bioinformatics of cellular processes
DESCRIPTION
EMBO Practical Course on Methods in Cell Biology: Exploring the Dynamics of Cellular Organization, European Molecular Biology Laboratory, Heidelberg, Germany, August 23-31, 2007TRANSCRIPT
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Bioinformatics of cellular processesProtein networks, signaling and regulation
Lars Juhl Jensen
EMBL Heidelberg
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functional networks
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data integration
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protein interactions
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genetic interactions
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gene coexpression
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genomic context methods
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gene neighborhood
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gene fusion
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phylogenetic profiles
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literature mining
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curated knowledge
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variable quality
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benchmarking
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probabilistic network
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signaling networks
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phosphoproteomics
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in vivo phosphosites
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kinases are unknown
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computational methods
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overprediction
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context
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scaffolders
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interaction networks
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NetworKIN
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benchmarking
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DNA damage response
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experimental validation
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dynamic networks
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the cell cycle
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microarrays
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expression profiles
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cell-cycle-regulated genes
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protein interactions
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temporal network
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global observations
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dynamic and static subunits
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consistent timing
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phosphorylation by CDK
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27% of dynamic proteins
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8% of static proteins
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targeted degradation
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44% of dynamic proteins
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29% of static proteins
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just-in-time assembly
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summary
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networks
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data integration
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highly specific predictions
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new biological principles
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Acknowledgments
The STRING database– Christian von Mering– Michael Kuhn– Berend Snel– Martijn Huynen– Sean Hooper– Samuel Chaffron– Julien Lagarde– Mathilde Foglierini– Peer Bork
• Cell-cycle regulation– Ulrik de Lichtenberg– Thomas Skøt Jensen– Søren Brunak– Peer Bork
The NetworKIN method– Rune Linding– Gerard Ostheimer– 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