Medical bioinformaticsCurrent 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