Evolutionary plasticity of cell-cycle regulation
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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 Evolutionary plasticity of cell-cycle regulation Presentation Transcript

  • Evolutionary plasticity of cell-cycle regulation Lars Juhl Jensen
  •  
  •  
  • sequence analysis
  • Jensen & Knudsen, Bioinformatics , 2000
  • Jensen, Gupta et al., Journal of Molecular Biology , 2002
  •  
  •  
  • data integration
  • Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
  • Jensen & Bork, Science , 2008
  • Campillos, Kuhn et al., Science , 2008
  •  
  •  
  •  
  • signaling networks
  • Miller, Jensen et al., Science Signaling , 2008
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  • text mining
  • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  • the cell cycle
  • complex process
  • one cell
  • two cells
  •  
  • regulation
  • gene expression
  • protein complexes
  • phosphorylation
  • targeted degradation
  • gene expression
  • cell cultures
  • S. cerevisiae
  •  
  • synchronization
  • microarrays
  •  
  • time courses
  • Gauthier et al., Nucleic Acids Research , 2007
  • cycling genes
  • renormalization
  • reanalysis
  • new scoring scheme
  • benchmarking
  • Gauthier et al., Nucleic Acids Research , 2007
  • protein complexes
  • interaction data
  • temporal network
  • de Lichtenberg, Jensen et al., Science , 2005
  • de Lichtenberg, Jensen et al., Science , 2005
  • hypothesis
  • just-in-time assembly
  • de Lichtenberg, Jensen et al., Cell Cycle , 2007
  • how can we test it?
  • evolutionary flexibility
  • reanalysis
  • microarray time courses
  • S. pombe
  • H. sapiens
  • A. thaliana
  • cycling genes
  • orthologous genes
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • protein complexes
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • phosphorylation
  •  
  • CDK substrate
  • low-throughput data
  • high-throughput data
  • NetPhosK
  • correlation
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • correlated changes
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • co-evolution
  • transcriptional regulation
  • posttranslational regulation
  • phosphoproteomics
  • SILAC study of HeLa cells
  • multi-block strategy
  • Olsen, Vermeulen et al., Science Signaling , 2010
  • cycling proteins
  • Olsen, Vermeulen et al., Science Signaling , 2010
  • regulation of kinases
  • Olsen, Vermeulen et al., Science Signaling , 2010
  • regulation by kinases
  • Olsen, Vermeulen et al., Science Signaling , 2010
  • evolution of cycles
  • other periodic processes
  • microarray time courses
  • ultradian cycle
  • S. cerevisiae
  • Trachana, Jensen & Bork, EMBO Reports , 2010
  • diurnal cycle
  • A. thaliana
  • Trachana, Jensen & Bork, EMBO Reports , 2010
  • mammals
  • Trachana, Jensen & Bork, EMBO Reports , 2010
  • paralogous genes
  • same cellular functions
  • different periodic processes
  • three independent lineages
  • summary
  • reanalysis
  • integration
  • high-throughput data
  • biological discoveries
  • Acknowledgments
    • Just-in-time assembly
      • Ulrik de Lichtenberg
      • Thomas Skøt Jensen
      • Søren Brunak
      • Peer Bork
    • Comparison with other cycling processes
      • Kalliopi Trachana
      • Peer Bork
    • Proteomics
      • Jesper V. Olsen
      • Michiel Vermeulen
      • Anna Santamaria
      • Chanchal Kumar
      • Martin Lee Miller
      • Florian Gnad
      • Jürgen Cox
      • Thomas Skøt Jensen
      • Erich A. Nigg
      • Søren Brunak
      • Matthias M ann
  • larsjuhljensen