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Networks of proteins and diseases

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Lars Juhl Jensen
Lars Juhl Jensen
Technology
1 of 99
Networks of proteins and diseases Lars Juhl Jensen
association networks
proteins
diseases
protein networks
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
gene fusion
Korbel et al., Nature Biotechnology, 2004
conserved neighborhood
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
curated knowledge
metabolic pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
integrate it all
many databases
different formats
different identifiers
variable quality
not comparable
hard work
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
missing most of the data
text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
cyclin dependent kinase 1
CDC2
expansion rules
CDC2
hCdc2
flexible matching
cyclin dependent kinase 1
cyclin-dependent kinase 1
“black list”
SDS
co-mentioning
within documents
within paragraphs
within sentences
weighted counts
localization and disease
general approach
suite of web resources
curated knowledge
experimental data
text mining
computational predictions
quality scores
proteins
compartments
compartments.jensenlab.org
tissues
tissues.jensenlab.org
diseases
evidence viewers
web services
compartments.jensenlab.org
download files
disease networks
electronic health records
Jensen et al., Nature Reviews Genetics, 2012
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
comorbidity
Jensen et al., Nature Reviews Genetics, 2012
Roque et al., PLoS Computational Biology, 2011
in Danish
multiple testing
confounding factors
age and gender
reporting bias
temporal correlation
diagnosis trajectories
Jensen et al., in preparation, 2013
diabetes progression
Jensen et al., in preparation, 2013
molecular basis
protein networks
Acknowledgments STRING Christian 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 Text mining Sune Frankild Evangelos Pafilis Alberto Santos Kalliopi Tsafou Janos Binder Heiko Horn Michael Kuhn Nigel Brown Reinhardt Schneider Sean O’Donoghue EHR mining Anders Boeck Jensen Peter Bjødstrup Jensen Francisco S. Roque Henriette Schmock Marlene Dalgaard Massimo Andreatta Thomas Hansen Karen Søeby Søren Bredkjær Anders Juul Tudor Oprea Pope Moseley Thomas Werge Søren Brunak
Networks of proteins and diseases

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