SlideShare une entreprise Scribd logo
1  sur  151
Télécharger pour lire hors ligne
Systems biology
Bioinformatics on complete biological
              systems




           Lars Juhl Jensen
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
data integration
association networks
guilt by association
Systems biology - Bioinformatics on complete biological systems
STRING
~2.6 million proteins
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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
Systems biology - Bioinformatics on complete biological systems
Systems biology - Bioinformatics on complete biological systems
Systems biology - Bioinformatics on complete biological systems
Cell




       Cellulosomes




                 Cellulose
experimental data
gene coexpression
Systems biology - Bioinformatics on complete biological systems
protein interactions
Jensen & Bork, Science, 2008
curated knowledge
complexes
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
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
Systems biology - Bioinformatics on complete biological systems
Systems biology - Bioinformatics on complete biological systems
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
Systems biology - Bioinformatics on complete biological systems
Systems biology - Bioinformatics on complete biological systems
corpora
~22 million abstracts
no access
~4 million full-text articles
Systems biology - Bioinformatics on complete biological systems
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
small molecules
proteins
compartments
tissues
diseases
organisms
environments
suite of web resources
common backend database
jensenlab.org
text mining
curated knowledge
experimental data
computational predictions
quality scores
web-centric databases
DISEASES
Systems biology - Bioinformatics on complete biological systems
Systems biology - Bioinformatics on complete biological systems
visualization
COMPARTMENTS
compartments.jensenlab.org
TISSUES
tissues.jensenlab.org
project onto networks
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
compartments.jensenlab.org
tissues.jensenlab.org
diseases.jensenlab.org
summary
bioinformatics
more than alignment
data/text mining
save you much time
Acknowledgments
      Protein            Literature mining
    networks             Sune Frankild
                         Evangelos Pafilis
Christian von Mering
                         Janos Binder
 Damian Szklarczyk
                         Kalliopi Tsafou
        Michael Kuhn
                         Alberto Santos
        Manuel Stark
                         Heiko Horn
   Samuel Chaffron
                         Michael Kuhn
       Chris Creevey
                         Nigel Brown
          Jean Muller
                         Reinhardt Schneider
       Tobias Doerks
                         Sean O’Donoghue
       Philippe Julien
     Alexander Roth
    Milan Simonovic
           Jan Korbel
         Berend Snel
      Martijn Huynen

Contenu connexe

Tendances

Activity 42 c a closer look
Activity 42 c a closer lookActivity 42 c a closer look
Activity 42 c a closer lookddegennaro
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsLars Juhl Jensen
 
Network biology: Large-scale data and text mining
Network biology: Large-scale data and text miningNetwork biology: Large-scale data and text mining
Network biology: Large-scale data and text miningLars Juhl Jensen
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningLars Juhl Jensen
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningLars Juhl Jensen
 
Unraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationUnraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationLars Juhl Jensen
 
IB Biology Core 2.1: Cell Theory
IB Biology Core 2.1: Cell TheoryIB Biology Core 2.1: Cell Theory
IB Biology Core 2.1: Cell TheoryJason de Nys
 
Scientific Highlights: The Reflect and NetPhorest web resources
Scientific Highlights: The Reflect and NetPhorest web resourcesScientific Highlights: The Reflect and NetPhorest web resources
Scientific Highlights: The Reflect and NetPhorest web resourcesLars Juhl Jensen
 
Cell theory choose your adventure
Cell theory choose your adventureCell theory choose your adventure
Cell theory choose your adventureWeavedan
 
Cell theory choose your adventure
Cell theory choose your adventureCell theory choose your adventure
Cell theory choose your adventureWeavedan
 
The cell theory
The cell theoryThe cell theory
The cell theorynorvely
 
Data integration and functional association networks
Data integration and functional association networksData integration and functional association networks
Data integration and functional association networksLars Juhl Jensen
 
Unraveling cellular phosphorylation networks using computational biology
Unraveling cellular phosphorylation networks using computational biologyUnraveling cellular phosphorylation networks using computational biology
Unraveling cellular phosphorylation networks using computational biologyLars Juhl Jensen
 
CVA Biology I - B10vrv3071
CVA Biology I - B10vrv3071CVA Biology I - B10vrv3071
CVA Biology I - B10vrv3071ClayVirtual
 
