Network biology

Lars Juhl Jensen

sequence analysis

Jensen, Gupta et al., Journal of Molecular Biology, 2002

data mining

de Lichtenberg, Jensen et al., Science, 2005

Campillos & Kuhn et al., Science, 2008

medical informatics

Part 1signaling networks

phosphoproteomics

Linding, Jensen, Ostheimer et al., Cell, 2007

in vivo phosphosites

kinases are unknown

sequence specificity

Miller, Jensen et al., Science Signaling, 2008

NetPhorest

data organization

Miller, Jensen et al., Science Signaling, 2008

automated pipeline

Miller, Jensen et al., Science Signaling, 2008

motif atlas

protein-specific

no context

co-activators

protein scaffolds

localization

expression

association network

Linding, Jensen, Ostheimer et al., Cell, 2007

NetworKIN

Linding, Jensen, Ostheimer et al., Cell, 2007

Part 2association networks

guilt by association

STRING

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

630 genomes

genomic context

gene fusion

Korbel et al., Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology, 2004

experimental data

protein interactions

Jensen & Bork, Science, 2008

genetic interactions

Beyer et al., Nature Reviews Genetics, 2007

gene coexpression

curated knowledge

protein complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many data types

many databases

different formats

different identifiers

variable quality

many parsers

identifier mapping

quality scores

calibrate vs. gold standard

von Mering et al., Nucleic Acids Research, 2005

orthology transfer

von Mering et al., Nucleic Acids Research, 2005

missing most of the data

Part 3text mining

exponential growth

some things are constant

~45 seconds per paper

computer

as smart as a dog

teach it specific tricks

named entity identification

Reflect

augmented browsing

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

comprehensive lexicon

orthographic variation

“black list”

information extraction

co-occurrence

scalable

>10 km<10 hours

no access

collaborate with publishers

AcknowledgmentsReflectSune FrankildHeiko HornEvangelos PafilisMichael KuhnReinhardt SchneiderSean O’Donoghue

STRINGDamian SzklarczykAndrea FranceschiniMichael KuhnMilan SimonovicAlexander RothPablo MinguezTobias DoerksManuel StarkJean MullerPeer BorkChristian von Mering

NetworKINHeiko HornMartin Lee MillerGerard OstheimerFrancesca DiellaClaus JørgensenRob RussellPeer BorkBenjamin TurkMichael YaffeTony PawsonRune Linding

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