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

1. USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica
http://labpib.fmrp.usp.br
Prof. Dr. Vêncio
rvencio@usp.br
Gene Expression: is it really complex or is it
just missing parts ?

2. Who are we ?

3. Who are we ?

4. Complex Systems

5. Complex Systems

6. Complex Systems

7. 2+2>4

8. 2+2>4

9. 2+2=5
1) Do we know all parts to sum them up ?
2) What are the interactions among parts ?

10. Biological Motivation
Joyce & Palsson, Nat Rev Mol Cell Biol (2006)

11. Biological Motivation
ncRNA
RNA-protein interaction
RNA-RNA interaction
structuromics
2012 update on Joyce & Palsson,
Nat Rev Mol Cell Biol (2006)

12. Biological Motivation
ncRNA
RNA-protein interaction
RNA-RNA interaction
structuromics
2012 update on Joyce & Palsson,
Nat Rev Mol Cell Biol (2006)

13. Biological Motivation … today
ncRNA
RNA-protein interaction
RNA-RNA interaction
structuromics
2012 update on Joyce & Palsson,
Nat Rev Mol Cell Biol (2006)

14. ~ 5 μm
from wikipedia's “halobacterium” entry
~ 1 cm
Bonneau et al., Cell (2007)
from webmineral.com Mineralogy Database's “halite” entry

15. Bonneau et al., Cell (2007)

16. Bonneau et al., Cell (2007)

17. 2+2=5
1) Do we know all parts to sum them up ?
2) What are the interactions among parts ?
Bonneau et al., Cell (2007)

18. 2+2=5
1) Do we know all parts to sum them up ?
No, ncRNAs are still missing
2) What are the interactions among parts ?
Some are known,
but protein-RNA are missing
Bonneau et al., Cell (2007)

19. ncRNA discovery by high-throughput sequencing RNA-seq
Wang et al., Nat Rev Gen (2009)

20. ncRNA discovery by high-throughput sequencing RNA-seq
Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates

21. ncRNA discovery by high-throughput sequencing RNA-seq
Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates

22. ncRNA discovery by high-throughput sequencing RNA-seq
There is a transcript
but there is no protein

23. Protein-RNA interaction discovery by RIP-Seq
Very similar to known
Chip-seq but for RNA
interactions
from wikipedia's “ChIP-sequencing” entry
Lívia Zaramela - PhD Candidate

24. Protein-RNA interaction discovery by RIP-Seq
Support Vectors
Marcos Abraão - PhD Candidate

25. So... back to the original question
is it really complex or is it just missing parts?

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. USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica
http://labpib.fmrp.usp.br
Prof. Dr. Vêncio
rvencio@usp.br

28. USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica
http://labpib.fmrp.usp.br
Prof. Dr. Vêncio
rvencio@usp.br
Thank 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.