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Systems biology
Large-scale biomedical data mining
Lars Juhl Jensen
association networks
who?
guilt by association
protein networks
Frishman et al., Modern Genome Annotation, 2009
computational predictions
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
text mining
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
confidence scores
signaling networks
what?
phosphoproteomics
sequence specificity
Miller, Jensen et al., Science Signaling, 2008
automated pipeline
Miller, Jensen et al., Science Signaling, 2008
cellular context
Linding, Jensen, Ostheimer et al., Cell, 2007
>2x better accuracy
dynamic networks
when?
cell-cycle regulation
microarray time courses
Gauthier et al., Nucleic Acids Research, 2007
protein interactions
temporal network
de Lichtenberg, Jensen et al., Science, 2005
just-in-time assembly
de Lichtenberg, Jensen et al., Cell Cycle, 2007
evolutionary flexibility
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
summary
data mining
specific predictions
systems properties
thank you!
NetPhorest
– Rune Linding
– Martin Lee Miller
– Francesca Diella
– Claus Jørgensen
– Michele Tinti
– Lei Li
– M...
larsjuhljensen
Systems biology: Large-scale biomedical data mining
Systems biology: Large-scale biomedical data mining
Systems biology: Large-scale biomedical data mining
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Systems biology: Large-scale biomedical data mining

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  • Integration
    Automation
    Collaboration
  • Atlas of human kinases
    Atlases for phospho-binding proteins
    Atlases for model organisms
    Ubiquitination would be welcome
  • Transcript of "Systems biology: Large-scale biomedical data mining"

    1. 1. Systems biology Large-scale biomedical data mining Lars Juhl Jensen
    2. 2. association networks
    3. 3. who?
    4. 4. guilt by association
    5. 5. protein networks
    6. 6. Frishman et al., Modern Genome Annotation, 2009
    7. 7. computational predictions
    8. 8. Korbel et al., Nature Biotechnology, 2004
    9. 9. experimental data
    10. 10. Jensen & Bork, Science, 2008
    11. 11. curated knowledge
    12. 12. Letunic & Bork, Trends in Biochemical Sciences, 2008
    13. 13. text mining
    14. 14. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
    15. 15. confidence scores
    16. 16. signaling networks
    17. 17. what?
    18. 18. phosphoproteomics
    19. 19. sequence specificity
    20. 20. Miller, Jensen et al., Science Signaling, 2008
    21. 21. automated pipeline
    22. 22. Miller, Jensen et al., Science Signaling, 2008
    23. 23. cellular context
    24. 24. Linding, Jensen, Ostheimer et al., Cell, 2007
    25. 25. >2x better accuracy
    26. 26. dynamic networks
    27. 27. when?
    28. 28. cell-cycle regulation
    29. 29. microarray time courses
    30. 30. Gauthier et al., Nucleic Acids Research, 2007
    31. 31. protein interactions
    32. 32. temporal network
    33. 33. de Lichtenberg, Jensen et al., Science, 2005
    34. 34. just-in-time assembly
    35. 35. de Lichtenberg, Jensen et al., Cell Cycle, 2007
    36. 36. evolutionary flexibility
    37. 37. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
    38. 38. summary
    39. 39. data mining
    40. 40. specific predictions
    41. 41. systems properties
    42. 42. thank you! NetPhorest – Rune Linding – Martin Lee Miller – Francesca Diella – Claus Jørgensen – Michele Tinti – Lei Li – Marilyn Hsiung – Sirlester A. Parker – Jennifer Bordeaux – Thomas Sicheritz-Pontén – Marina Olhovsky – Adrian Pasculescu – Jes Alexander – Stefan Knapp – Nikolaj Blom – Peer Bork – Shawn Li – Gianni Cesareni – Tony Pawson – Benjamin E. Turk – Michael B. Yaffe – Søren Brunak STRING – Christian von Mering – Damian Szklarczyk – Michael Kuhn – Manuel Stark – Samuel Chaffron – Chris Creevey – Jean Muller – Tobias Doerks – Philippe Julien – Alexander Roth – Milan Simonovic – Jan Korbel – Berend Snel – Martijn Huynen – Peer Bork Reflect – Sune Frankild – Heiko Horn – Evangelos Pafilis – Michael Kuhn – Nigel Brown – Reinhardt Schneider – Sean O’Donoghue NetworKIN – Rune Linding – Heiko Horn – Gerard Ostheimer – Martin Lee Miller – Francesca Diella – Karen Colwill – Jing Jin – Pavel Metalnikov – Vivian Nguyen – Adrian Pasculescu – Jin Gyoon Park – Leona D. Samson – Rob Russell – Peer Bork – Michael Yaffe – Tony Pawson Cyclebase – Ulrik de Lichtenberg – Thomas Skøt Jensen – Nicholas Paul Gauthier – Rasmus Wernersson – Søren Brunak
    43. 43. larsjuhljensen
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