Just-in-time assembly: Transcriptional and post-translational cell-cycle regulation of protein complexes

851 views

Published on

Centre for Computational and Systems Biology (CoSBi), Trento, Italy, January 12, 2010.

Published in: Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
851
On SlideShare
0
From Embeds
0
Number of Embeds
5
Actions
Shares
0
Downloads
21
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Just-in-time assembly: Transcriptional and post-translational cell-cycle regulation of protein complexes

  1. 1. Just-in-time assembly Transcriptional and post-translational cell-cycle regulation of protein complexes Lars Juhl Jensen
  2. 3. sequence analysis
  3. 4. Jensen & Knudsen, Bioinformatics , 2000
  4. 5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
  5. 7. data integration
  6. 8. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  7. 9. Jensen & Bork, Science , 2008
  8. 10. Campillos, Kuhn et al., Science , 2008
  9. 12. signaling networks
  10. 13. Linding, Jensen, Ostheimer et al., Cell , 2007
  11. 14. text mining
  12. 15. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  13. 16. the cell cycle
  14. 17. complex process
  15. 18. one cell
  16. 19. two cells
  17. 21. regulation
  18. 22. gene expression
  19. 23. protein complexes
  20. 24. phosphorylation
  21. 25. targeted degradation
  22. 26. gene expression
  23. 27. cell cultures
  24. 28. S. cerevisiae
  25. 30. synchronization
  26. 31. microarrays
  27. 33. time courses
  28. 34. Gauthier et al., Nucleic Acids Research , 2007
  29. 35. cycling genes
  30. 36. renormalization
  31. 37. reanalysis
  32. 38. new scoring scheme
  33. 39. benchmarking
  34. 40. Gauthier et al., Nucleic Acids Research , 2007
  35. 41. protein complexes
  36. 42. interaction data
  37. 43. temporal network
  38. 44. de Lichtenberg, Jensen et al., Science , 2005
  39. 45. de Lichtenberg, Jensen et al., Science , 2005
  40. 46. hypothesis
  41. 47. just-in-time assembly
  42. 48. de Lichtenberg, Jensen et al., Cell Cycle , 2007
  43. 49. how can we test it?
  44. 50. evolutionary flexibility
  45. 51. reanalysis
  46. 52. microarray time courses
  47. 53. S. pombe
  48. 54. H. sapiens
  49. 55. A. thaliana
  50. 56. cycling genes
  51. 57. orthologous genes
  52. 58. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  53. 59. protein complexes
  54. 60. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  55. 61. phosphorylation
  56. 63. CDK substrate
  57. 64. low-throughput data
  58. 65. high-throughput data
  59. 66. NetPhosK
  60. 67. correlation
  61. 68. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  62. 69. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  63. 70. correlated changes
  64. 71. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  65. 72. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  66. 73. co-evolution
  67. 74. transcriptional regulation
  68. 75. posttranslational regulation
  69. 76. phosphoproteomics
  70. 77. SILAC study of HeLa cells
  71. 78. multi-block strategy
  72. 79. Olsen, Vermeulen et al., Science Signaling , 2010
  73. 80. cycling proteins
  74. 81. Olsen, Vermeulen et al., Science Signaling , 2010
  75. 82. regulation of kinases
  76. 83. Olsen, Vermeulen et al., Science Signaling , 2010
  77. 84. regulation by kinases
  78. 85. Olsen, Vermeulen et al., Science Signaling , 2010
  79. 86. evolution of cycles
  80. 87. other periodic processes
  81. 88. microarray time courses
  82. 89. ultradian cycle
  83. 90. S. cerevisiae
  84. 91. Trachana, Jensen & Bork, EMBO Reports , 2010
  85. 92. diurnal cycle
  86. 93. A. thaliana
  87. 94. Trachana, Jensen & Bork, EMBO Reports , 2010
  88. 95. mammals
  89. 96. Trachana, Jensen & Bork, EMBO Reports , 2010
  90. 97. paralogous genes
  91. 98. same cellular functions
  92. 99. different periodic processes
  93. 100. three independent lineages
  94. 101. summary
  95. 102. reanalysis
  96. 103. integration
  97. 104. high-throughput data
  98. 105. biological discoveries
  99. 106. Acknowledgments <ul><li>Just-in-time assembly </li></ul><ul><ul><li>Ulrik de Lichtenberg </li></ul></ul><ul><ul><li>Thomas Skøt Jensen </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Comparison with other cycling processes </li></ul><ul><ul><li>Kalliopi Trachana </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Proteomics </li></ul><ul><ul><li>Jesper V. Olsen </li></ul></ul><ul><ul><li>Michiel Vermeulen </li></ul></ul><ul><ul><li>Anna Santamaria </li></ul></ul><ul><ul><li>Chanchal Kumar </li></ul></ul><ul><ul><li>Martin Lee Miller </li></ul></ul><ul><ul><li>Florian Gnad </li></ul></ul><ul><ul><li>Jürgen Cox </li></ul></ul><ul><ul><li>Thomas Skøt Jensen </li></ul></ul><ul><ul><li>Erich A. Nigg </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><ul><li>Matthias M ann </li></ul></ul>
  100. 107. larsjuhljensen

×