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Protein networksA basis for large-scale data mining
Lars Juhl Jensen
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Phase 1association networks
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who?
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STRING
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Jensen, Kuhn et al., Nucleic Acids Research, 2009
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genomic context
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Korbel et al., Nature Biotechnology, 2004
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gene coexpression
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protein interactions
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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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literature mining
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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confidence scores
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von Mering et al., Nucleic Acids Research, 2005
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transfer by orthology
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probabilistic integration
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Frishman et al., Modern Genome Annotation, 2009
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Phase 2signaling networks
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what?
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phosphoproteomics
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signaling events
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sequence motifs
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Miller, Jensen et al., Science Signaling, 2008
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NetPhorest
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Miller, Jensen et al., Science Signaling, 2008
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NetworKIN
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Linding, Jensen, Ostheimer et al., Cell, 2007
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benchmarking
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Linding, Jensen, Ostheimer et al., Cell, 2007
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context is crucial
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use cases
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DNA damage response
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Linding, Jensen, Ostheimer et al., Cell, 2007
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cell-cycle kinases
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Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling, 2010
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Phase 3dynamic 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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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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individual genes
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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protein complexes
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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phosphorylation
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co-evolution
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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summary
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networks
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data integration
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specific predictions
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systems properties
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thank you!
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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– 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
Cyclebase.org– Ulrik de Lichtenberg– Thomas Skøt Jensen– Nicholas Paul Gauthier– Rasmus Wernersson– Søren Brunak
NetworKIN.info– 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
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larsjuhljensen