Advanced bioinformatics methods for proteomics

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  • Integration Automation Collaboration
  • Advanced bioinformatics methods for proteomics

    1. 1. Advanced bioinformaticsmethods for proteomics Lars Juhl Jensen
    2. 2. three parts
    3. 3. signaling networks
    4. 4. association networks
    5. 5. text mining
    6. 6. Part 1signaling networks
    7. 7. phosphoproteomics
    8. 8. Linding, Jensen, Ostheimer et al., Cell, 2007
    9. 9. in vivo phosphosites
    10. 10. kinases are unknown
    11. 11. sequence specificity
    12. 12. Miller, Jensen et al., Science Signaling, 2008
    13. 13. NetPhorest
    14. 14. automated pipeline
    15. 15. Miller, Jensen et al., Science Signaling, 2008
    16. 16. motif atlas
    17. 17. kinases
    18. 18. phospho-binding proteins
    19. 19. phosphatases
    20. 20. protein-specific
    21. 21. no context
    22. 22. co-activators
    23. 23. protein scaffolds
    24. 24. localization
    25. 25. expression
    26. 26. association network
    27. 27. Linding, Jensen, Ostheimer et al., Cell, 2007
    28. 28. NetworKIN
    29. 29. Linding, Jensen, Ostheimer et al., Cell, 2007
    30. 30. Part 2association networks
    31. 31. guilt by association
    32. 32. STRING
    33. 33. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    34. 34. >1100 genomes
    35. 35. computational predictions
    36. 36. genomic context
    37. 37. gene fusion
    38. 38. Korbel et al., Nature Biotechnology, 2004
    39. 39. phylogenetic profiles
    40. 40. Korbel et al., Nature Biotechnology, 2004
    41. 41. experimental data
    42. 42. physical interactions
    43. 43. Jensen & Bork, Science, 2008
    44. 44. genetic interactions
    45. 45. Beyer et al., Nature Reviews Genetics, 2007
    46. 46. gene coexpression
    47. 47. curated knowledge
    48. 48. pathways
    49. 49. Letunic & Bork, Trends in Biochemical Sciences, 2008
    50. 50. many data types
    51. 51. many databases
    52. 52. different formats
    53. 53. different identifiers
    54. 54. variable quality
    55. 55. not comparable
    56. 56. spread over 1100+ genomes
    57. 57. quality scores
    58. 58. von Mering et al., Nucleic Acids Research, 2005
    59. 59. calibrate vs. gold standard
    60. 60. von Mering et al., Nucleic Acids Research, 2005
    61. 61. orthology transfer
    62. 62. missing most of the data
    63. 63. Part 3text mining
    64. 64. >10 km
    65. 65. too much to read
    66. 66. computer
    67. 67. as smart as a dog
    68. 68. teach it specific tricks
    69. 69. named entity recognition
    70. 70. identify the concepts
    71. 71. proteins
    72. 72. small molecules
    73. 73. comprehensive lexicon
    74. 74. orthographic variation
    75. 75. “black list”
    76. 76. Reflect
    77. 77. augmented browsing
    78. 78. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
    79. 79. information extraction
    80. 80. formalize the facts
    81. 81. co-mentioning
    82. 82. global statistical analysis
    83. 83. NLPNatural Language Processing
    84. 84. parsing individual sentences
    85. 85. summary
    86. 86. computational biology
    87. 87. data mining
    88. 88. text mining
    89. 89. save you much time
    90. 90. AcknowledgmentsNetPhorest NetworKIN STRING ReflectRune Linding Rune Linding Christian von Mering Sune FrankildMartin Lee Miller Heiko Horn Damian Szklarczyk Heiko HornErwin Schoof Gerard Ostheimer Michael Kuhn Evangelos PafilisFrancesca Diella Martin Lee Miller Manuel Stark Michael KuhnClaus Jørgensen Francesca Diella Samuel Chaffron Nigel BrownMichele Tinti Karen Colwill Chris Creevey ReinhardtLei Li Jing Jin Jean Muller SchneiderMarilyn Hsiung Pavel Metalnikov Tobias Doerks Sean O’DonoghueSirlester A. Parker Vivian Nguyen Philippe JulienJennifer Bordeaux Adrian Pasculescu Alexander RothThomas Sicheritz-Pontén Jin Gyoon Park Milan SimonovicMarina Olhovsky Leona D. Samson Jan KorbelAdrian Pasculescu Rob Russell Berend SnelJes Alexander Peer Bork Martijn HuynenStefan Knapp Michael Yaffe Peer BorkNikolaj Blom Tony PawsonPeer BorkShawn LiGianni CesareniTony PawsonBenjamin E. TurkMichael B. YaffeSøren Brunak
    91. 91. larsjuhljensen

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