Cellular Network Biology
Lars Juhl Jensen
proteome analysis
mass spectrometry
proteins
modifications
biological context
evolutionary conservation
Weinert et al., Science Signaling, 2011
protein networks
Hendriks et al., NSMB, 2017
data integration
string-db.org
9.6 million proteins
functional associations
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
experimental data
Jensen & Bork, Science, 2008
genomic context
Korbel et al., Nature Biotechnology, 2004
many databases
different formats
different identifiers
variable quality
most is missing
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
dictionary
cyclin dependent kinase 1
CDC2
“black list”
SDS
co-mentioning
relation extraction
medical data
Jensen et al., Nature Reviews Genetics, 2012
diagnosis trajectories
Jensen et al., Nature Communications, 2014
adverse drug reactions
clinical narrative
medication data
Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
Adverse event
ADR of
additional drug
Identification start
clinical proteomics
Cellular Network Biology

Cellular Network Biology