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 ]
    43. 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
    44.  
    45. no new discoveries
    46. text mining
    47. undiscovered links
    48.  
    49. Raynaud’s syndrome
    50. fish oil
    51.  
    52. temporal trends
    53.  
    54. buzzwords
    55.  
    56. association networks
    57.  
    58.  
    59. information extraction
    60.  
    61. curated knowledge
    62.  
    63. experimental data
    64.  
    65.  
    66. genomic context
    67.  
    68.  
    69.  
    70. variable reliability
    71. raw quality scores
    72.  
    73.  
    74.  
    75. not comparable
    76. benchmarking
    77. calibrate vs. gold standard
    78.  
    79. probabilistic scores
    80. spread over many species
    81. transfer by orthology
    82.  
    83. combine all evidence
    84. P = 1-(1-P 1 ) . (1-P 2 ) . (1-P 3 ) …
    85.  
    86. signaling networks
    87. phosphoproteomics
    88.  
    89. phosphorylation sites
    90. kinases are unknown
    91. computational methods
    92.  
    93.  
    94. kinase families
    95. overprediction
    96. context
    97. co-activators
    98. scaffolders
    99. association networks
    100.  
    101. NetworKIN
    102.  
    103. benchmarking
    104.  
    105. 2.5-fold better accuracy
    106. ATM signaling
    107.  
    108. experimental validation
    109. ATM phosphorylates Rad50
    110.  
    111. Cdk1 phosphorylates 53BP1
    112.  
    113. multiple reaction monitoring
    114.  
    115. 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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