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!