network biology
TRANSCRIPT
Network biology
Lars Juhl Jensen
three parts
protein networks
localization and diseases
disease networks
protein networks
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
text mining
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
von Mering et al., Nucleic Acids Research, 2005
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
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
molecular basis
protein networks
Acknowledgments
STRINGChristian von MeringDamian SzklarczykMichael KuhnManuel StarkSamuel ChaffronChris CreeveyJean MullerTobias DoerksPhilippe JulienAlexander RothMilan SimonovicJan KorbelBerend SnelMartijn HuynenPeer Bork
Text miningSune FrankildEvangelos PafilisAlberto SantosKalliopi TsafouJanos BinderHeiko HornMichael KuhnNigel BrownReinhardt SchneiderSean O’Donoghue
EHR miningAnders Boeck JensenPeter Bjødstrup JensenFrancisco S. RoqueHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulTudor OpreaPope MoseleyThomas WergeSøren Brunak
