networks of proteins and diseases
TRANSCRIPT
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Networks of proteins and diseases
Lars Juhl Jensen
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association networks
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proteins
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diseases
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protein networks
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STRING
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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computational predictions
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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conserved neighborhood
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Korbel et al., Nature Biotechnology, 2004
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experimental data
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physical interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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metabolic pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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integrate it all
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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hard work
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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calibrate vs. gold standard
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missing most of the data
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text mining
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>10 km
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too much to read
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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comprehensive lexicon
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cyclin dependent kinase 1
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CDC2
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expansion rules
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CDC2
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hCdc2
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flexible matching
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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“black list”
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SDS
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co-mentioning
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within documents
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within paragraphs
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within sentences
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weighted counts
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localization and disease
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general approach
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suite of web resources
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curated knowledge
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experimental data
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text mining
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computational predictions
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quality scores
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proteins
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compartments
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compartments.jensenlab.org
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tissues
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tissues.jensenlab.org
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diseases
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evidence viewers
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web services
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compartments.jensenlab.org
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download files
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disease networks
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electronic health records
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Jensen et al., Nature Reviews Genetics, 2012
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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unstructured data
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comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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Roque et al., PLoS Computational Biology, 2011
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in Danish
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multiple testing
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confounding factors
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age and gender
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reporting bias
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temporal correlation
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diagnosis trajectories
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Jensen et al., in preparation, 2013
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diabetes progression
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Jensen et al., in preparation, 2013
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molecular basis
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protein networks
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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
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