 28. motif atlas
    22. 29. sequence specificity
    23. 30. no context
    24. 31. network context
    25. 32. Linding, Jensen, Ostheimer et al., Cell , 2007
    26. 33. guilt by association
    27. 35. STRING
    28. 36. 630 genomes
    29. 37. computational predictions
    30. 38. gene fusion
    31. 39. Korbel et al., Nature Biotechnology , 2004
    32. 40. experimental data
    33. 41. physical interactions
    34. 42. Jensen & Bork, Science , 2008
    35. 43. gene coexpression
    36. 45. curated knowledge
    37. 46. Letunic & Bork, Trends in Biochemical Sciences , 2008
    38. 47. >10 km
    39. 48. literature mining
    40. 49. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    41. 50. not comparable
    42. 51. confidence scores
    43. 52. von Mering et al., Nucleic Acids Research , 2005
    44. 53. cross-species integration
    45. 54. von Mering et al., Nucleic Acids Research , 2005
    46. 55. association network
    47. 56. Linding, Jensen, Ostheimer et al., Cell , 2007
    48. 57. integrate with motifs
    49. 58. NetworKIN
    50. 59. Linding, Jensen, Ostheimer et al., Cell , 2007
    51. 60. >2x better accuracy
    52. 61. drug repositioning
    53. 62. new uses for old drugs
    54. 63. drug–drug network
    55. 64. shared target(s)
    56. 65. chemical similarity
    57. 66. Campillos & Kuhn et al., Science , 2008
    58. 67. similar drugs share targets
    59. 68. Campillos & Kuhn et al., Science , 2008
    60. 69. only trivial predictions
    61. 70. phenotypic similarity
    62. 71. chemical perturbations
    63. 72. phenotypic readouts
    64. 73. drug treatment
    65. 74. side effects
    66. 75. no database
    67. 76. package inserts
    68. 77. Campillos & Kuhn et al., Science , 2008
    69. 78. text mining
    70. 79. side-effect ontology
    71. 80. Campillos & Kuhn et al., Science , 2008
    72. 81. manual validation
    73. 82. SIDER Kuhn et al., Molecular Systems Biology , 2010
    74. 83. side-effect correlations
    75. 84. Campillos & Kuhn et al., Science , 2008
    76. 85. GSC weighting
    77. 86. side-effect frequencies
    78. 87. Campillos & Kuhn et al., Science , 2008
    79. 88. raw similarity score
    80. 89. Campillos & Kuhn et al., Science , 2008
    81. 90. p-values
    82. 91. Campillos & Kuhn et al., Science , 2008
    83. 92. side-effect similarity
    84. 93. chemical similarity
    85. 94. Campillos & Kuhn et al., Science , 2008
    86. 95. confidence scores
    87. 96. drug–drug network
    88. 97. Campillos & Kuhn et al., Science , 2008
    89. 98. categorization
    90. 99. Campillos & Kuhn et al., Science , 2008
    91. 100. experimental validation
    92. 101. 20 drug–drug pairs
    93. 102. in vitro binding assays
    94. 103. K i <10 µM for 11 of 20
    95. 104. cell assays
    96. 105. 9 of 9 showed activity
    97. 106. work in progress
    98. 107. link side-effects to targets
    99. 108. direct target prediction
    100. 109. thank you! <ul><li>NetPhorest </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 </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Damian Szklarczyk </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>Reflect </li></ul><ul><ul><li>Sune Frankild </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><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><li>NetworKIN </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Gerard Ostheimer </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><li>Side effect </li></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Anne-Claude Gavin </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul>
    101. 110. larsjuhljensen

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