protein networks: a basis for large-scale data mining
DESCRIPTION
MiTiN Consortium Meeting, Institute for Research in Biomedicine, Barcelona, Spain, March 9, 2010.TRANSCRIPT
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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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Frishman et al., Modern Genome Annotation, 2009
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STRING
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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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literature mining
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confidence scores
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cross-species transfer
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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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NetPhorest
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automation
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Miller, Jensen et al., Science Signaling, 2008
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specificity atlas
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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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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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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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AcknowledgmentsNetPhorest.info
– Rune Linding– Martin Lee Miller– Heiko Horn– 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
Cyclebase.org– Ulrik de Lichtenberg– Thomas Skøt Jensen– Nicholas Paul Gauthier– Rasmus Wernersson– Søren Brunak
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
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larsjuhljensen