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Medical bioinformatics: Current trends, industry needs, and core competencies

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Lars Juhl Jensen
Lars Juhl Jensen
Wissenschaft
1 von 95
Medical bioinformatics Current trends, industry needs, and core competences Lars Juhl Jensen
Ph.D.
postdoc
staff scientist
group leader
cofounder
current trends
compressive genomics
next generation sequencing
scaling challenge
Loh et al., Nature Biotechnology, 2012
exponential cost increase
store only differences
work on compressed data
sublinear scaling
new algorithms needed
network biology
beyond pathways
no discoveries
protein networks
STRING
Franceschini et al., Nucleic Acids Research, 2013
regulation
cell cycle
de Lichtenberg, Jensen et al., Science, 2005
disease phenotypes
heart development
Lage et al., Molecular Systems Biology, 2010
diabetes
Bergholdt et al., Diabetes, 2013
applied text mining
biomedical literature
>10 km
too much to read
full-text articles
electronic health records
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
temporal correlations
diagnosis trajectories
Jensen et al., submitted, 2013
adverse drug reactions
Eriksson et al., submitted, 2013
industry needs
goals
biomarker discovery
target discovery
ADR prediction
data sources
in-house data
expression profiles
screening assays
security
legal agreements
poorly standardized
public data
expression profiles
interaction networks
literature
unawareness
patient data
security
privacy
core competencies
biological data mining
quantity is not the problem
many data types
different formats
different identifiers
different quality
scripting language
biological understanding
statistical mindset
medical text mining
free text
in Norwegian
by busy doctors
text-mining techniques
information extraction
named entity recognition
dictionary construction
medical knowledge
speak Norwegian
summary
custom solution
no standard software
interdisciplinary team
outsourcing

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Medical bioinformatics: Current trends, industry needs, and core competencies