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Mining and communicating biomedical knowledge
Lars Juhl Jensen
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Part 1complex regulation
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cell-cycle regulation
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microarrays
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time courses
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Gauthier et al., Nucleic Acids Research, 2007
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protein interactions
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Jensen & Bork, Science, 2008
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temporal network
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de Lichtenberg, Jensen et al., Science, 2005
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just-in-time assembly
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de Lichtenberg, Jensen et al., Cell Cycle, 2007
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evolutionary flexibility
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individual genes
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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protein complexes
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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just-in-time assembly
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Part 2buried knowledge
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exponential growth
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some things are constant
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~45 seconds per paper
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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new uses for old drugs
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Campillos & Kuhn et al., Science, 2008
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augmented browsing
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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semantic indexing
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>10 km<10 hours
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Part 3science communication
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~150 years ago
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today
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incremental evolution
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historical baggage
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subscription charges
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space restrictions
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issues
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editorial filtering
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pre-publication peer review
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the world has changed
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internet economy
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publishing is changing
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open access
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free to download
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free to reuse
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same publication process
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publish first
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filter later
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post-publication peer review
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conference reporting
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Brumfiel, Nature, 2009
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Saunders et al., PLoS Computational Biology, 2009
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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!