In Silico and Text-Based Analysisof Cellular Networks
Lars Juhl Jensen
association networks
guilt by association
computational predictions
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
gene coexpression
physical interactions
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
different formats
different identifiers
von Mering et al., Nucleic Acids Research, 2005
score calibration
von Mering et al., Nucleic Acids Research, 2005
missing most of the data
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
cyclin dependent kinase 1
orthographic variation
spaces and hyphens
cyclin dependent kinase 1
cyclin-dependent kinase 1
prefixes and suffixes
within paragraphs
Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
chemical networks
Kuhn et al., Nucleic Acids Research, 2014stitch-db.org
subcellular localization
Binder et al., Database, 2014compartments.jensenlab.org
tissue expression
tissues.jensenlab.org Santos et al., submitted, 2015
cell-cycle expression
Santos et al., Nucleic Acids Research, 2015cyclebase.org
disease associations
diseases.jensenlab.org Frankild et al., Methods, 2015
AcknowledgmentsMolecular networks
Michael KuhnDamian Szklarczyk
Andrea Franceschini Milan SimonovicAlexander Roth
Sune Pletscher-FrankildJianyi Lin
Pablo MinguezChristian von Mering
Peer Bork
Time and spaceAlberto SantosSune Pletscher-FrankildJanos BinderKalliopi TsafouChristian StolteAlbert PallejaHeiko HornRasmus WernerssonReinhardt SchneiderSean O’ Donoghue