Current research topics (those I am allowed to talk about) Lars Juhl Jensen EMBL Heidelberg
literature mining
why?
 
too much to read
information retrieval
finding the papers
ad hoc  retrieval
user-specified query
“ yeast  AND  cell cycle”
stemming
yeast / yeasts
dynamic query expansion
yeast /  S. cerevisiae
 
 
 
 
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming st...
no tool will find it
entity recognition
identifying the substance(s)
Mitotic cyclin ( Clb2 )-bound  Cdc28  (Cdk1 homolog) directly phosphorylated  Swe1  and this modification served as a prim...
good synonyms list
orthographic variation
CDC28
Cdc28p
disambiguation
hairy
SDS
APC
Cdc2
 
 
still too much to read
information extraction
formalizing the facts
co-mentioning
 
statistical methods
NLP Natural Language Processing
<ul><li>Gene  and protein  names </li></ul><ul><li>Cue words for entity recognition </li></ul><ul><li>Verbs for relation e...
Mitotic cyclin ( Clb2 )-bound  Cdc28  (Cdk1 homolog) directly phosphorylated  Swe1  and this modification served as a prim...
 
no new discoveries
text mining
undiscovered links
 
Raynaud’s syndrome
fish oil
 
temporal trends
 
buzzwords
 
association networks
 
 
information extraction
 
curated knowledge
 
experimental data
 
 
genomic context
 
 
 
variable reliability
raw quality scores
 
 
 
not comparable
benchmarking
calibrate vs. gold standard
 
probabilistic scores
spread over many species
transfer by orthology
 
combine all evidence
P = 1-(1-P 1 ) . (1-P 2 ) . (1-P 3 ) …
 
signaling networks
phosphoproteomics
 
phosphorylation sites
kinases are unknown
computational methods
 
 
kinase families
overprediction
context
co-activators
scaffolders
association networks
 
NetworKIN
 
benchmarking
 
2.5-fold better accuracy
ATM signaling
 
experimental validation
ATM phosphorylates Rad50
 
Cdk1 phosphorylates 53BP1
 
multiple reaction monitoring
 
Acknowledgments <ul><li>Reflect & NLP </li></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Jasmin Saric </li...
Upcoming SlideShare
Loading in …5
×

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

613 views

Published on

PhD Program in Computational Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, April 29-May 2, 2008

Published in: Technology, Health & Medicine
  • Be the first to comment

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

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

×