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
AcknowledgmentsNetPhorest.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
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