Computational approaches to cell cycle analysis: Current research topics (those I am allowed to talk about)

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    Computational approaches to cell cycle analysis: Current research topics (those I am allowed to talk about) - Presentation Transcript

    1. Current research topics (those I am allowed to talk about) Lars Juhl Jensen EMBL Heidelberg
    2. literature mining
    3. why?
    4.  
    5. too much to read
    6. information retrieval
    7. finding the papers
    8. ad hoc retrieval
    9. user-specified query
    10. “ yeast AND cell cycle”
    11. stemming
    12. yeast / yeasts
    13. dynamic query expansion
    14. yeast / S. cerevisiae
    15.  
    16.  
    17.  
    18.  
    19. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation
    20. no tool will find it
    21. entity recognition
    22. identifying the substance(s)
    23. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
    24. good synonyms list
    25. orthographic variation
    26. CDC28
    27. Cdc28p
    28. disambiguation
    29. hairy
    30. SDS
    31. APC
    32. Cdc2
    33.  
    34.  
    35. still too much to read
    36. information extraction
    37. formalizing the facts
    38. co-mentioning
    39.  
    40. statistical methods
    41. NLP Natural Language Processing
      • Gene and protein names
      • Cue words for entity recognition
      • Verbs for relation extraction
      • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
    42. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
    43.  
    44. no new discoveries
    45. text mining
    46. undiscovered links
    47.  
    48. Raynaud’s syndrome
    49. fish oil
    50.  
    51. temporal trends
    52.  
    53. buzzwords
    54.  
    55. association networks
    56.  
    57.  
    58. information extraction
    59.  
    60. curated knowledge
    61.  
    62. experimental data
    63.  
    64.  
    65. genomic context
    66.  
    67.  
    68.  
    69. variable reliability
    70. raw quality scores
    71.  
    72.  
    73.  
    74. not comparable
    75. benchmarking
    76. calibrate vs. gold standard
    77.  
    78. probabilistic scores
    79. spread over many species
    80. transfer by orthology
    81.  
    82. combine all evidence
    83. P = 1-(1-P 1 ) . (1-P 2 ) . (1-P 3 ) …
    84.  
    85. signaling networks
    86. phosphoproteomics
    87.  
    88. phosphorylation sites
    89. kinases are unknown
    90. computational methods
    91.  
    92.  
    93. kinase families
    94. overprediction
    95. context
    96. co-activators
    97. scaffolders
    98. association networks
    99.  
    100. NetworKIN
    101.  
    102. benchmarking
    103.  
    104. 2.5-fold better accuracy
    105. ATM signaling
    106.  
    107. experimental validation
    108. ATM phosphorylates Rad50
    109.  
    110. Cdk1 phosphorylates 53BP1
    111.  
    112. multiple reaction monitoring
    113.  
    114. Acknowledgments
      • Reflect & NLP
        • Evangelos Pafilis
        • Jasmin Saric
        • Rossitza Ouzounova
        • Sean O’Donoghue
        • Isabel Rojas
      • STRING & STITCH
        • Christian von Mering
        • Michael Kuhn
        • Manuel Stark
        • Samuel Chaffron
        • Philippe Julien
        • Tobias Doerks
        • Jan Korbel
        • Berend Snel
        • Martijn Huynen
        • Peer Bork
      • NetworKIN & NetPhorest
        • Rune Linding
        • Martin Lee Miller
        • Gerard Ostheimer
        • Francesca Diella
        • Karen Colwill
        • Jing Jin
        • Pavel Metalnikov
        • Vivian Nguyen
        • Adrian Pasculescu
        • Jin Gyoon Park
        • Leona D. Samson
        • Nikolaj Blom
        • Rob Russell
        • Peer Bork
        • Søren Brunak
        • Michael Yaffe
        • Tony Pawson

    + Lars Juhl JensenLars Juhl Jensen, 2 years ago

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    PhD Program in Computational Biology, Instituto Gul more

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