Bioinformatics of cellular processesProtein networks, signaling and regulation

Lars Juhl Jensen

EMBL Heidelberg

functional networks

data integration

protein interactions

genetic interactions

gene coexpression

genomic context methods

gene neighborhood

gene fusion

phylogenetic profiles

literature mining

curated knowledge

variable quality

benchmarking

probabilistic network

signaling networks

phosphoproteomics

in vivo phosphosites

kinases are unknown

computational methods

overprediction

context

scaffolders

interaction networks

NetworKIN

benchmarking

DNA damage response

experimental validation

dynamic networks

the cell cycle

microarrays

expression profiles

cell-cycle-regulated genes

protein interactions

temporal network

global observations

dynamic and static subunits

consistent timing

phosphorylation by CDK

27% of dynamic proteins

8% of static proteins

targeted degradation

44% of dynamic proteins

29% of static proteins

just-in-time assembly

summary

networks

data integration

highly specific predictions

new biological principles

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