Network biology and data mining techniques

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Lars Juhl Jensen

Network biology Lars Juhl Jensen

sequence analysis

Jensen, Gupta et al., Journal of Molecular Biology , 2002

data mining

de Lichtenberg, Jensen et al., Science , 2005

Campillos & Kuhn et al., Science , 2008

medical informatics

Part 1 signaling networks

phosphoproteomics

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

in vivo phosphosites

kinases are unknown

sequence specificity

Miller, Jensen et al., Science Signaling , 2008

NetPhorest

data organization

Miller, Jensen et al., Science Signaling , 2008

automated pipeline

Miller, Jensen et al., Science Signaling , 2008

motif atlas

protein-specific

no context

co-activators

protein scaffolds

localization

expression

association network

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

NetworKIN

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

Part 2 association networks

guilt by association

STRING

Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011

630 genomes

genomic context

gene fusion

Korbel et al., Nature Biotechnology , 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology , 2004

experimental data

protein interactions

Jensen & Bork, Science , 2008

genetic interactions

Beyer et al., Nature Reviews Genetics , 2007

gene coexpression

curated knowledge

protein complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences , 2008

many data types

many databases

different formats

different identifiers

variable quality

many parsers

identifier mapping

quality scores

calibrate vs. gold standard

von Mering et al., Nucleic Acids Research , 2005

orthology transfer

von Mering et al., Nucleic Acids Research , 2005

missing most of the data

Part 3 text mining

exponential growth

some things are constant

~45 seconds per paper

computer

as smart as a dog

teach it specific tricks

named entity identification

Reflect

augmented browsing

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

comprehensive lexicon

orthographic variation

“ black list”

information extraction

co-occurrence

scalable

>10 km <10 hours

no access

collaborate with publishers

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larsjuhljensen

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Network biology and data mining techniques

1. Network biology Lars Juhl Jensen

2.

3.

4. sequence analysis

5. Jensen, Gupta et al., Journal of Molecular Biology , 2002

6.

7.

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

10. Campillos & Kuhn et al., Science , 2008

11.

12.

13.

14. medical informatics

15.

16. Part 1 signaling networks

17. phosphoproteomics

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

19. in vivo phosphosites

20. kinases are unknown

21. sequence specificity

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

24. data organization

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

26. automated pipeline

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

28. motif atlas

29.

30. protein-specific

32. co-activators

33. protein scaffolds

34. localization

36. association network

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

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

40.

41. Part 2 association networks

42. guilt by association

43.

45. Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011

46. 630 genomes

47. genomic context

48. gene fusion

49. Korbel et al., Nature Biotechnology , 2004

50. phylogenetic profiles

51. Korbel et al., Nature Biotechnology , 2004

52. experimental data

53. protein interactions

54. Jensen & Bork, Science , 2008

55. genetic interactions

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

57. gene coexpression

58.

59. curated knowledge

60. protein complexes

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

63. many data types

64. many databases

65. different formats

66. different identifiers

67. variable quality

68. many parsers

69. identifier mapping

70. quality scores

71. calibrate vs. gold standard

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

73. orthology transfer

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

75. missing most of the data

76. Part 3 text mining

77. exponential growth

78.

79.

80. some things are constant

81.

82. ~45 seconds per paper

84. as smart as a dog

85. teach it specific tricks

86.

87.

88. named entity identification

90. augmented browsing

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

92. comprehensive lexicon

93. orthographic variation

94. “ black list”

95. information extraction

96. co-occurrence

97.

99. >10 km <10 hours

101.

102. collaborate with publishers

103.

104.

105. larsjuhljensen

Notas do Editor

Integration Automation Collaboration
Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome