Lars Juhl Jensen
Medical network analysis
Linking diseases and genes through
data and text mining
electronic health registries
disease trajectories
community resources
linking genes and diseases
electronic health registries
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
structured data
Jensen et al., Nature Reviews Genetics, 2012
civil registration system
established in 1968
CPR number
Jensen et al., Nature Reviews Genetics, 2012
national discharge registry
14 years
6.2 million patients
119 million diagnoses
Jensen et al., Nature Reviews Genetics, 2012
reimbursement
statistical analysis
comorbidity
contingency table
Jensen et al., Nature Reviews Genetics, 2012
confounding factors
“known knowns”
sex
age
type of hospital encounter
Jensen et al., Nature Communications, 2014
“known unknowns”
smoking
diet
“unknown unknowns”
reporting biases
matched controls
temporal correlations
disease trajectories
Jensen et al., Nature Communications, 2014
clustering
trajectory networks
Jensen et al., Nature Communications, 2014
specific questions
alcohol-related sepsis
Beck et al., Scientific Reports, 2016
community resources
string-db.org
functional associations
DISEASES
disease–gene associations
curated knowledge
protein complexes
pathways
established disease genes
experimental data
physical interactions
Jensen & Bork, Science, 2008
coexpression
GWAS
text mining
>10 km
named entity recognition
gene/protein dictionary
disease dictionary
many databases
different formats
different identifiers
variable quality
not comparable
hard work
(Ph.D. students)
quality scores
affinity purification
von Mering et al., Nucleic Acids Research, 2005
cooccurrence score
score calibration
von Mering et al., Nucleic Acids Research, 2005
implicit weighting by quality
common scale
visualization
Cytoscape
Thank you

Medical network analysis: Linking diseases and genes through data and text mining