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Network biology - A basis for large-scale biomedica data mining

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Lars Juhl Jensen
Lars Juhl Jensen
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Network biology A basis for large-scale biomedical data mining Lars Juhl Jensen
 
 
sequence analysis
Jensen, Gupta et al., Journal of Molecular Biology , 2002
 
 
data mining
de Lichtenberg, Jensen et al., Science , 2005
 
 
 
data mining
text mining
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
signaling networks
phosphoproteomics
Linding, Jensen, Ostheimer et al., Cell , 2007
in vivo phosphosites
kinases are unknown
sequence motifs
Miller, Jensen et al., Science Signaling , 2008
NetPhorest
data organization
Miller, Jensen et al., Science Signaling , 2008
automated pipeline
Miller, Jensen et al., Science Signaling , 2008
motif atlas
sequence specificity
no context
network context
Linding, Jensen, Ostheimer et al., Cell , 2007
guilt by association
 
STRING
630 genomes
computational predictions
gene fusion
Korbel et al., Nature Biotechnology , 2004
experimental data
physical interactions
Jensen & Bork, Science , 2008
gene coexpression
 
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences , 2008
>10 km
literature mining
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
not comparable
confidence scores
von Mering et al., Nucleic Acids Research , 2005
cross-species integration
von Mering et al., Nucleic Acids Research , 2005
association network
Linding, Jensen, Ostheimer et al., Cell , 2007
integrate with motifs
NetworKIN
Linding, Jensen, Ostheimer et al., Cell , 2007
>2x better accuracy
drug repositioning
new uses for old drugs
drug–drug network
shared target(s)
chemical similarity
Campillos & Kuhn et al., Science , 2008
similar drugs share targets
Campillos & Kuhn et al., Science , 2008
only trivial predictions
phenotypic similarity
chemical perturbations
phenotypic readouts
drug treatment
side effects
no database
package inserts
Campillos & Kuhn et al., Science , 2008
text mining
side-effect ontology
Campillos & Kuhn et al., Science , 2008
manual validation
SIDER Kuhn et al., Molecular Systems Biology , 2010
side-effect correlations
Campillos & Kuhn et al., Science , 2008
GSC weighting
side-effect frequencies
Campillos & Kuhn et al., Science , 2008
raw similarity score
Campillos & Kuhn et al., Science , 2008
p-values
Campillos & Kuhn et al., Science , 2008
side-effect similarity
chemical similarity
Campillos & Kuhn et al., Science , 2008
confidence scores
drug–drug network
Campillos & Kuhn et al., Science , 2008
categorization
Campillos & Kuhn et al., Science , 2008
experimental validation
20 drug–drug pairs
in vitro binding assays
K i <10 µM for 11 of 20
cell assays
9 of 9 showed activity
work in progress
link side-effects to targets
direct target prediction
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Network biology - A basis for large-scale biomedica data mining

Notes de l'éditeur

  1. Integration Automation Collaboration