Mining and communicating biomedical knowledge

Lars Juhl Jensen

Part 1complex regulation

cell-cycle regulation

microarrays

time courses

Gauthier et al., Nucleic Acids Research, 2007

protein interactions

Jensen & Bork, Science, 2008

temporal network

de Lichtenberg, Jensen et al., Science, 2005

just-in-time assembly

de Lichtenberg, Jensen et al., Cell Cycle, 2007

evolutionary flexibility

individual genes

Jensen, Jensen, de Lichtenberg et al., Nature, 2006

protein complexes

Jensen, Jensen, de Lichtenberg et al., Nature, 2006

just-in-time assembly

Part 2buried knowledge

exponential growth

some things are constant

~45 seconds per paper

computer

as smart as a dog

teach it specific tricks

named entity recognition

new uses for old drugs

Campillos & Kuhn et al., Science, 2008

augmented browsing

Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009

semantic indexing

>10 km<10 hours

Part 3science communication

~150 years ago

today

incremental evolution

historical baggage

subscription charges

space restrictions

issues

editorial filtering

pre-publication peer review

the world has changed

internet economy

publishing is changing

open access

free to download

free to reuse

same publication process

publish first

filter later

post-publication peer review

conference reporting

Brumfiel, Nature, 2009

Saunders et al., PLoS Computational Biology, 2009

Thanks

Past and present colleagues at– Center for Biological Sequence Analysis– European Molecular Biology Laboratory– Novo Nordisk Foundation Center for Protein Research

The bloggers who made it happen at ISMB

The Lundbeck Foundation

All of you who are here today!