Networks of proteins and diseases
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Networks of proteins and diseases
Lars Juhl Jensen
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three parts
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protein networks
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localization and diseases
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disease networks
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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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experimental data
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Jensen & Bork, Science, 2008
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curated knowledge
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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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>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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CDK1
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CDC2
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orthographic variation
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cyclin-dependent kinase 1
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hCdc2
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“black list”
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SDS
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information extraction
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co-mentioning
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localization and disease
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proteins
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compartments
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tissues
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diseases
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suite of web resources
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jensenlab.org
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text mining
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curated knowledge
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experimental data
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computational predictions
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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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project onto networks
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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compartments.jensenlab.org
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tissues.jensenlab.org
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diseases.jensenlab.org
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disease networks
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medical data
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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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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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comorbidity matrix
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Roque et al., PLoS Computational Biology, 2011
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comorbidity network
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temporal correlation
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Jensen et al., in preparation, 2012
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disease trajectories
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Jensen et al., in preparation, 2012
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molecular basis
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protein networks
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Acknowledgments
STRINGChristian 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 miningSune Frankild
Evangelos Pafilis
Janos Binder
Kalliopi Tsafou
Alberto Santos
Heiko Horn
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue
EHR miningAnders 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
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Thank you!