Advanced bioinformatics methods for proteomics
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The document discusses several advanced bioinformatics methods and computational tools for proteomics research, including NetPhorest, STRING, Reflect, and NetworKIN. It describes how these tools use machine learning techniques and large protein-protein interaction datasets to build models for predicting kinase-substrate relationships and mapping sequence motifs, helping to organize big proteomics data and generate testable hypotheses to guide experimental validation work.
Advanced bioinformatics methods for proteomics
- 1. Advanced bioinformatics methods for proteomics Lars Juhl Jensen
- 7. Miller, Jensen et al., Science Signaling, 2008
- 8. NetPhorest
- 10. Miller, Jensen et al., Science Signaling, 2008
- 12. Miller, Jensen et al., Science Signaling, 2008
- 15. motif atlas
- 17. 179 kinases
- 18. 89 SH2 domains
- 19. 8 PTB domains
- 20. BRCT domains
- 21. WW domains
- 22. 14-3-3 proteins
- 24. protein-specific
- 25. no context
- 27. Linding, Jensen, Ostheimer et al., Cell, 2007
- 30. STRING
- 31. Jensen, Kuhn et al., Nucleic Acids Research, 2009
- 33. gene fusion
- 34. Korbel et al., Nature Biotechnology, 2004
- 36. Korbel et al., Nature Biotechnology, 2004
- 39. Jensen & Bork, Science, 2008
- 41. Beyer et al., Nature Reviews Genetics, 2007
- 45. Letunic & Bork, Trends in Biochemical Sciences, 2008
- 46. >10 km
- 48. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
- 49. co-mentioning
- 52. different names
- 53. variable quality
- 54. not comparable
- 55. spread over 630 genomes
- 57. von Mering et al., Nucleic Acids Research, 2005
- 59. von Mering et al., Nucleic Acids Research, 2005
- 60. Linding, Jensen, Ostheimer et al., Cell, 2007
- 61. integration
- 62. NetworKIN
- 63. Linding, Jensen, Ostheimer et al., Cell, 2007
- 65. use case
- 67. Linding, Jensen, Ostheimer et al., Cell, 2007
- 70. Linding, Jensen, Ostheimer et al., Cell, 2007
- 71. summary
- 73. network analysis
- 75. save much time in the lab
- 76. 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
- 77. larsjuhljensen