1. Systems biology
Large-scale biomedical data mining
Lars Juhl Jensen

6. Phase 1
association networks

7. who?

9. protein networks

10. Jensen, Kuhn et al., Nucleic Acids Research, 2009

11. genomic context

12. gene fusion

13. Korbel et al., Nature Biotechnology, 2004

14. conserved neighborhood

15. Korbel et al., Nature Biotechnology, 2004

16. phylogenetic profiles

17. Korbel et al., Nature Biotechnology, 2004

18. gene coexpression

20. protein interactions

21. Jensen & Bork, Science, 2008

22. genetic interactions

23. Beyer et al., Nature Reviews Genetics, 2007

24. curated knowledge

25. Letunic & Bork, Trends in Biochemical Sciences, 2008

26. >10 km

27. text mining

28. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009

29. co-mentioning

30. NLP
Natural Language Processing

31. different formats

32. different names

33. variable quality

34. not comparable

35. spread over 630 genomes

36. confidence scores

37. von Mering et al., Nucleic Acids Research, 2005

38. transfer by orthology

39. von Mering et al., Nucleic Acids Research, 2005

40. Frishman et al., Modern Genome Annotation, 2009

41. Phase 2
signaling networks

42. what?

43. phosphoproteomics

45. kinases are unknown

46. sequence motifs

47. machine-learning methods

48. Miller, Jensen et al., Science Signaling, 2008

49. peptide assays

50. Miller, Jensen et al., Science Signaling, 2008

51. automated pipeline

52. Miller, Jensen et al., Science Signaling, 2008

54. sequence specificity

55. no context

56. network context

57. Linding, Jensen, Ostheimer et al., Cell, 2007

58. Linding, Jensen, Ostheimer et al., Cell, 2007

59. >2x better accuracy

60. context is crucial

61. example

62. DNA damage response

63. Linding, Jensen, Ostheimer et al., Cell, 2007

64. small-scale validation

65. Linding, Jensen, Ostheimer et al., Cell, 2007

66. Phase 3
dynamic networks

67. when?

68. cell-cycle regulation

70. microarray time courses

71. Gauthier et al., Nucleic Acids Research, 2007

72. protein interactions

73. temporal network

74. de Lichtenberg, Jensen et al., Science, 2005

75. de Lichtenberg, Jensen et al., Science, 2005

76. just-in-time assembly

77. de Lichtenberg, Jensen et al., Cell Cycle, 2007

78. evolutionary flexibility

79. individual genes

80. Jensen, Jensen, de Lichtenberg et al., Nature, 2006

81. protein complexes

82. Jensen, Jensen, de Lichtenberg et al., Nature, 2006

83. phosphorylation

84. co-evolution

85. Jensen, Jensen, de Lichtenberg et al., Nature, 2006

86. summary

87. data mining

88. specific predictions

89. systems properties

91. thank you!

92. 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
– Damian Szklarczyk
– 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
Reflect.ws
– Sune Frankild
– Heiko Horn
– Evangelos Pafilis
– Michael Kuhn
– Nigel Brown
– Reinhardt Schneider
– Sean O’Donoghue
NetworKIN.info
– Rune Linding
– Heiko Horn
– Gerard Ostheimer
– 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
Cyclebase.org
– Ulrik de Lichtenberg
– Thomas Skøt Jensen
– Nicholas Paul Gauthier
– Rasmus Wernersson
– Søren Brunak

93. larsjuhljensen