European Bioinformatics Institute, Hinxton, England, May 21, 2007

1. Just-in-time assembly Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes Lars Juhl Jensen EMBL Heidelberg

2. the cell cycle

3. grow and divide

4. one cell

5. two cells

6. four phases

7. G 1 phase

8. growth

9. S phase

10. DNA replication

11. G 2 phase

12. growth

13. M phase

14. cell division

16. regulation

17. gene expression

18. phosphorylation

19. targeted degradation

20. protein interactions

21. molecular biology

22. one gene

23. one postdoc

24. many types of data

25. a single gene

26. high-throughput biology

27. one lab

28. one technology

29. all the relevant genes

30. a single type of data

31. systems biology

32. many types of data

33. all the relevant genes

34. data integration

35. expression data

36. cell cultures

38. synchronization

39. microarrays

41. time courses

43. expression profiles

45. list of genes

46. periodically expressed

47. S. cerevisiae

48. expression data

49. Cho et al.

50. Spellman et al.

51. computational methods

52. Zhao et al.

53. Langmead et al.

54. Johansson et al.

55. Wichert et al.

56. Luan and Li

57. Lu et al.

58. Ahdesm äki et al.

59. Willbrand et al.

60. Chen

61. Qiu et al.

62. Ahnert et al.

63. Glynn et al.

64. Andersson et al.

65. Lu et al.

66. Xu et al.

67. Liew et al.

68. no benchmarking

69. reanalysis

70. benchmarking

72. no progress

73. no benchmarking

74. S. pombe

75. H. sapiens

76. A. thaliana

77. reanalysis

78. benchmarking

79. list of genes

80. periodically expressed

81. four organisms

82. orthologous groups

83. sequence similarity

85. not conserved

86. others had seen the same

87. Ota et al.

88. Rustici et al.

89. Dyczkowski and Vingron

90. no explanation

91. a long time ago in a journal far, far away …

92. (Science, 2005)

93. temporal network

95. dynamic and static subunits

96. just-in-time assembly

98. evolutionary flexibility

99. different organisms

100. different dynamic subunits

101. manual curation

102. protein complexes

106. different time scales

107. time warping

108. same color = same phase

109. deoxynucleotide synthesis

111. dynamic subunits

112. time of peak expression

113. time of action

114. just-in-time assembly

116. CDK substrates

117. Phospho.ELM

118. Übersax et al.

119. Loog et al.

120. NetPhosK

121. correlation

123. Fisher’s exact test

125. cell cycle vs. non-cell cycle

126. correlated changes

128. Fisher’s exact test

130. co-evolution

131. transcriptional regulation

132. phosphorylation

133. targeted degradation

134. just-in-time assembly

136. summary

137. reanalysis

138. benchmarking

139. integration

140. high-throughput data

141. reproduce what is know

142. biological discoveries

143. testable hypotheses

144. protein complex regulation

145. evolution

147. Thank you!

148. Questions?