Large-scale data and text mining
Upcoming SlideShare
Loading in...5
×
 

Like this? Share it with your network

Share

Large-scale data and text mining

on

  • 783 views

Hagedorn Research Institute, Gentofte, Denmark, October 8, 2009.

Hagedorn Research Institute, Gentofte, Denmark, October 8, 2009.

Statistics

Views

Total Views
783
Views on SlideShare
780
Embed Views
3

Actions

Likes
1
Downloads
19
Comments
0

1 Embed 3

http://www.slideshare.net 3

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

Large-scale data and text mining Presentation Transcript

  • 1. Large-scale data and text mining Lars Juhl Jensen
  • 2.  
  • 3.  
  • 4. function prediction
  • 5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
  • 6.  
  • 7.  
  • 8. cell-cycle regulation
  • 9. de Lichtenberg, Jensen et al., Science , 2005
  • 10. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • 11. phosphorylation
  • 12.  
  • 13. signaling networks
  • 14. upstream events
  • 15. downstream events
  • 16. NetworKIN
  • 17.  
  • 18. sequence motifs
  • 19. NetPhorest
  • 20. automated pipeline
  • 21. Miller, Jensen et al., Science Signaling , 2008
  • 22. data organization
  • 23. Miller, Jensen et al., Science Signaling , 2008
  • 24. compilation of datasets
  • 25. redundancy reduction
  • 26. training and evaluation
  • 27. motif atlas
  • 28.  
  • 29. model organisms
  • 30. other modifications
  • 31. protein networks
  • 32. functional associations
  • 33.  
  • 34. STRING
  • 35. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  • 36. 630 genomes
  • 37. genomic context
  • 38. Korbel et al., Nature Biotechnology , 2004
  • 39. Korbel et al., Nature Biotechnology , 2004
  • 40. Korbel et al., Nature Biotechnology , 2004
  • 41. physical interactions
  • 42. Jensen & Bork, Science , 2008
  • 43. genetic interactions
  • 44. Beyer et al., Nature Reviews Genetics , 2007
  • 45. gene coexpression
  • 46.  
  • 47. curated knowledge
  • 48. Letunic & Bork, Trends in Biochemical Sciences , 2008
  • 49. literature mining
  • 50. >10 km
  • 51.  
  • 52. confidence scores
  • 53. cross-species integration
  • 54. visualization
  • 55. Frishman et al., Modern Genome Annotation , 2009
  • 56. small molecules
  • 57. STITCH
  • 58. Kuhn et al., Nucleic Acids Research , 2008
  • 59. kinase inhibitor screens
  • 60. Fedorov et al., PNAS , 2007
  • 61. new targets for old drugs
  • 62. chemical similarity
  • 63. Campillos & Kuhn et al., Science , 2008
  • 64. side-effect similarity
  • 65. information on side effects
  • 66. package inserts
  • 67. Campillos, Kuhn et al., Science , 2008
  • 68. text mining
  • 69. side-effect ontology
  • 70. Campillos, Kuhn et al., Science , 2008
  • 71. side-effect correlations
  • 72. Campillos, Kuhn et al., Science , 2008
  • 73. side-effect frequencies
  • 74. Campillos & Kuhn et al., Science , 2008
  • 75. combined similarity score
  • 76. Campillos, Kuhn et al., Science , 2008
  • 77. thousands of predictions
  • 78. categorization
  • 79. Campillos, Kuhn et al., Science , 2008
  • 80. 20 drug–drug relations
  • 81. Campillos, Kuhn et al., Science , 2008
  • 82. in vitro binding assays
  • 83. K i <10 µM for 11 of 20
  • 84. cell assays
  • 85. 9 of 9 showed activity
  • 86. augmented browsing
  • 87. Reflect
  • 88.  
  • 89. collaborate publishers
  • 90.  
  • 91. Acknowledgments
    • NetPhorest.info
      • Rune Linding
      • Martin Lee Miller
      • Francesca Diella
      • Claus Jørgensen
      • Michele Tinti
      • Lei Li
      • Marilyn Hsiung
      • Sirlester A. Parker
      • Jennifer Bordeaux
      • Thomas Sicheritz-Pontén
      • Marina Olhovsky
      • Adrian Pasculescu
      • Jes Alexander
      • Stefan Knapp
      • Nikolaj Blom
      • Peer Bork
      • Shawn Li
      • Gianni Cesareni
      • Tony Pawson
      • Benjamin E. Turk
      • Michael B. Yaffe
      • Søren Brunak
    • STRING-DB.org
      • Christian von Mering
      • Michael Kuhn
      • Manuel Stark
      • Samuel Chaffron
      • Chris Creevey
      • Jean Muller
      • Tobias Doerks
      • Philippe Julien
      • Alexander Roth
      • Milan Simonovic
      • Jan Korbel
      • Berend Snel
      • Martijn Huynen
      • Peer Bork
      • STITCH-DB.org
      • Michael Kuhn
      • Damian Szklarczyk
      • Andrea Franceschini
      • Monica Campillos
      • Christian von Mering
      • Lars Juhl Jensen
      • Andreas Beyer
      • Peer Bork
    • NetworKIN.info
      • Rune Linding
      • Gerard Ostheimer
      • Heiko Horn
      • Martin Lee Miller
      • Francesca Diella
      • Karen Colwill
      • Jing Jin
      • Pavel Metalnikov
      • Vivian Nguyen
      • Adrian Pasculescu
      • Jin Gyoon Park
      • Leona D. Samson
      • Rob Russell
      • Peer Bork
      • Michael Yaffe
      • Tony Pawson
      • Reflect.ws
      • Sean O’Donoghue
      • Heiko Horn
      • Evangelos Pafilis
      • Michael Kuhn
      • Nigel Brown
      • Reinhardt Schneider
  • 92. larsjuhljensen