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Large-scale data and text mining

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Lars Juhl Jensen
Lars Juhl Jensen

The document discusses Lars Juhl Jensen's work in large-scale data and text mining including developing databases and tools for predicting protein function, modeling cell cycle regulation and signaling networks, compiling datasets on protein interactions and functional associations, text mining of biomedical literature, and developing databases of drug-drug and drug-target interactions. It acknowledges collaborators on various projects involving NetPhorest, STRING, STITCH, NetworKIN, and Reflect.

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Large-scale data and text mining Lars Juhl Jensen
 
 
function prediction
Jensen, Gupta et al., Journal of Molecular Biology , 2002
 
 
cell-cycle regulation
de Lichtenberg, Jensen et al., Science , 2005
Jensen, Jensen, de Lichtenberg et al., Nature , 2006
phosphorylation
 
signaling networks
upstream events
downstream events
NetworKIN
 
sequence motifs
NetPhorest
automated pipeline
Miller, Jensen et al., Science Signaling , 2008
data organization
Miller, Jensen et al., Science Signaling , 2008
compilation of datasets
redundancy reduction
training and evaluation
motif atlas
 
model organisms
other modifications
protein networks
functional associations
 
STRING
Jensen, Kuhn et al., Nucleic Acids Research , 2009
630 genomes
genomic context
Korbel et al., Nature Biotechnology , 2004
Korbel et al., Nature Biotechnology , 2004
Korbel et al., Nature Biotechnology , 2004
physical interactions
Jensen & Bork, Science , 2008
genetic interactions
Beyer et al., Nature Reviews Genetics , 2007
gene coexpression
 
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences , 2008
literature mining
>10 km
 
confidence scores
cross-species integration
visualization
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
new targets for old drugs
chemical similarity
Campillos & Kuhn et al., Science , 2008
side-effect similarity
information on side effects
package inserts
Campillos, Kuhn et al., Science , 2008
text mining
side-effect ontology
Campillos, Kuhn et al., Science , 2008
side-effect correlations
Campillos, Kuhn et al., Science , 2008
side-effect frequencies
Campillos & Kuhn et al., Science , 2008
combined similarity score
Campillos, Kuhn et al., Science , 2008
thousands of predictions
categorization
Campillos, Kuhn et al., Science , 2008
20 drug–drug relations
Campillos, Kuhn et al., Science , 2008
in vitro binding assays
K i <10 µM for 11 of 20
cell assays
9 of 9 showed activity
augmented browsing
Reflect
 
collaborate publishers
 
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larsjuhljensen

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Mais de Lars Juhl Jensen (20)

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Network Biology: A crash course on STRING and Cytoscape
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STRING & related databases: Large-scale integration of heterogeneous data
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Tagger: Rapid dictionary-based named entity recognition
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Medical text mining: Linking diseases, drugs, and adverse reactions
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The Art of Counting: Scoring and ranking co-occurrences in literature
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Large-scale data and text mining