USP – University of Sao Paulo          LabPIB – Laboratório de Processamento de Informação Biológica          http://labpi...
Who are we ?
Who are we ?
Complex Systems
Complex Systems
Complex Systems
2+2>4
2+2>4
2+2=51) Do we know all parts to sum them up ?2) What are the interactions among parts ?
Biological Motivation                        Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
Biological Motivation                        ncRNA                                RNA-protein interaction                 ...
Biological Motivation                        ncRNA                                RNA-protein interaction                 ...
Biological Motivation … today                                ncRNA                                        RNA-protein inte...
~ 5 μmfrom wikipedias “halobacterium” entry                                  ~ 1 cm                                       ...
Bonneau et al., Cell (2007)
Bonneau et al., Cell (2007)
2+2=51) Do we know all parts to sum them up ?2) What are the interactions among parts ?                                  B...
2+2=51) Do we know all parts to sum them up ?       No, ncRNAs are still missing2) What are the interactions among parts ?...
ncRNA discovery by high-throughput sequencing RNA-seq                                        Wang et al., Nat Rev Gen (2009)
ncRNA discovery by high-throughput sequencing RNA-seq           Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Can...
ncRNA discovery by high-throughput sequencing RNA-seq           Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Can...
ncRNA discovery by high-throughput sequencing RNA-seqThere is a transcriptbut there is no protein
Protein-RNA interaction discovery by RIP-SeqVery similar to knownChip-seq but for RNAinteractions                      fro...
Protein-RNA interaction discovery by RIP-Seq                                     Support Vectors                      Marc...
So... back to the original question  is it really complex or is it just missing parts?
So... back to the original question  is it really complex or is it just missing parts?  Probably both.               http:...
USP – University of Sao PauloLabPIB – Laboratório de Processamento de Informação Biológicahttp://labpib.fmrp.usp.brProf. D...
USP – University of Sao Paulo          LabPIB – Laboratório de Processamento de Informação Biológica          http://labpi...
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IEA - Expressão gênica: é complexo mesmo ou só estão faltando partes?

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Evento organizado pelo Instituto de Estudos Avançados da USP, Polo Ribeirão Preto (IEA-RP).
Mais informações: http://www.iearp.blogspot.com.br/2012/09/perspectivas-sobre-aplicacoes-de_18.html

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IEA - Expressão gênica: é complexo mesmo ou só estão faltando partes?

  1. 1. USP – University of Sao Paulo LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br Prof. Dr. Vêncio rvencio@usp.brGene Expression: is it really complex or is itjust missing parts ?
  2. 2. Who are we ?
  3. 3. Who are we ?
  4. 4. Complex Systems
  5. 5. Complex Systems
  6. 6. Complex Systems
  7. 7. 2+2>4
  8. 8. 2+2>4
  9. 9. 2+2=51) Do we know all parts to sum them up ?2) What are the interactions among parts ?
  10. 10. Biological Motivation Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
  11. 11. Biological Motivation ncRNA RNA-protein interaction RNA-RNA interaction structuromics 2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
  12. 12. Biological Motivation ncRNA RNA-protein interaction RNA-RNA interaction structuromics 2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
  13. 13. Biological Motivation … today ncRNA RNA-protein interaction RNA-RNA interaction structuromics 2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
  14. 14. ~ 5 μmfrom wikipedias “halobacterium” entry ~ 1 cm Bonneau et al., Cell (2007)from webmineral.com Mineralogy Databases “halite” entry
  15. 15. Bonneau et al., Cell (2007)
  16. 16. Bonneau et al., Cell (2007)
  17. 17. 2+2=51) Do we know all parts to sum them up ?2) What are the interactions among parts ? Bonneau et al., Cell (2007)
  18. 18. 2+2=51) Do we know all parts to sum them up ? No, ncRNAs are still missing2) What are the interactions among parts ? Some are known, but protein-RNA are missing Bonneau et al., Cell (2007)
  19. 19. ncRNA discovery by high-throughput sequencing RNA-seq Wang et al., Nat Rev Gen (2009)
  20. 20. ncRNA discovery by high-throughput sequencing RNA-seq Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates
  21. 21. ncRNA discovery by high-throughput sequencing RNA-seq Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates
  22. 22. ncRNA discovery by high-throughput sequencing RNA-seqThere is a transcriptbut there is no protein
  23. 23. Protein-RNA interaction discovery by RIP-SeqVery similar to knownChip-seq but for RNAinteractions from wikipedias “ChIP-sequencing” entry Lívia Zaramela - PhD Candidate
  24. 24. Protein-RNA interaction discovery by RIP-Seq Support Vectors Marcos Abraão - PhD Candidate
  25. 25. So... back to the original question is it really complex or is it just missing parts?
  26. 26. So... back to the original question is it really complex or is it just missing parts? Probably both. http://www.systemsbiology.org.au/
  27. 27. USP – University of Sao PauloLabPIB – Laboratório de Processamento de Informação Biológicahttp://labpib.fmrp.usp.brProf. Dr. Vênciorvencio@usp.br
  28. 28. USP – University of Sao Paulo LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br Prof. Dr. Vêncio rvencio@usp.brThank you for your attention! “ Simplicity is a great virtue but it requires hard work to achieve it and education to appreciate it. And to make matters worse: complexity sells better ” -- E. Dijkstra.
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