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Advanced bioinformaticsmethods for proteomics
Lars Juhl Jensen
three parts
signaling networks
association networks
text mining
Part 1signaling networks
phosphoproteomics
Linding, Jensen, Ostheimer et al., Cell, 2007
in vivo phosphosites
kinases are unknown
sequence specificity
Miller, Jensen et al., Science Signaling, 2008
NetPhorest
Miller, Jensen et al., Science Signaling, 2008
motif atlas
kinases
phospho-binding proteins
phosphatases
protein-specific
no context
co-activators
protein scaffolds
localization
expression
association network
Linding, Jensen, Ostheimer et al., Cell, 2007
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
web interface
Part 2association networks
guilt by association
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
>1100 genomes
computational predictions
genomic context
gene fusion
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
gene coexpression
curated knowledge
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
von Mering et al., Nucleic Acids Research, 2005
missing most of the data
Part 3text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
proteins
cellular components
compartments.jensenlab.org
tissues
tissues.jensenlab.org
diseases
orthographic variation
singular vs. plural
spaces and hyphens
“black list”
information extraction
co-mentioning
NLPNatural Language Processing
Gene and protein names
Cue words for entity recognition
Verbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
summary
bioinformatics
more than BLAST
data/text mining
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
Text-miningSune Frankild
Evangelos Pafilis
Janos Binder
Heiko Horn
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue
larsjuhljensen