Evolutionconnection mitochondriaplastids
Evolutionconnection mitochondriaplastidsEvolutionconnection mitochondriaplastids
Evolutionconnection mitochondriaplastidsElsa von Licy
 
The endosymbiosis theory associated with mitochondria and chloroplast
The  endosymbiosis  theory associated  with  mitochondria  and  chloroplastThe  endosymbiosis  theory associated  with  mitochondria  and  chloroplast
The endosymbiosis theory associated with mitochondria and chloroplastMayur Saikia
 

Tendances (20)

Activity 42 c a closer look
Activity 42 c a closer lookActivity 42 c a closer look
Activity 42 c a closer look
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomics
 
Network biology: Large-scale data and text mining
Network biology: Large-scale data and text miningNetwork biology: Large-scale data and text mining
Network biology: Large-scale data and text mining
 
Cells power point
Cells power pointCells power point
Cells power point
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
 
Unraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationUnraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integration
 
How dna works
How dna worksHow dna works
How dna works
 
IB Biology Core 2.1: Cell Theory
IB Biology Core 2.1: Cell TheoryIB Biology Core 2.1: Cell Theory
IB Biology Core 2.1: Cell Theory
 
Scientific Highlights: The Reflect and NetPhorest web resources
Scientific Highlights: The Reflect and NetPhorest web resourcesScientific Highlights: The Reflect and NetPhorest web resources
Scientific Highlights: The Reflect and NetPhorest web resources
 
Toran1
Toran1Toran1
Toran1
 
Cell theory choose your adventure
Cell theory choose your adventureCell theory choose your adventure
Cell theory choose your adventure
 
Cell theory choose your adventure
Cell theory choose your adventureCell theory choose your adventure
Cell theory choose your adventure
 
The cell theory
The cell theoryThe cell theory
The cell theory
 
Data integration and functional association networks
Data integration and functional association networksData integration and functional association networks
Data integration and functional association networks
 
Unraveling cellular phosphorylation networks using computational biology
Unraveling cellular phosphorylation networks using computational biologyUnraveling cellular phosphorylation networks using computational biology
Unraveling cellular phosphorylation networks using computational biology
 
Endosymbiotic theory
 Endosymbiotic theory Endosymbiotic theory
Endosymbiotic theory
 
CVA Biology I - B10vrv3071
CVA Biology I - B10vrv3071CVA Biology I - B10vrv3071
CVA Biology I - B10vrv3071
 
Evolutionconnection mitochondriaplastids
Evolutionconnection mitochondriaplastidsEvolutionconnection mitochondriaplastids
Evolutionconnection mitochondriaplastids
 
The endosymbiosis theory associated with mitochondria and chloroplast
The  endosymbiosis  theory associated  with  mitochondria  and  chloroplastThe  endosymbiosis  theory associated  with  mitochondria  and  chloroplast
The endosymbiosis theory associated with mitochondria and chloroplast
 

En vedette

Data integration and visualization
Data integration and visualizationData integration and visualization
Data integration and visualizationLars Juhl Jensen
 
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...Lars Juhl Jensen
 
Complementing patient records with registry data on cormormidity
Complementing patient records with registry data on cormormidityComplementing patient records with registry data on cormormidity
Complementing patient records with registry data on cormormidityLars Juhl Jensen
 
Networks of proteins and diseases
Networks of proteins and diseasesNetworks of proteins and diseases
Networks of proteins and diseasesLars Juhl Jensen
 
Turning big data and text collections into web resrouces
Turning big data and text collections into web resroucesTurning big data and text collections into web resrouces
Turning big data and text collections into web resroucesLars Juhl Jensen
 
Mining heterogeneous data: Understanding systems at the level of complexes an...
Mining heterogeneous data: Understanding systems at the level of complexes an...Mining heterogeneous data: Understanding systems at the level of complexes an...
Mining heterogeneous data: Understanding systems at the level of complexes an...Lars Juhl Jensen
 
Provenance Evidence in the Fellows' Library at Jesus College, Oxford
Provenance Evidence in the Fellows' Library at Jesus College, OxfordProvenance Evidence in the Fellows' Library at Jesus College, Oxford
Provenance Evidence in the Fellows' Library at Jesus College, OxfordEmma Jones
 
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...Managing the Maturity of Tourism Destinations: the Challenge of Governance an...
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...FEST
 
