Download - Large-scale data and text mining
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Large-scale data and text mining
Lars Juhl Jensen
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function prediction
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Jensen, Gupta et al., Journal of Molecular Biology, 2002
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cell-cycle regulation
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de Lichtenberg, Jensen et al., Science, 2005
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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phosphorylation
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signaling networks
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upstream events
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downstream events
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NetworKIN
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sequence motifs
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NetPhorest
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automated pipeline
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Miller, Jensen et al., Science Signaling, 2008
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data organization
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Miller, Jensen et al., Science Signaling, 2008
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compilation of datasets
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redundancy reduction
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training and evaluation
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motif atlas
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model organisms
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other modifications
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protein networks
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functional associations
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STRING
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Jensen, Kuhn et al., Nucleic Acids Research, 2009
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630 genomes
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genomic context
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Korbel et al., Nature Biotechnology, 2004
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Korbel et al., Nature Biotechnology, 2004
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Korbel et al., Nature Biotechnology, 2004
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physical interactions
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Jensen & Bork, Science, 2008
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genetic interactions
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Beyer et al., Nature Reviews Genetics, 2007
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gene coexpression
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curated knowledge
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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literature mining
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>10 km
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confidence scores
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cross-species integration
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visualization
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Frishman et al., Modern Genome Annotation, 2009
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small molecules
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STITCH
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Kuhn et al., Nucleic Acids Research, 2008
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kinase inhibitor screens
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Fedorov et al., PNAS, 2007
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new targets for old drugs
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chemical similarity
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Campillos & Kuhn et al., Science, 2008
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side-effect similarity
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information on side effects
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package inserts
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Campillos, Kuhn et al., Science, 2008
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text mining
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side-effect ontology
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Campillos, Kuhn et al., Science, 2008
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side-effect correlations
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Campillos, Kuhn et al., Science, 2008
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side-effect frequencies
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Campillos & Kuhn et al., Science, 2008
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combined similarity score
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Campillos, Kuhn et al., Science, 2008
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thousands of predictions
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categorization
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Campillos, Kuhn et al., Science, 2008
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20 drug–drug relations
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Campillos, Kuhn et al., Science, 2008
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in vitro binding assays
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Ki<10 µM for 11 of 20
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cell assays
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9 of 9 showed activity
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augmented browsing
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Reflect
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collaborate publishers
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AcknowledgmentsNetPhorest.info
– Rune Linding– Martin Lee Miller– Francesca Diella– Claus Jørgensen– Michele Tinti– Lei Li– Marilyn Hsiung– Sirlester A. Parker– Jennifer Bordeaux– Thomas Sicheritz-Pontén– Marina Olhovsky– Adrian Pasculescu– Jes Alexander– Stefan Knapp– Nikolaj Blom– Peer Bork– Shawn Li– Gianni Cesareni– Tony Pawson– Benjamin E. Turk– Michael B. Yaffe– Søren Brunak
STRING-DB.org– Christian von Mering– Michael Kuhn– Manuel Stark– Samuel Chaffron– Chris Creevey– Jean Muller– Tobias Doerks– Philippe Julien– Alexander Roth– Milan Simonovic– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
STITCH-DB.org– Michael Kuhn– Damian Szklarczyk– Andrea Franceschini– Monica Campillos– Christian von Mering– Lars Juhl Jensen– Andreas Beyer– Peer Bork
NetworKIN.info– Rune Linding– Gerard Ostheimer– Heiko Horn– Martin Lee Miller– Francesca Diella– Karen Colwill– Jing Jin– Pavel Metalnikov– Vivian Nguyen– Adrian Pasculescu– Jin Gyoon Park– Leona D. Samson– Rob Russell– Peer Bork– Michael Yaffe– Tony Pawson
– Reflect.ws– Sean O’Donoghue– Heiko Horn– Evangelos Pafilis– Michael Kuhn– Nigel Brown– Reinhardt Schneider
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larsjuhljensen