Unraveling signaling networks by data integration

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

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Unraveling signaling networks by data integration

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

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