ETIS European Tourism Indicators System - Cinzia De Marzo
ETIS European Tourism Indicators System - Cinzia De MarzoETIS European Tourism Indicators System - Cinzia De Marzo
ETIS European Tourism Indicators System - Cinzia De MarzoFEST
 
Significaciones que niños y niñas de n.s.e. medio están construyendo ace...
Significaciones que niños y niñas de n.s.e. medio están      construyendo ace...Significaciones que niños y niñas de n.s.e. medio están      construyendo ace...
Significaciones que niños y niñas de n.s.e. medio están construyendo ace...Marco Nazel
 
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...JJ Liang
 
Integración transdisciplinaria
Integración transdisciplinariaIntegración transdisciplinaria
Integración transdisciplinariaJanettadry
 
[PPS] Desierto de Atacama
[PPS] Desierto de Atacama[PPS] Desierto de Atacama
[PPS] Desierto de AtacamaJosue Rodriguez
 
CompositeBuild_partner (Eng)
CompositeBuild_partner (Eng)CompositeBuild_partner (Eng)
CompositeBuild_partner (Eng)Redenex
 

En vedette (15)

Data integration and visualization
Data integration and visualizationData integration and visualization
Data integration and visualization
 
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...
Just-in-time assembly: Transcriptional and post-translational cell-cycle regu...
 
Mining the Antibodypedia
Mining the AntibodypediaMining the Antibodypedia
Mining the Antibodypedia
 
Complementing patient records with registry data on cormormidity
Complementing patient records with registry data on cormormidityComplementing patient records with registry data on cormormidity
Complementing patient records with registry data on cormormidity
 
Networks of proteins and diseases
Networks of proteins and diseasesNetworks of proteins and diseases
Networks of proteins and diseases
 
Turning big data and text collections into web resrouces
Turning big data and text collections into web resroucesTurning big data and text collections into web resrouces
Turning big data and text collections into web resrouces
 
Mining heterogeneous data: Understanding systems at the level of complexes an...
Mining heterogeneous data: Understanding systems at the level of complexes an...Mining heterogeneous data: Understanding systems at the level of complexes an...
Mining heterogeneous data: Understanding systems at the level of complexes an...
 
Provenance Evidence in the Fellows' Library at Jesus College, Oxford
Provenance Evidence in the Fellows' Library at Jesus College, OxfordProvenance Evidence in the Fellows' Library at Jesus College, Oxford
Provenance Evidence in the Fellows' Library at Jesus College, Oxford
 
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...Managing the Maturity of Tourism Destinations: the Challenge of Governance an...
Managing the Maturity of Tourism Destinations: the Challenge of Governance an...
 
ETIS European Tourism Indicators System - Cinzia De Marzo
ETIS European Tourism Indicators System - Cinzia De MarzoETIS European Tourism Indicators System - Cinzia De Marzo
ETIS European Tourism Indicators System - Cinzia De Marzo
 
Significaciones que niños y niñas de n.s.e. medio están construyendo ace...
Significaciones que niños y niñas de n.s.e. medio están      construyendo ace...Significaciones que niños y niñas de n.s.e. medio están      construyendo ace...
Significaciones que niños y niñas de n.s.e. medio están construyendo ace...
 
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...
3G GPS WIFI Portable DVR Body Worn Camera for Police Law Enforcement from Ric...
 
Integración transdisciplinaria
Integración transdisciplinariaIntegración transdisciplinaria
Integración transdisciplinaria
 
[PPS] Desierto de Atacama
[PPS] Desierto de Atacama[PPS] Desierto de Atacama
[PPS] Desierto de Atacama
 
CompositeBuild_partner (Eng)
CompositeBuild_partner (Eng)CompositeBuild_partner (Eng)
CompositeBuild_partner (Eng)
 

Similaire à Systems biology - Bioinformatics on complete biological systems

Networks of proteins and diseases
Networks of proteins and diseasesNetworks of proteins and diseases
Networks of proteins and diseasesLars Juhl Jensen
 
Mining text and data on chemicals
Mining text and data on chemicalsMining text and data on chemicals
Mining text and data on chemicalsLars Juhl Jensen
 
Integration of heterogeneous data
Integration of heterogeneous dataIntegration of heterogeneous data
Integration of heterogeneous dataLars Juhl Jensen
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningLars Juhl Jensen
 
