Protein–protein interaction networks
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This document discusses protein-protein interaction networks, outlining various phases including association, signaling, and dynamic networks. It highlights key studies and methodologies such as literature mining, phosphoproteomics, and evolutionary flexibility in understanding protein interactions. It emphasizes the importance of data integration and context for making specific predictions in biological systems.
Protein–protein interaction networks
- 1. Protein–protein interaction networks Lars Juhl Jensen
- 6. Phase 1 association networks
- 7. who?
- 9. STRING
- 10. Jensen, Kuhn et al., Nucleic Acids Research , 2009
- 11. STITCH
- 12. Kuhn et al., Nucleic Acids Research , 2010
- 13. 630 genomes
- 16. genomic context
- 17. Korbel et al., Nature Biotechnology , 2004
- 18. Korbel et al., Nature Biotechnology , 2004
- 19. Korbel et al., Nature Biotechnology , 2004
- 23. Jensen & Bork, Science , 2008
- 25. Beyer et al., Nature Reviews Genetics , 2007
- 27. Letunic & Bork, Trends in Biochemical Sciences , 2008
- 29. >10 km
- 32. benchmarking
- 33. von Mering et al., Nucleic Acids Research , 2005
- 35. protein mode
- 36. von Mering et al., Nucleic Acids Research , 2005
- 37. COG mode
- 38. von Mering et al., Nucleic Acids Research , 2005
- 40. Frishman et al., Modern Genome Annotation , 2009
- 41. Phase 2 signaling networks
- 42. what?
- 45. signaling events
- 46. sequence motifs
- 47. Miller, Jensen et al., Science Signaling , 2008
- 48. NetPhorest
- 49. Miller, Jensen et al., Science Signaling , 2008
- 51. NetworKIN
- 52. Linding, Jensen, Ostheimer et al., Cell , 2007
- 53. benchmarking
- 54. Linding, Jensen, Ostheimer et al., Cell , 2007
- 56. use cases
- 58. Linding, Jensen, Ostheimer et al., Cell , 2007
- 60. Olsen, Vermeulen et al., Science Signaling , 2010
- 61. Phase 3 dynamic networks
- 62. when?
- 66. Gauthier et al., Nucleic Acids Research , 2007
- 68. temporal network
- 69. de Lichtenberg, Jensen et al., Science , 2005
- 70. de Lichtenberg, Jensen et al., Science , 2005
- 72. de Lichtenberg, Jensen et al., Cell Cycle , 2007
- 74. individual genes
- 75. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
- 77. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
- 78. phosphorylation
- 79. co-evolution
- 80. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
- 81. summary
- 82. networks
- 83. data integration
- 87. Acknowledgments NetPhorest.info 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-DB.org Christian von Mering 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 Cyclebase.org Ulrik de Lichtenberg Thomas Skøt Jensen Nicholas Paul Gauthier Rasmus Wernersson Søren Brunak NetworKIN.info Rune Linding Gerard Ostheimer Heiko Horn 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
- 88. larsjuhljensen