Kinetic Analysis of Protein Assembly on the Basis of the ...
Protein networks: A basis for large-scale data mining
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Protein networks A basis for large-scale data mining Lars Juhl Jensen
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MiTiN Consortium Meeting, Institute for Research in Biomedicine, Barcelona, Spain, March 9, 2010.
Transcript of Protein networks: A basis for large-scale data mining
Protein networksA basis for large-scale data mining
Lars Juhl Jensen
Phase 1association networks
who?
Frishman et al., Modern Genome Annotation, 2009
STRING
computational predictions
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
literature mining
confidence scores
cross-species transfer
Phase 2signaling networks
what?
phosphoproteomics
signaling events
NetPhorest
automation
Miller, Jensen et al., Science Signaling, 2008
specificity atlas
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
benchmarking
Linding, Jensen, Ostheimer et al., Cell, 2007
context is crucial
Phase 3dynamic networks
when?
cell-cycle regulation
microarray time courses
Gauthier et al., Nucleic Acids Research, 2007
protein interactions
temporal network
de Lichtenberg, Jensen et al., Science, 2005
de Lichtenberg, Jensen et al., Science, 2005
just-in-time assembly
de Lichtenberg, Jensen et al., Cell Cycle, 2007
evolutionary flexibility
individual genes
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
summary
networks
data integration
specific predictions
systems properties
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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