Networks of proteins and diseases
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Transcript of Networks of proteins and diseases
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Networks of proteins and diseases
Lars Juhl Jensen
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sequence analysis
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protein networks
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de Lichtenberg, Jensen et al., Science, 2005
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adverse drug reactions
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Campillos, Kuhn et al., Science, 2008
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group leader
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cofounder
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data mining
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proteomics
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text mining
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biomedical literature
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electronic health records
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protein networks
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guilt by association
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STRING
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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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gene neighborhood
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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experimental data
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gene coexpression
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protein interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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complexes
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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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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CDC2
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cyclin dependent kinase 1
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expansion rules
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hCdc2
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CDC2
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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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augmented browsing
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Reflect
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browser add-on
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real-time text mining
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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information extraction
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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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text corpus
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~22 million abstracts
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no access
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~4 million full-text articles
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localization and disease
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general approach
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COMPARTMENTS
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TISSUES
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DISEASES
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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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common identifiers
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quality scores
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visualization
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compartments.jensenlab.org
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tissues.jensenlab.org
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dissemination
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web interfaces
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web services
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diseases.jensenlab.org
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bulk download
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disease networks
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medical data
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electronic health records
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central registries
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individual hospitals
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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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in Danish
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by busy doctors
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confounding factors
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age and gender
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reporting bias
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custom dictionaries
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typo rules
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age/gender matching
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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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temporal correlation
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diagnosis trajectories
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Jensen et al., in preparation, 2013
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pharmocovigilance
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adverse drug reactions
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Eriksson et al., submitted, 2013
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ADR profiles
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Eriksson et al., submitted, 2013
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ADR frequencies
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Eriksson et al., submitted, 2013
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molecular basis
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protein networks
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AcknowledgmentsSTRINGChristian von MeringDamian SzklarczykMichael KuhnManuel StarkSamuel ChaffronChris CreeveyJean MullerTobias DoerksPhilippe JulienAlexander RothMilan SimonovicJan KorbelBerend SnelMartijn HuynenPeer Bork
Text miningSune FrankildEvangelos PafilisKalliopi TsafouAlberto SantosJanos 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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Thank you!