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Unraveling signaling networks by data integration

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Lars Juhl Jensen
Lars Juhl Jensen

CPR Seminar, University of Copenhagen, Copenhagen, Denmark, February 6, 2009

Technologie
1 von 100
Unraveling signaling networks by data integration
Lars Juhl Jensen
 
 
promoter analysis
Jensen & Knudsen, Bioinformatics , 2000
genome visualization
Pedersen, Jensen et al., Journal of Molecular Biology , 2000
function prediction
Jensen, Gupta et al., Journal of Molecular Biology , 2002
 
 
data integration
Jensen & Bork, Drug Discovery Today: TARGETS , 2004
Gavin, Aloy et al., Nature , 2006
cell-cycle regulation
de Lichtenberg, Jensen et al., Science , 2005
Jensen, Jensen, de Lichtenberg et al., Nature , 2006
drug repurposing
Campillos, Kuhn et al., Science , 2008
signaling networks
phosphoproteomics
Linding, Jensen, Ostheimer et al., Cell , 2007
in vivo phosphosites
kinases are unknown
peptide assays
Miller, Jensen et al., Science Signaling , 2008
kinase-specific
in vitro
no context
machine-learning methods
Phospho.ELM
Miller, Jensen et al., Science Signaling , 2008
kinase-specific
no context
context
association networks
Linding, Jensen, Ostheimer et al., Cell , 2007
NetworKIN
Linding, Jensen, Ostheimer et al., Cell , 2007
sequence motifs
NetPhorest
Miller, Jensen et al., Science Signaling , 2008
data organization
Miller, Jensen et al., Science Signaling , 2008
automated pipeline
compilation of datasets
redundancy reduction
training and evaluation
classifier selection
motif atlas
 
179 kinases
93 SH2 domains
8 PTB domains
BRCT domains
WW domains
14-3-3 proteins
comparison
Miller, Jensen et al., Science Signaling , 2008
association networks
STRING
functional associations
630 genomes
genomic context
gene fusion
Korbel et al., Nature Biotechnology , 2004
conserved neighborhood
Korbel et al., Nature Biotechnology , 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology , 2004
primary experimental data
protein interactions
Jensen & Bork, Science , 2008
gene coexpression
 
literature mining
 
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences , 2008
benchmarking
von Mering et al., Nucleic Acids Research , 2005
transfer by orthology
combine all evidence
Frishman et al., Modern Genome Annotation , 2009
small molecules
STITCH
Kuhn et al., Nucleic Acids Research , 2008
kinase inhibitor screens
Fedorov et al., PNAS , 2007
design optimal experiments
multiple reaction monitoring
Linding, Jensen, Ostheimer et al., Cell , 2007
high-throughput validation
NetworKIN predictions
augmented browsing
Reflect
 
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Unraveling signaling networks by data integration