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Network biology

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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 Lars Juhl Jensen
  • 2.  
  • 3.  
  • 4. sequence analysis
  • 5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
  • 6.  
  • 7.  
  • 8. data mining
  • 9. de Lichtenberg, Jensen et al., Science , 2005
  • 10. Campillos & Kuhn et al., Science , 2008
  • 11.  
  • 12.  
  • 13.  
  • 14. medical informatics
  • 15.  
  • 16. Part 1 signaling networks
  • 17. phosphoproteomics
  • 18. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 19. in vivo phosphosites
  • 20. kinases are unknown
  • 21. sequence specificity
  • 22. Miller, Jensen et al., Science Signaling , 2008
  • 23. NetPhorest
  • 24. data organization
  • 25. Miller, Jensen et al., Science Signaling , 2008
  • 26. automated pipeline
  • 27. Miller, Jensen et al., Science Signaling , 2008
  • 28. motif atlas
  • 29.  
  • 30. protein-specific
  • 31. no context
  • 32. co-activators
  • 33. protein scaffolds
  • 34. localization
  • 35. expression
  • 36. association network
  • 37. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 38. NetworKIN
  • 39. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 40.  
  • 41. Part 2 association networks
  • 42. guilt by association
  • 43.  
  • 44. STRING
  • 45. Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
  • 46. 630 genomes
  • 47. genomic context
  • 48. gene fusion
  • 49. Korbel et al., Nature Biotechnology , 2004
  • 50. phylogenetic profiles
  • 51. Korbel et al., Nature Biotechnology , 2004
  • 52. experimental data
  • 53. protein interactions
  • 54. Jensen & Bork, Science , 2008
  • 55. genetic interactions
  • 56. Beyer et al., Nature Reviews Genetics , 2007
  • 57. gene coexpression
  • 58.  
  • 59. curated knowledge
  • 60. protein complexes
  • 61. pathways
  • 62. Letunic & Bork, Trends in Biochemical Sciences , 2008
  • 63. many data types
  • 64. many databases
  • 65. different formats
  • 66. different identifiers
  • 67. variable quality
  • 68. many parsers
  • 69. identifier mapping
  • 70. quality scores
  • 71. calibrate vs. gold standard
  • 72. von Mering et al., Nucleic Acids Research , 2005
  • 73. orthology transfer
  • 74. von Mering et al., Nucleic Acids Research , 2005
  • 75. missing most of the data
  • 76. Part 3 text mining
  • 77. exponential growth
  • 78.  
  • 79.  
  • 80. some things are constant
  • 81.  
  • 82. ~45 seconds per paper
  • 83. computer
  • 84. as smart as a dog
  • 85. teach it specific tricks
  • 86.  
  • 87.  
  • 88. named entity identification
  • 89. Reflect
  • 90. augmented browsing
  • 91. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  • 92. comprehensive lexicon
  • 93. orthographic variation
  • 94. “ black list”
  • 95. information extraction
  • 96. co-occurrence
  • 97.  
  • 98. scalable
  • 99. >10 km <10 hours
  • 100. no access
  • 101.  
  • 102. collaborate with publishers
  • 103.  
  • 104. Acknowledgments
      • Reflect
      • Sune Frankild
      • Heiko Horn
      • Evangelos Pafilis
      • Michael Kuhn
      • Reinhardt Schneider
      • Sean O’Donoghue
      • STRING
      • Damian Szklarczyk
      • Andrea Franceschini
      • Michael Kuhn
      • Milan Simonovic
      • Alexander Roth
      • Pablo Minguez
      • Tobias Doerks
      • Manuel Stark
      • Jean Muller
      • Peer Bork
      • Christian von Mering
      • NetworKIN
      • Heiko Horn
      • Martin Lee Miller
      • Gerard Ostheimer
      • Francesca Diella
      • Claus Jørgensen
      • Rob Russell
      • Peer Bork
      • Benjamin Turk
      • Michael Yaffe
      • Tony Pawson
      • Rune Linding
  • 105. larsjuhljensen