Network biology: Large-scale biomedical data and text mining
Systems biology: Large-scale biomedical data mining
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Transcript of Systems biology: Large-scale biomedical data mining
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Systems biologyLarge-scale biomedical data mining
Lars Juhl Jensen
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association networks
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who?
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guilt by association
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protein networks
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Frishman et al., Modern Genome Annotation, 2009
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computational predictions
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Korbel et al., Nature Biotechnology, 2004
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experimental data
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Jensen & Bork, Science, 2008
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curated knowledge
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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text mining
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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confidence scores
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signaling networks
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what?
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phosphoproteomics
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sequence specificity
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Miller, Jensen et al., Science Signaling, 2008
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automated pipeline
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Miller, Jensen et al., Science Signaling, 2008
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cellular context
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Linding, Jensen, Ostheimer et al., Cell, 2007
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>2x better accuracy
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dynamic networks
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when?
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cell-cycle regulation
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microarray time courses
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Gauthier et al., Nucleic Acids Research, 2007
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protein interactions
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temporal network
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de Lichtenberg, Jensen et al., Science, 2005
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just-in-time assembly
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de Lichtenberg, Jensen et al., Cell Cycle, 2007
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evolutionary flexibility
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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summary
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data mining
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specific predictions
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systems properties
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thank you!NetPhorest
– 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– Christian von Mering– Damian Szklarczyk– 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
Reflect– Sune Frankild– Heiko Horn– Evangelos Pafilis– Michael Kuhn– Nigel Brown– Reinhardt Schneider– Sean O’Donoghue
NetworKIN– Rune Linding– Heiko Horn– Gerard Ostheimer– 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
Cyclebase– Ulrik de Lichtenberg– Thomas Skøt Jensen– Nicholas Paul Gauthier– Rasmus Wernersson– Søren Brunak
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