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Advanced bioinformatics methods for proteomics

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Lars Juhl Jensen
Lars Juhl Jensen
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Advanced bioinformatics methods for proteomics Lars Juhl Jensen
three parts
signaling networks
association networks
text mining
Part 1 signaling 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
automated pipeline
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
Part 2 association 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
genetic interactions
Beyer et al., Nature Reviews Genetics, 2007
gene coexpression
curated knowledge
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many data types
many databases
different formats
different identifiers
variable quality
not comparable
spread over 1100+ genomes
quality scores
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 3 text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
identify the concepts
proteins
small molecules
comprehensive lexicon
orthographic variation
“black list”
Reflect
augmented browsing
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
information extraction
formalize the facts
co-mentioning
global statistical analysis
NLP Natural Language Processing
parsing individual sentences
summary
computational biology
data mining
text mining
save you much time
Acknowledgments NetPhorest NetworKIN STRING Reflect Rune Linding Rune Linding Christian von Mering Sune Frankild Martin Lee Miller Heiko Horn Damian Szklarczyk Heiko Horn Erwin Schoof Gerard Ostheimer Michael Kuhn Evangelos Pafilis Francesca Diella Martin Lee Miller Manuel Stark Michael Kuhn Claus Jørgensen Francesca Diella Samuel Chaffron Nigel Brown Michele Tinti Karen Colwill Chris Creevey Reinhardt Lei Li Jing Jin Jean Muller Schneider Marilyn Hsiung Pavel Metalnikov Tobias Doerks Sean O’Donoghue Sirlester A. Parker Vivian Nguyen Philippe Julien Jennifer Bordeaux Adrian Pasculescu Alexander Roth Thomas Sicheritz-Pontén Jin Gyoon Park Milan Simonovic Marina Olhovsky Leona D. Samson Jan Korbel Adrian Pasculescu Rob Russell Berend Snel Jes Alexander Peer Bork Martijn Huynen Stefan Knapp Michael Yaffe Peer Bork Nikolaj Blom Tony Pawson Peer Bork Shawn Li Gianni Cesareni Tony Pawson Benjamin E. Turk Michael B. Yaffe Søren Brunak
larsjuhljensen
Advanced bioinformatics methods for proteomics

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Notes de l'éditeur

  1. Integration Automation Collaboration