Network biology: Large-scale biomedical data and text mining
Network biology: Large-scale biomedical data and text miningNetwork biology: Large-scale biomedical data and text mining
Network biology: Large-scale biomedical data and text miningLars Juhl Jensen
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsLars Juhl Jensen
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsLars Juhl Jensen
 
Visualization of large-scale protein and disease networks
Visualization of large-scaleprotein and disease networksVisualization of large-scaleprotein and disease networks
Visualization of large-scale protein and disease networksLars Juhl Jensen
 
Network biology: Large-scale data integration and text mining
Network biology: Large-scale data integration and text miningNetwork biology: Large-scale data integration and text mining
Network biology: Large-scale data integration and text miningLars Juhl Jensen
 
Network biology - Large-scale data integration and text mining
Network biology - Large-scale data integration and text miningNetwork biology - Large-scale data integration and text mining
Network biology - Large-scale data integration and text miningLars Juhl Jensen
 
The STRING database and related tools
The STRING database and related toolsThe STRING database and related tools
The STRING database and related toolsLars Juhl Jensen
 
Data integration: The STITCH database of protein-small molecule interactions
Data integration: The STITCH database of protein-small molecule interactionsData integration: The STITCH database of protein-small molecule interactions
Data integration: The STITCH database of protein-small molecule interactionsLars Juhl Jensen
 
Systems biology - Understanding biology at the systems level
Systems biology - Understanding biology at the systems levelSystems biology - Understanding biology at the systems level
Systems biology - Understanding biology at the systems levelLars Juhl Jensen
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsLars Juhl Jensen
 
STRING - Modeling of biological systems through cross-species data integ...
STRING - Modeling of biological systems through cross-species data integ...STRING - Modeling of biological systems through cross-species data integ...
STRING - Modeling of biological systems through cross-species data integ...Lars Juhl Jensen
 
Unraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationUnraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationLars Juhl Jensen
 
Mining molecules from text and data
Mining molecules from text and dataMining molecules from text and data
Mining molecules from text and dataLars Juhl Jensen
 

Similaire à Systems biology - Bioinformatics on complete biological systems (20)

Networks of proteins and diseases
Networks of proteins and diseasesNetworks of proteins and diseases
Networks of proteins and diseases
 
Mining text and data on chemicals
Mining text and data on chemicalsMining text and data on chemicals
Mining text and data on chemicals
 
Integration of heterogeneous data
Integration of heterogeneous dataIntegration of heterogeneous data
Integration of heterogeneous data
 
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data miningProtein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
 
Disease Systems Biology
Disease Systems BiologyDisease Systems Biology
Disease Systems Biology
 
Network biology: Large-scale biomedical data and text mining
Network biology: Large-scale biomedical data and text miningNetwork biology: Large-scale biomedical data and text mining
Network biology: Large-scale biomedical data and text mining
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomics
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomics
 
Visualization of large-scale protein and disease networks
Visualization of large-scaleprotein and disease networksVisualization of large-scaleprotein and disease networks
Visualization of large-scale protein and disease networks
 
Network biology
Network biologyNetwork biology
Network biology
 
Network biology: Large-scale data integration and text mining
Network biology: Large-scale data integration and text miningNetwork biology: Large-scale data integration and text mining
Network biology: Large-scale data integration and text mining
 
Network biology - Large-scale data integration and text mining
Network biology - Large-scale data integration and text miningNetwork biology - Large-scale data integration and text mining
Network biology - Large-scale data integration and text mining
 
The STRING database and related tools
The STRING database and related toolsThe STRING database and related tools
The STRING database and related tools
 
Data integration: The STITCH database of protein-small molecule interactions
Data integration: The STITCH database of protein-small molecule interactionsData integration: The STITCH database of protein-small molecule interactions
Data integration: The STITCH database of protein-small molecule interactions
 
Mining biomedical texts
Mining biomedical textsMining biomedical texts
Mining biomedical texts
 
Systems biology - Understanding biology at the systems level
Systems biology - Understanding biology at the systems levelSystems biology - Understanding biology at the systems level
Systems biology - Understanding biology at the systems level
 
Advanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomicsAdvanced bioinformatics methods for proteomics
Advanced bioinformatics methods for proteomics
 
STRING - Modeling of biological systems through cross-species data integ...
STRING - Modeling of biological systems through cross-species data integ...STRING - Modeling of biological systems through cross-species data integ...
STRING - Modeling of biological systems through cross-species data integ...
 
Unraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integrationUnraveling signaling networks by large-scale data integration
Unraveling signaling networks by large-scale data integration
 
Mining molecules from text and data
Mining molecules from text and dataMining molecules from text and data
Mining molecules from text and data
 

Plus de Lars Juhl Jensen

One tagger, many uses: Illustrating the power of dictionary-based named entit...
One tagger, many uses: Illustrating the power of dictionary-based named entit...One tagger, many uses: Illustrating the power of dictionary-based named entit...
One tagger, many uses: Illustrating the power of dictionary-based named entit...Lars Juhl Jensen
 
One tagger, many uses: Simple text-mining strategies for biomedicine
One tagger, many uses: Simple text-mining strategies for biomedicineOne tagger, many uses: Simple text-mining strategies for biomedicine
One tagger, many uses: Simple text-mining strategies for biomedicineLars Juhl Jensen
 
Extract 2.0: Text-mining-assisted interactive annotation
Extract 2.0: Text-mining-assisted interactive annotationExtract 2.0: Text-mining-assisted interactive annotation
Extract 2.0: Text-mining-assisted interactive annotationLars Juhl Jensen
 
Network visualization: A crash course on using Cytoscape
Network visualization: A crash course on using CytoscapeNetwork visualization: A crash course on using Cytoscape
Network visualization: A crash course on using CytoscapeLars Juhl Jensen
 
STRING & STITCH : Network integration of heterogeneous data
STRING & STITCH: Network integration of heterogeneous dataSTRING & STITCH: Network integration of heterogeneous data
STRING & STITCH : Network integration of heterogeneous dataLars Juhl Jensen
 
Biomedical text mining: Automatic processing of unstructured text
Biomedical text mining: Automatic processing of unstructured textBiomedical text mining: Automatic processing of unstructured text
Biomedical text mining: Automatic processing of unstructured textLars Juhl Jensen
 
Medical network analysis: Linking diseases and genes through data and text mi...
Medical network analysis: Linking diseases and genes through data and text mi...Medical network analysis: Linking diseases and genes through data and text mi...
Medical network analysis: Linking diseases and genes through data and text mi...Lars Juhl Jensen
 
Network Biology: A crash course on STRING and Cytoscape
Network Biology: A crash course on STRING and CytoscapeNetwork Biology: A crash course on STRING and Cytoscape
Network Biology: A crash course on STRING and CytoscapeLars Juhl Jensen
 
Cellular Network Biology: Large-scale integration of data and text
Cellular Network Biology: Large-scale integration of data and textCellular Network Biology: Large-scale integration of data and text
Cellular Network Biology: Large-scale integration of data and textLars Juhl Jensen
 
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...Lars Juhl Jensen
 
STRING & related databases: Large-scale integration of heterogeneous data
STRING & related databases: Large-scale integration of heterogeneous dataSTRING & related databases: Large-scale integration of heterogeneous data
STRING & related databases: Large-scale integration of heterogeneous dataLars Juhl Jensen
 
Tagger: Rapid dictionary-based named entity recognition
Tagger: Rapid dictionary-based named entity recognitionTagger: Rapid dictionary-based named entity recognition
Tagger: Rapid dictionary-based named entity recognitionLars Juhl Jensen
 
Network Biology: Large-scale integration of data and text
Network Biology: Large-scale integration of data and textNetwork Biology: Large-scale integration of data and text
Network Biology: Large-scale integration of data and textLars Juhl Jensen
 
Medical text mining: Linking diseases, drugs, and adverse reactions
Medical text mining: Linking diseases, drugs, and adverse reactionsMedical text mining: Linking diseases, drugs, and adverse reactions
Medical text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen
 
Network biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textNetwork biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textLars Juhl Jensen
 
Medical data and text mining: Linking diseases, drugs, and adverse reactions
Medical data and text mining: Linking diseases, drugs, and adverse reactionsMedical data and text mining: Linking diseases, drugs, and adverse reactions
Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen
 
Network biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textNetwork biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textLars Juhl Jensen
 
Biomarker bioinformatics: Network-based candidate prioritization
Biomarker bioinformatics: Network-based candidate prioritizationBiomarker bioinformatics: Network-based candidate prioritization
Biomarker bioinformatics: Network-based candidate prioritizationLars Juhl Jensen
 

Plus de Lars Juhl Jensen (20)

One tagger, many uses: Illustrating the power of dictionary-based named entit...
One tagger, many uses: Illustrating the power of dictionary-based named entit...One tagger, many uses: Illustrating the power of dictionary-based named entit...
One tagger, many uses: Illustrating the power of dictionary-based named entit...
 
