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Centre for Computational and Systems Biology (CoSBi), Trento, Italy, January 12, 2010.
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Just-in-time assemblyTranscriptional and post-translational
cell-cycle regulation of protein complexes
Lars Juhl Jensen
sequence analysis
Jensen & Knudsen, Bioinformatics, 2000
Jensen, Gupta et al., Journal of Molecular Biology, 2002
data integration
Jensen, Kuhn et al., Nucleic Acids Research, 2009
Jensen & Bork, Science, 2008
Campillos, Kuhn et al., Science, 2008
signaling networks
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 othercycling 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 Mann
larsjuhljensen
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