Large-scale data and text mining Lars Juhl Jensen

function prediction

Jensen, Gupta et al., Journal of Molecular Biology , 2002

cell-cycle regulation

de Lichtenberg, Jensen et al., Science , 2005

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

phosphorylation

signaling networks

upstream events

downstream events

NetworKIN

sequence motifs

NetPhorest

automated pipeline

Miller, Jensen et al., Science Signaling , 2008

data organization

Miller, Jensen et al., Science Signaling , 2008

compilation of datasets

redundancy reduction

training and evaluation

motif atlas

model organisms

other modifications

protein networks

functional associations

STRING

Jensen, Kuhn et al., Nucleic Acids Research , 2009

630 genomes

genomic context

Korbel et al., Nature Biotechnology , 2004

Korbel et al., Nature Biotechnology , 2004

Korbel et al., Nature Biotechnology , 2004

physical interactions

Jensen & Bork, Science , 2008

genetic interactions

Beyer et al., Nature Reviews Genetics , 2007

gene coexpression

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences , 2008

literature mining

>10 km

confidence scores

cross-species integration

visualization

Frishman et al., Modern Genome Annotation , 2009

small molecules

STITCH

Kuhn et al., Nucleic Acids Research , 2008

kinase inhibitor screens

Fedorov et al., PNAS , 2007

augmented browsing

Reflect

collaborate publishers

Acknowledgments NetPhorest.info 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-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 STITCH-DB.org Michael Kuhn Damian Szklarczyk Andrea Franceschini Monica Campillos Christian von Mering Lars Juhl Jensen Andreas Beyer Peer Bork 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 Reflect.ws Sean O’Donoghue Heiko Horn Evangelos Pafilis Michael Kuhn Nigel Brown Reinhardt Schneider

NetPhorest.info

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-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

STITCH-DB.org

Michael Kuhn

Damian Szklarczyk

Andrea Franceschini

Monica Campillos

Christian von Mering

Lars Juhl Jensen

Andreas Beyer

Peer Bork

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

Reflect.ws

Sean O’Donoghue

Heiko Horn

Evangelos Pafilis

Michael Kuhn

Nigel Brown

Reinhardt Schneider

larsjuhljensen