Network biology

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Network biology

  1. 1. Network biology Lars Juhl Jensen
  2. 2. three parts
  3. 3. protein networks
  4. 4. localization and diseases
  5. 5. disease networks
  6. 6. protein networks
  7. 7. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  8. 8. computational predictions
  9. 9. Korbel et al., Nature Biotechnology, 2004
  10. 10. experimental data
  11. 11. Jensen & Bork, Science, 2008
  12. 12. curated knowledge
  13. 13. Letunic & Bork, Trends in Biochemical Sciences, 2008
  14. 14. text mining
  15. 15. many databases
  16. 16. different formats
  17. 17. different identifiers
  18. 18. variable quality
  19. 19. not comparable
  20. 20. hard work
  21. 21. quality scores
  22. 22. von Mering et al., Nucleic Acids Research, 2005
  23. 23. calibrate vs. gold standard
  24. 24. von Mering et al., Nucleic Acids Research, 2005
  25. 25. localization and disease
  26. 26. general approach
  27. 27. suite of web resources
  28. 28. curated knowledge
  29. 29. experimental data
  30. 30. text mining
  31. 31. computational predictions
  32. 32. quality scores
  33. 33. proteins
  34. 34. compartments
  35. 35. compartments.jensenlab.org
  36. 36. tissues
  37. 37. tissues.jensenlab.org
  38. 38. diseases
  39. 39. disease networks
  40. 40. electronic health records
  41. 41. Jensen et al., Nature Reviews Genetics, 2012
  42. 42. structured data
  43. 43. Jensen et al., Nature Reviews Genetics, 2012
  44. 44. unstructured data
  45. 45. comorbidity
  46. 46. Jensen et al., Nature Reviews Genetics, 2012
  47. 47. Roque et al., PLoS Computational Biology, 2011
  48. 48. in Danish
  49. 49. multiple testing
  50. 50. confounding factors
  51. 51. age and gender
  52. 52. reporting bias
  53. 53. temporal correlation
  54. 54. diagnosis trajectories
  55. 55. Jensen et al., in preparation, 2013
  56. 56. molecular basis
  57. 57. protein networks
  58. 58. Acknowledgments 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 Text mining Sune Frankild Evangelos Pafilis Alberto Santos Kalliopi Tsafou Janos Binder Heiko Horn Michael Kuhn Nigel Brown Reinhardt Schneider Sean O’Donoghue EHR mining Anders Boeck Jensen Peter Bjødstrup Jensen Francisco S. Roque Henriette Schmock Marlene Dalgaard Massimo Andreatta Thomas Hansen Karen Søeby Søren Bredkjær Anders Juul Tudor Oprea Pope Moseley Thomas Werge Søren Brunak

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