Gene Expression: is it really complex or is it
just missing parts ?
USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br
Prof. Dr. Vê[email protected]
Who are we ?
Who are we ?
Complex Systems
Complex Systems
Complex Systems
2 + 2 > 4
2 + 2 > 4
2 + 2 = 5
1) Do we know all parts to sum them up ?
2) What are the interactions among parts ?
Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
Biological Motivation
2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
RNA-protein interaction
RNA-RNA interaction
structuromics
ncRNA
Biological Motivation
RNA-protein interaction
RNA-RNA interaction
ncRNA
Biological Motivation
2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
structuromics
RNA-protein interaction
RNA-RNA interaction
ncRNA
Biological Motivation … today
2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)
structuromics
Bonneau et al., Cell (2007)
from wikipedia's “halobacterium” entry
~ 5 μm
from webmineral.com Mineralogy Database's “halite” entry
~ 1 cm
Bonneau et al., Cell (2007)
Bonneau et al., Cell (2007)
Bonneau et al., Cell (2007)
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)
2 + 2 = 5
1) Do we know all parts to sum them up ?
2) What are the interactions among parts ?
No, ncRNAs are still missing
Some are known,
but protein-RNA are missing
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 Candidates
ncRNA discovery by high-throughput sequencing RNA-seq
Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates
ncRNA discovery by high-throughput sequencing RNA-seq
There is a transcript
but there is no protein
Protein-RNA interaction discovery by RIP-Seq
Lívia Zaramela - PhD Candidate
Very similar to known
Chip-seq but for RNA
interactions
from wikipedia's “ChIP-sequencing” entry
Protein-RNA interaction discovery by RIP-Seq
Marcos Abraão - PhD Candidate
Support Vectors
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://www.systemsbiology.org.au/
USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br
Prof. Dr. Vê[email protected]
Thank you for your attention!
USP – University of Sao Paulo
LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br
Prof. Dr. Vê[email protected]
“ 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.