Advanced bioinformaticsmethods for proteomics
Lars Juhl Jensen
signaling networks
association networks
Part 1signaling networks
Linding, Jensen, Ostheimer et al., Cell, 2007
in vivo phosphosites
kinases are unknown
sequence specificity
Miller, Jensen et al., Science Signaling, 2008
automated pipeline
Miller, Jensen et al., Science Signaling, 2008
phospho-binding proteins
protein scaffolds
association network
Linding, Jensen, Ostheimer et al., Cell, 2007
Linding, Jensen, Ostheimer et al., Cell, 2007
Part 2association networks
guilt by association
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
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
different formats
different identifiers
spread over 1100+ genomes
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
von Mering et al., Nucleic Acids Research, 2005
orthology transfer
missing most of the data
Part 3text mining
as smart as a dog
teach it specific tricks
named entity recognition
identify the concepts
comprehensive lexicon
orthographic variation
augmented browsing
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
information extraction
formalize the facts
global statistical analysis
NLPNatural Language Processing
parsing individual sentences
computational biology
save you much time
AcknowledgmentsNetPhorestRune Linding
Martin Lee Miller
Erwin Schoof
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
STRINGChristian 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
NetworKINRune 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
ReflectSune Frankild
Heiko Horn
Evangelos Pafilis
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue