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Large-scale data and text mining

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Hagedorn Research Institute, Gentofte, Denmark, October 8, 2009.

Hagedorn Research Institute, Gentofte, Denmark, October 8, 2009.

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    Large-scale data and text mining Large-scale data and text mining Presentation Transcript

    • 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
    •  
    • Acknowledgments
      • NetPhorest.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
    • larsjuhljensen