Saturday, August 30, 2014

Saturday Morning Video: Life at the Speed of Light - Craig Venter ( and some remarks )

We mentioned Craig Venter before ( How Can Compressive Sensing and Advanced Matrix Factorizations enable Synthetic Biology ? ), he is a very inspiring speaker. This presentation by him is no exception. In fact, I believe there are a lot many issues that need to be addressed in this exploration and I have decided to create the Paris BioSciences Meetup group as a result. We'll about the scientific and technical aspect of some of the issues mentioned in this video and more, come join us if you are in the Paris area. Without further ado:

A fascinating aspect of their work is how Craig's team devise a way to figure out which gene is good for life and which one it is not. Mostly by knocking them one by one and finding out which ones allow the cell to survive. This looks like a combinatorial approach. Maybe a group testing approach ( connected to comprressive sensing) might help. At about 38 minutes, he also makes the case that much of the genome is oversampled so that a specific capacity can be replaced by a different set of genes. 

I note that his team uses a mix of previous and the new PacBio long read technology. 

It was in the video we mentioned back in 2012 that sometimes a 1 base pair means the difference between life and death of the cell. There may be redundancy at the gene level but a one base pair difference between life and death point to other issues. 

From an engineering standpoint, I note that the optics of the Illumina had to be reframed after the road trip (at 58 minutes).

Relevant blog entries:
  1. Videos and Slides: Next-Generation Sequencing Technologies - Elaine Mardis (2014)
  2. Improving Pacific Biosciences' Single Molecule Real Time Sequencing Technology through Advanced Matrix Factorization ?
  3. DNA Sequencing, Information Theory, Advanced Matrix Factorization and all that...
  4. It's quite simply, the stuff of Life...

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