Systems biologyLarge-scale biomedical data mining

Lars Juhl Jensen

association networks

who?

guilt by association

protein networks

Frishman et al., Modern Genome Annotation, 2009

computational predictions

Korbel et al., Nature Biotechnology, 2004

experimental data

Jensen & Bork, Science, 2008

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences, 2008

text mining

Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009

confidence scores

signaling networks

what?

phosphoproteomics

sequence specificity

Miller, Jensen et al., Science Signaling, 2008

automated pipeline

Miller, Jensen et al., Science Signaling, 2008

cellular context

Linding, Jensen, Ostheimer et al., Cell, 2007

>2x better accuracy

dynamic 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

just-in-time assembly

de Lichtenberg, Jensen et al., Cell Cycle, 2007

evolutionary flexibility

Jensen, Jensen, de Lichtenberg et al., Nature, 2006

summary

data mining

specific predictions

systems properties

thank you!NetPhorest

– 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– 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

Reflect– Sune Frankild– Heiko Horn– Evangelos Pafilis– Michael Kuhn– Nigel Brown– Reinhardt Schneider– Sean O’Donoghue

NetworKIN– 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

Cyclebase– Ulrik de Lichtenberg– Thomas Skøt Jensen– Nicholas Paul Gauthier– Rasmus Wernersson– Søren Brunak

larsjuhljensen