Evolutionary plasticity of cell-cycle regulation

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  • Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome
  • Evolutionary plasticity of cell-cycle regulation

    1. 1. Evolutionary plasticity of cell-cycle regulation Lars Juhl Jensen
    2. 4. sequence analysis
    3. 5. Jensen & Knudsen, Bioinformatics , 2000
    4. 6. Jensen, Gupta et al., Journal of Molecular Biology , 2002
    5. 9. data integration
    6. 10. Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
    7. 11. Jensen & Bork, Science , 2008
    8. 12. Campillos, Kuhn et al., Science , 2008
    9. 16. signaling networks
    10. 17. Miller, Jensen et al., Science Signaling , 2008
    11. 18. Linding, Jensen, Ostheimer et al., Cell , 2007
    12. 19. text mining
    13. 20. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    14. 21. the cell cycle
    15. 22. complex process
    16. 23. one cell
    17. 24. two cells
    18. 26. regulation
    19. 27. gene expression
    20. 28. protein complexes
    21. 29. phosphorylation
    22. 30. targeted degradation
    23. 31. gene expression
    24. 32. cell cultures
    25. 33. S. cerevisiae
    26. 35. synchronization
    27. 36. microarrays
    28. 38. time courses
    29. 39. Gauthier et al., Nucleic Acids Research , 2007
    30. 40. cycling genes
    31. 41. renormalization
    32. 42. reanalysis
    33. 43. new scoring scheme
    34. 44. benchmarking
    35. 45. Gauthier et al., Nucleic Acids Research , 2007
    36. 46. protein complexes
    37. 47. interaction data
    38. 48. temporal network
    39. 49. de Lichtenberg, Jensen et al., Science , 2005
    40. 50. de Lichtenberg, Jensen et al., Science , 2005
    41. 51. hypothesis
    42. 52. just-in-time assembly
    43. 53. de Lichtenberg, Jensen et al., Cell Cycle , 2007
    44. 54. how can we test it?
    45. 55. evolutionary flexibility
    46. 56. reanalysis
    47. 57. microarray time courses
    48. 58. S. pombe
    49. 59. H. sapiens
    50. 60. A. thaliana
    51. 61. cycling genes
    52. 62. orthologous genes
    53. 63. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    54. 64. protein complexes
    55. 65. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    56. 66. phosphorylation
    57. 68. CDK substrate
    58. 69. low-throughput data
    59. 70. high-throughput data
    60. 71. NetPhosK
    61. 72. correlation
    62. 73. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    63. 74. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    64. 75. correlated changes
    65. 76. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    66. 77. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    67. 78. co-evolution
    68. 79. transcriptional regulation
    69. 80. posttranslational regulation
    70. 81. phosphoproteomics
    71. 82. SILAC study of HeLa cells
    72. 83. multi-block strategy
    73. 84. Olsen, Vermeulen et al., Science Signaling , 2010
    74. 85. cycling proteins
    75. 86. Olsen, Vermeulen et al., Science Signaling , 2010
    76. 87. regulation of kinases
    77. 88. Olsen, Vermeulen et al., Science Signaling , 2010
    78. 89. regulation by kinases
    79. 90. Olsen, Vermeulen et al., Science Signaling , 2010
    80. 91. evolution of cycles
    81. 92. other periodic processes
    82. 93. microarray time courses
    83. 94. ultradian cycle
    84. 95. S. cerevisiae
    85. 96. Trachana, Jensen & Bork, EMBO Reports , 2010
    86. 97. diurnal cycle
    87. 98. A. thaliana
    88. 99. Trachana, Jensen & Bork, EMBO Reports , 2010
    89. 100. mammals
    90. 101. Trachana, Jensen & Bork, EMBO Reports , 2010
    91. 102. paralogous genes
    92. 103. same cellular functions
    93. 104. different periodic processes
    94. 105. three independent lineages
    95. 106. summary
    96. 107. reanalysis
    97. 108. integration
    98. 109. high-throughput data
    99. 110. biological discoveries
    100. 111. 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>
    101. 112. larsjuhljensen

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