• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
Systems biology - Bioinformatics on complete biological systems
 

Systems biology - Bioinformatics on complete biological systems

on

  • 312 views

 

Statistics

Views

Total Views
312
Views on SlideShare
312
Embed Views
0

Actions

Likes
1
Downloads
92
Comments
0

0 Embeds 0

No embeds

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    Systems biology - Bioinformatics on complete biological systems Systems biology - Bioinformatics on complete biological systems Presentation Transcript

    • Lars Juhl Jensen Systems biology Bioinformatics on complete biological systems
    • can a biologist fix a radio?
    • Lazebnik, Biochemistry, 2004
    • one gene
    • one postdoc
    • knockout phenotype
    • name the gene
    • Lazebnik, Biochemistry, 2004
    • all aspects
    • one gene
    • high-throughput biology
    • one technology
    • one lab
    • all genes
    • one aspect
    • systems biology
    • complete systems
    • all aspects
    • all genes
    • systems-level properties
    • two subfields
    • mathematical modeling
    • small systems
    • data integration
    • large systems
    • mathematical modeling
    • small systems
    • Chen, Mol. Biol. Cell, 2004
    • many equations
    • Chen, Mol. Biol. Cell, 2004
    • simulation
    • Chen, Mol. Biol. Cell, 2004
    • many parameters
    • Chen, Mol. Biol. Cell, 2004
    • equires detailed knowledge
    • network biology
    • association networks
    • guilt by association
    • protein networks
    • STRING
    • >1100 organisms
    • ~2.6 million proteins
    • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    • Exercise 1 Go to http://string-db.org Query for CDC28 in budding yeast Try different evidence views Show only high-confidence links Show only experimental evidence
    • genomic context
    • gene fusion
    • Korbel et al., Nature Biotechnology, 2004
    • operons
    • Korbel et al., Nature Biotechnology, 2004
    • bidirectional promoters
    • Korbel et al., Nature Biotechnology, 2004
    • phylogenetic profiles
    • Korbel et al., Nature Biotechnology, 2004
    • a real example
    • Cell Cellulosomes Cellulose
    • experimental data
    • gene coexpression
    • protein interactions
    • Jensen & Bork, Science, 2008
    • genetic interactions
    • Beyer et al., Nature Reviews Genetics, 2007
    • curated knowledge
    • complexes
    • pathways
    • Letunic & Bork, Trends in Biochemical Sciences, 2008
    • chemical networks
    • STITCH
    • STRING + 300k chemicals
    • drugs
    • metabolites
    • known drug targets
    • high-throughput assays
    • metabolic pathways
    • Exercise 2 Go to http://stitch-db.org Query for TYMS in human What is the role of thymidylate? What is the role of dUMP What is the role of Permetrexed
    • many databases
    • different formats
    • different identifiers
    • variable quality
    • not comparable
    • hard work
    • quality scores
    • von Mering et al., Nucleic Acids Research, 2005
    • calibrate vs. gold standard
    • missing most of the data
    • text mining
    • >10 km
    • too much to read
    • computer
    • as smart as a dog
    • teach it specific tricks
    • named entity recognition
    • comprehensive lexicon
    • cyclin dependent kinase 1
    • CDK1
    • CDC2
    • flexible matching
    • spaces and hyphens
    • cyclin dependent kinase 1
    • cyclin-dependent kinase 1
    • orthographic variation
    • CDC2
    • hCdc2
    • “black list”
    • SDS
    • information extraction
    • count co-mentioning
    • within documents
    • within paragraphs
    • within sentences
    • scoring scheme
    • proteins
    • small molecules
    • compartments
    • tissues
    • phenotypes
    • diseases
    • adverse drug reactions
    • organisms
    • environments
    • Exercise 3 Go to http://diseases.jensenlab.org Find TYMS disease associations nspect the text-mining evidence Find genes linked to colorectal cance Explore the gene network
    • text corpus
    • ~22 million abstracts
    • no access
    • ~4 million full-text articles
    • augmented browsing
    • Reflect
    • browser add-on
    • real-time text mining
    • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
    • localization and disease
    • suite of web resources
    • common backend database
    • curated knowledge
    • experimental data
    • text mining
    • computational predictions
    • unified identifiers
    • quality scores
    • visualization
    • COMPARTMENTS
    • compartments.jensenlab.org
    • TISSUES
    • tissues.jensenlab.org
    • more to come
    • summary
    • bioinformatics
    • more than alignment
    • data/text mining
    • save you much time
    • questions?