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Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
Network biology: A basis for large-scale biomedical data mining
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Network biology: A basis for large-scale biomedical data mining

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  • Integration
    Automation
    Collaboration
  • Atlas of human kinases
    Atlases for phospho-binding proteins
    Atlases for model organisms
    Ubiquitination would be welcome
  • Transcript

    • 1. Network biology A basis for large-scale biomedical data mining Lars Juhl Jensen
    • 2. sequence analysis
    • 3. Jensen, Gupta et al., Journal of Molecular Biology, 2002
    • 4. data mining
    • 5. de Lichtenberg, Jensen et al., Science, 2005
    • 6. data mining
    • 7. text mining
    • 8. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
    • 9. signaling networks
    • 10. phosphoproteomics
    • 11. in vivo phosphosites
    • 12. kinases are unknown
    • 13. sequence motifs
    • 14. Miller, Jensen et al., Science Signaling, 2008
    • 15. NetPhorest
    • 16. data organization
    • 17. Miller, Jensen et al., Science Signaling, 2008
    • 18. automated pipeline
    • 19. Miller, Jensen et al., Science Signaling, 2008
    • 20. compilation of datasets
    • 21. training and evaluation
    • 22. motif atlas
    • 23. 179 kinases
    • 24. 89 SH2 domains
    • 25. 8 PTB domains
    • 26. BRCT domains
    • 27. WW domains
    • 28. 14-3-3 proteins
    • 29. phosphatases
    • 30. sequence specificity
    • 31. in vitro
    • 32. network context
    • 33. Linding, Jensen, Ostheimer et al., Cell, 2007
    • 34. STRING
    • 35. Jensen, Kuhn et al., Nucleic Acids Research, 2009
    • 36. 630 genomes
    • 37. 2.5 million proteins
    • 38. genomic context
    • 39. gene fusion
    • 40. Korbel et al., Nature Biotechnology, 2004
    • 41. phylogenetic profiles
    • 42. Korbel et al., Nature Biotechnology, 2004
    • 43. primary experimental data
    • 44. physical interactions
    • 45. Jensen & Bork, Science, 2008
    • 46. gene coexpression
    • 47. curated knowledge
    • 48. Letunic & Bork, Trends in Biochemical Sciences, 2008
    • 49. literature mining
    • 50. not comparable
    • 51. confidence scores
    • 52. von Mering et al., Nucleic Acids Research, 2005
    • 53. cross-species integration
    • 54. Linding, Jensen, Ostheimer et al., Cell, 2007
    • 55. putting it all together
    • 56. NetworKIN
    • 57. Linding, Jensen, Ostheimer et al., Cell, 2007
    • 58. >2x better accuracy
    • 59. use case
    • 60. DNA damage response
    • 61. Linding, Jensen, Ostheimer et al., Cell, 2007
    • 62. experimental validation
    • 63. ATM phosphorylates Rad50
    • 64. Linding, Jensen, Ostheimer et al., Cell, 2007
    • 65. drug repositioning
    • 66. new uses for old drugs
    • 67. drug–drug network
    • 68. shared target(s)
    • 69. chemical similarity
    • 70. Tanimoto coefficients
    • 71. Campillos & Kuhn et al., Science, 2008
    • 72. Campillos & Kuhn et al., Science, 2008
    • 73. similar drugs share targets
    • 74. only trivial predictions
    • 75. phenotypic similarity
    • 76. chemical perturbations
    • 77. phenotypic readouts
    • 78. drug treatment
    • 79. side effects
    • 80. no database
    • 81. package inserts
    • 82. Campillos & Kuhn et al., Science, 2008
    • 83. text mining
    • 84. side-effect ontology
    • 85. backtracking
    • 86. Campillos & Kuhn et al., Science, 2008
    • 87. side-effect correlations
    • 88. Campillos & Kuhn et al., Science, 2008
    • 89. GSC weighting
    • 90. side-effect frequencies
    • 91. Campillos & Kuhn et al., Science, 2008
    • 92. raw similarity score
    • 93. Campillos & Kuhn et al., Science, 2008
    • 94. p-values
    • 95. Campillos & Kuhn et al., Science, 2008
    • 96. side-effect similarity
    • 97. chemical similarity
    • 98. Campillos & Kuhn et al., Science, 2008
    • 99. confidence scores
    • 100. drug–drug network
    • 101. Campillos & Kuhn et al., Science, 2008
    • 102. categorization
    • 103. Campillos & Kuhn et al., Science, 2008
    • 104. experimental validation
    • 105. 20 drug–drug pairs
    • 106. in vitro binding assays
    • 107. Ki<10 µM for 11 of 20
    • 108. cell assays
    • 109. 9 of 9 showed activity
    • 110. work in progress
    • 111. link side-effects to targets
    • 112. direct target prediction
    • 113. STITCH
    • 114. Kuhn et al., Nucleic Acids Research, 2010
    • 115. thank you!
    • 116. Acknowledgments NetPhorest.info – Rune Linding – Martin Lee Miller – Francesca Diella – Claus Jørgensen – Michele Tinti – Lei Li – Marilyn Hsiung – Sirlester A. Parker – Jennifer Bordeaux – Thomas Sicheritz-Pontén – Marina Olhovsky – Adrian Pasculescu – Jes Alexander – Stefan Knapp – Nikolaj Blom – Peer Bork – Shawn Li – Gianni Cesareni – Tony Pawson – Benjamin E. Turk – Michael B. Yaffe – Søren Brunak STRING-DB.org – Christian von Mering – Damian Szklarczyk – Michael Kuhn – Manuel Stark – Samuel Chaffron – Chris Creevey – Jean Muller – Tobias Doerks – Philippe Julien – Alexander Roth – Milan Simonovic – Jan Korbel – Berend Snel – Martijn Huynen – Peer Bork Side effect – Monica Campillos – Michael Kuhn – Christian von Mering – Anne-Claude Gavin – Peer Bork NetworKIN.info – Rune Linding – Gerard Ostheimer – Heiko Horn – Martin Lee Miller – Francesca Diella – Karen Colwill – Jing Jin – Pavel Metalnikov – Vivian Nguyen – Adrian Pasculescu – Jin Gyoon Park – Leona D. Samson – Rob Russell – Peer Bork – Michael Yaffe – Tony Pawson
    • 117. larsjuhljensen

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