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Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
Unraveling signaling networks by data integration
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Unraveling signaling networks by data integration

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CPR Seminar, University of Copenhagen, Copenhagen, Denmark, February 6, 2009

CPR Seminar, University of Copenhagen, Copenhagen, Denmark, February 6, 2009

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  • 1. Unraveling signaling networks by data integration
  • 2. Lars Juhl Jensen
  • 3.  
  • 4.  
  • 5. promoter analysis
  • 6. Jensen & Knudsen, Bioinformatics , 2000
  • 7. genome visualization
  • 8. Pedersen, Jensen et al., Journal of Molecular Biology , 2000
  • 9. function prediction
  • 10. Jensen, Gupta et al., Journal of Molecular Biology , 2002
  • 11.  
  • 12.  
  • 13. data integration
  • 14. Jensen & Bork, Drug Discovery Today: TARGETS , 2004
  • 15. Gavin, Aloy et al., Nature , 2006
  • 16. cell-cycle regulation
  • 17. de Lichtenberg, Jensen et al., Science , 2005
  • 18. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • 19. drug repurposing
  • 20. Campillos, Kuhn et al., Science , 2008
  • 21. signaling networks
  • 22. phosphoproteomics
  • 23. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 24. in vivo phosphosites
  • 25. kinases are unknown
  • 26. peptide assays
  • 27. Miller, Jensen et al., Science Signaling , 2008
  • 28. kinase-specific
  • 29. in vitro
  • 30. no context
  • 31. machine-learning methods
  • 32. Phospho.ELM
  • 33. Miller, Jensen et al., Science Signaling , 2008
  • 34. kinase-specific
  • 35. no context
  • 36. context
  • 37. association networks
  • 38. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 39. NetworKIN
  • 40. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 41. sequence motifs
  • 42. NetPhorest
  • 43. Miller, Jensen et al., Science Signaling , 2008
  • 44. data organization
  • 45. Miller, Jensen et al., Science Signaling , 2008
  • 46. automated pipeline
  • 47. compilation of datasets
  • 48. redundancy reduction
  • 49. training and evaluation
  • 50. classifier selection
  • 51. motif atlas
  • 52.  
  • 53. 179 kinases
  • 54. 93 SH2 domains
  • 55. 8 PTB domains
  • 56. BRCT domains
  • 57. WW domains
  • 58. 14-3-3 proteins
  • 59. comparison
  • 60. Miller, Jensen et al., Science Signaling , 2008
  • 61. association networks
  • 62. STRING
  • 63. functional associations
  • 64. 630 genomes
  • 65. genomic context
  • 66. gene fusion
  • 67. Korbel et al., Nature Biotechnology , 2004
  • 68. conserved neighborhood
  • 69. Korbel et al., Nature Biotechnology , 2004
  • 70. phylogenetic profiles
  • 71. Korbel et al., Nature Biotechnology , 2004
  • 72. primary experimental data
  • 73. protein interactions
  • 74. Jensen & Bork, Science , 2008
  • 75. gene coexpression
  • 76.  
  • 77. literature mining
  • 78.  
  • 79. curated knowledge
  • 80. Letunic & Bork, Trends in Biochemical Sciences , 2008
  • 81. benchmarking
  • 82. von Mering et al., Nucleic Acids Research , 2005
  • 83. transfer by orthology
  • 84. combine all evidence
  • 85. Frishman et al., Modern Genome Annotation , 2009
  • 86. small molecules
  • 87. STITCH
  • 88. Kuhn et al., Nucleic Acids Research , 2008
  • 89. kinase inhibitor screens
  • 90. Fedorov et al., PNAS , 2007
  • 91. design optimal experiments
  • 92. multiple reaction monitoring
  • 93. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 94. high-throughput validation
  • 95. NetworKIN predictions
  • 96. augmented browsing
  • 97. Reflect
  • 98.  
  • 99. Acknowledgments <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>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>STITCH.embl.de </li></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>NetPhorest.info </li></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.embl.de </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>Philippe Julien </li></ul></ul><ul><ul><li>Tobias Doerks </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.ws </li></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Heiko Horn </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>
  • 100. &nbsp;

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