One tagger, many uses: Simple text-mining strategies for biomedicine
One tagger, many uses: Simple text-mining strategies for biomedicineOne tagger, many uses: Simple text-mining strategies for biomedicine
One tagger, many uses: Simple text-mining strategies for biomedicine
 
Extract 2.0: Text-mining-assisted interactive annotation
Extract 2.0: Text-mining-assisted interactive annotationExtract 2.0: Text-mining-assisted interactive annotation
Extract 2.0: Text-mining-assisted interactive annotation
 
Network visualization: A crash course on using Cytoscape
Network visualization: A crash course on using CytoscapeNetwork visualization: A crash course on using Cytoscape
Network visualization: A crash course on using Cytoscape
 
STRING & STITCH : Network integration of heterogeneous data
STRING & STITCH: Network integration of heterogeneous dataSTRING & STITCH: Network integration of heterogeneous data
STRING & STITCH : Network integration of heterogeneous data
 
Biomedical text mining: Automatic processing of unstructured text
Biomedical text mining: Automatic processing of unstructured textBiomedical text mining: Automatic processing of unstructured text
Biomedical text mining: Automatic processing of unstructured text
 
Medical network analysis: Linking diseases and genes through data and text mi...
Medical network analysis: Linking diseases and genes through data and text mi...Medical network analysis: Linking diseases and genes through data and text mi...
Medical network analysis: Linking diseases and genes through data and text mi...
 
Network Biology: A crash course on STRING and Cytoscape
Network Biology: A crash course on STRING and CytoscapeNetwork Biology: A crash course on STRING and Cytoscape
Network Biology: A crash course on STRING and Cytoscape
 
Cellular networks
Cellular networksCellular networks
Cellular networks
 
Cellular Network Biology: Large-scale integration of data and text
Cellular Network Biology: Large-scale integration of data and textCellular Network Biology: Large-scale integration of data and text
Cellular Network Biology: Large-scale integration of data and text
 
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...
Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...
 
STRING & related databases: Large-scale integration of heterogeneous data
STRING & related databases: Large-scale integration of heterogeneous dataSTRING & related databases: Large-scale integration of heterogeneous data
STRING & related databases: Large-scale integration of heterogeneous data
 
Tagger: Rapid dictionary-based named entity recognition
Tagger: Rapid dictionary-based named entity recognitionTagger: Rapid dictionary-based named entity recognition
Tagger: Rapid dictionary-based named entity recognition
 
Network Biology: Large-scale integration of data and text
Network Biology: Large-scale integration of data and textNetwork Biology: Large-scale integration of data and text
Network Biology: Large-scale integration of data and text
 
Medical text mining: Linking diseases, drugs, and adverse reactions
Medical text mining: Linking diseases, drugs, and adverse reactionsMedical text mining: Linking diseases, drugs, and adverse reactions
Medical text mining: Linking diseases, drugs, and adverse reactions
 
Network biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textNetwork biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and text
 
Medical data and text mining: Linking diseases, drugs, and adverse reactions
Medical data and text mining: Linking diseases, drugs, and adverse reactionsMedical data and text mining: Linking diseases, drugs, and adverse reactions
Medical data and text mining: Linking diseases, drugs, and adverse reactions
 
Cellular Network Biology
Cellular Network BiologyCellular Network Biology
Cellular Network Biology
 
Network biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and textNetwork biology: Large-scale integration of data and text
Network biology: Large-scale integration of data and text
 
Biomarker bioinformatics: Network-based candidate prioritization
Biomarker bioinformatics: Network-based candidate prioritizationBiomarker bioinformatics: Network-based candidate prioritization
Biomarker bioinformatics: Network-based candidate prioritization
 

Systems biology - Bioinformatics on complete biological systems