MIPS Retreat, Kloster Frauenchiemsee, Chiemsee, Germany, July 9-10, 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 this before

87. Ota et al.

88. Rustici et al.

89. Dyczkowski and Vingron

90. technical issues

91. orthology definitions

92. no reanalysis

93. different analysis methods

94. no error estimates

95. no biological explanation

96. turn back time …

97. temporal network

98. S. cerevisiae cell cycle

100. dynamic and static subunits

101. just-in-time assembly

103. evolutionary flexibility

104. different organisms

105. different dynamic subunits

106. manual curation

107. protein complexes

111. different time scales

112. time warping

114. same color = same phase

115. DNA polymerases

117. dynamic subunits

118. time of peak expression

119. time of action

120. just-in-time assembly

122. CDK substrates

123. Übersax et al.

124. Loog et al.

125. Phospho.ELM

126. NetPhosK

127. correlation

129. Fisher’s exact test

131. cell cycle vs. non-cell cycle

132. correlated changes

134. Fisher’s exact test

136. co-evolution

137. transcriptional regulation

138. phosphorylation

139. targeted degradation

140. just-in-time assembly

143. Thank you!

144. Questions?