Network biology

683 views

Published on

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
683
On SlideShare
0
From Embeds
0
Number of Embeds
5
Actions
Shares
0
Downloads
9
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • Integration Automation Collaboration
  • Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome
  • Network biology

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

    ×