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

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  • 1. Systems biologyBioinformatics on complete biological systems Lars Juhl Jensen
  • 2. can a biologist fix a radio?
  • 3. Lazebnik, Biochemistry, 2004
  • 4. one gene
  • 5. one postdoc
  • 6. knockout phenotype
  • 7. name the gene
  • 8. Lazebnik, Biochemistry, 2004
  • 9. all aspects
  • 10. one gene
  • 11. high-throughput biology
  • 12. one technology
  • 13. one lab
  • 14. all genes
  • 15. one aspect
  • 16. systems biology
  • 17. complete systems
  • 18. all aspects
  • 19. all genes
  • 20. systems-level properties
  • 21. two subfields
  • 22. mathematical modeling
  • 23. small systems
  • 24. data integration
  • 25. large systems
  • 26. mathematical modeling
  • 27. small systems
  • 28. Chen, Mol. Biol. Cell, 2004
  • 29. many equations
  • 30. Chen, Mol. Biol. Cell, 2004
  • 31. simulation
  • 32. Chen, Mol. Biol. Cell, 2004
  • 33. many parameters
  • 34. Chen, Mol. Biol. Cell, 2004
  • 35. equires detailed knowledge
  • 36. data integration
  • 37. association networks
  • 38. guilt by association
  • 39. STRING
  • 40. ~2.6 million proteins
  • 41. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • 42. genomic context
  • 43. gene fusion
  • 44. Korbel et al., Nature Biotechnology, 2004
  • 45. operons
  • 46. Korbel et al., Nature Biotechnology, 2004
  • 47. bidirectional promoters
  • 48. Korbel et al., Nature Biotechnology, 2004
  • 49. phylogenetic profiles
  • 50. Korbel et al., Nature Biotechnology, 2004
  • 51. a real example
  • 52. Cell Cellulosomes Cellulose
  • 53. experimental data
  • 54. gene coexpression
  • 55. protein interactions
  • 56. Jensen & Bork, Science, 2008
  • 57. curated knowledge
  • 58. complexes
  • 59. pathways
  • 60. Letunic & Bork, Trends in Biochemical Sciences, 2008
  • 61. many databases
  • 62. different formats
  • 63. different identifiers
  • 64. variable quality
  • 65. not comparable
  • 66. hard work
  • 67. quality scores
  • 68. von Mering et al., Nucleic Acids Research, 2005
  • 69. calibrate vs. gold standard
  • 70. missing most of the data
  • 71. text mining
  • 72. >10 km
  • 73. too much to read
  • 74. computer
  • 75. as smart as a dog
  • 76. teach it specific tricks
  • 77. named entity recognition
  • 78. comprehensive lexicon
  • 79. cyclin dependent kinase 1
  • 80. CDK1
  • 81. CDC2
  • 82. flexible matching
  • 83. spaces and hyphens
  • 84. cyclin dependent kinase 1
  • 85. cyclin-dependent kinase 1
  • 86. orthographic variation
  • 87. CDC2
  • 88. hCdc2
  • 89. “black list”
  • 90. SDS
  • 91. information extraction
  • 92. count co-mentioning
  • 93. within documents
  • 94. within paragraphs
  • 95. within sentences
  • 96. scoring scheme
  • 97. corpora
  • 98. ~22 million abstracts
  • 99. no access
  • 100. ~4 million full-text articles
  • 101. augmented browsing
  • 102. Reflect
  • 103. browser add-on
  • 104. real-time text mining
  • 105. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
  • 106. localization and disease
  • 107. small molecules
  • 108. proteins
  • 109. compartments
  • 110. tissues
  • 111. diseases
  • 112. organisms
  • 113. environments
  • 114. suite of web resources
  • 115. common backend database
  • 116. jensenlab.org
  • 117. text mining
  • 118. curated knowledge
  • 119. experimental data
  • 120. computational predictions
  • 121. quality scores
  • 122. web-centric databases
  • 123. DISEASES
  • 124. visualization
  • 125. COMPARTMENTS
  • 126. compartments.jensenlab.org
  • 127. TISSUES
  • 128. tissues.jensenlab.org
  • 129. project onto networks
  • 130. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • 131. compartments.jensenlab.org
  • 132. tissues.jensenlab.org
  • 133. diseases.jensenlab.org
  • 134. summary
  • 135. bioinformatics
  • 136. more than alignment
  • 137. data/text mining
  • 138. save you much time
  • 139. Acknowledgments Protein Literature mining networks Sune Frankild Evangelos PafilisChristian 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

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