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Network biology - Large-scale biomedical data and text mining

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Lars Juhl Jensen
Lars Juhl Jensen
TechnologieFormation
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Network biology Large-scale biomedical data and text mining Lars Juhl Jensen
three parts
one thing in common
guilt by association
Part 1 protein networks
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
>1100 genomes
genomic context
gene fusion
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
many data types
many databases
different formats
different identifiers
variable quality
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
von Mering et al., Nucleic Acids Research, 2005
orthology transfer
Part 2 literature mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
identify the concepts
proteins
compartments
tissues
diseases
comprehensive lexicon
orthographic variation
“black list”
information extraction
co-mentioning
http://diseases.jensenlab.org
abstracts
restricted full-text access
collaborate with publishers
Part 3 medical informatics
electronic health records
Jensen et al., Nature Reviews Genetics, 2012
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
in Danish
by busy doctors
about psychiatric patients
comorbidity
Jensen et al., Nature Reviews Genetics, 2012
multiple testing
Roque et al., PLoS Computational Biology, 2011
patient clustering
Roque et al., PLoS Computational Biology, 2011
cluster characterization
Roque et al., PLoS Computational Biology, 2011
temporal correlation
medication
adverse drug events
pharmacovigilance
Acknowledgments STRING Text mining EPR mining Damian Szklarczyk Sune Frankild Francisco S Roque Andrea Franceschini Heiko Horn Peter B Jensen Michael Kuhn Evangelos Pafilis Robert Eriksson Milan Simonovic Janos Binder Henriette Schmock Alexander Roth Reinhardt Schneider Marlene Dalgaard Pablo Minguez Sean O’Donoghue Massimo Andreatta Tobias Doerks Thomas Hansen Manuel Stark Karen Søeby Jean Muller Søren Bredkjær Peer Bork Anders Juul Christian von Mering Thomas Werge Søren Brunak
larsjuhljensen
Thank you

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