Saturday, December 10, 2011

Sequencing species.... by the thousands

 When I was giving my first steps in the field of comparative genomics, there was not much to think about when deciding which genomic datasets to use: one would just take them all. With only a few dozens of genomes, mostly of bacteria, one could have everything at hand, in the local disk, just need to update every couple of months by adding one or two more...

 These times have definitely passed, and now the flow of newly sequenced genomes is... well, overwhelming (see figure below, taken from Genomes Online). This is both a blessing and a curse for us doing comparative genomics, since we have an unprecedented amount of data which enables more resolution, but we are increasingly facing novel technical and analyitical challenges.

 Just to give a taste of this avalanche of genomes from different species (projects for sequencing genomes for a given species, such as the 1000 genomes is another story) that is coming, I here list some of the projects I am aware of that aim at sequencing thousands of genomes from a given taxonomic group.

As expected, in this kind of projects it is way more easy to come up with a bold number, than to actually define the list of species that are actually going to be sequenced. At least this is what I can tell from my involvement in the i5K initiative, in which prioritisation of species to be sequenced is not simple, since usually one wants to weigh in different criteria (phylogenetic relevance, biological, economical, and clinical importance, etc).   

 I'm sure I missed some, and, in addition, there is a growing flow of genomes that are sequenced by independent groups, including my modest own group. One common weakness of this large, and small-scale initiatives is that they sometimes come with the cost for covering the genome sequencing but do not account for the necessary bioinformatics analyses to actually make sense of the data. With the sequencing costs dropping and the potential analyses becoming more complex, the actual costs of sequencing projects will more and more be on the side of the analysis beyond the assembly and annotation phases. As a result, many bioinformatics groups are streching their resources to contribute to genomics projects without getting any specific funding.

In my opinion the planning of a sequencing project should account for all the downstream phases with their associated costs. With such an approach we may end up having a handful of genomes less, but we will definitely learn more from them. 

Monday, December 5, 2011

Watch the talks from the CRG Symposium: Computational Biology of Molecular Sequences.

 If you missed the opportunity to attend physically our past symposium on "Computational Biology of molecules" (see this past post), you can now watch the videos of the talks (read message below).

Dear all,

All contents of the 10th CRG Annual Symposium on Computational Biology of Molecular Sequences, celebrated last 10th and 11th of November, are now available online.

Leading scientists in computational biology came together in Barcelona on the occasion of the tenth edition of the CRG Annual Symposium, which focused on computational biology of molecular sequences, organized by the Centre for Genomic Regulation (CRG). The auditorium of the Barcelona Biomedical Research Park (PRBB) hosted the event, celebrated from Thursday 10 to Friday 11 November 2011.
In the microsite you can find the inaugural video of the Symposium, videos of the talks, interviews with some of the speakers, participants and organizers of the event and two summary videos that capture the major points of all sessions. There are also available two articles that summarize the talks and news related to the field of computational biology of sequencing.

We hope that these resources are useful for you!

Click here to visit the 10th CRG Annual Symposium web.

Saturday, December 3, 2011

SESBE: Spanish Society for Evolutionary Biology

 Last week I went to Madrid to attend the 3rd congress of the Spanish Society for Evolutionary Biology (SESBE). This is a relatively new (7 years) society that embraces evolutionary biology as a whole, from palaeontology and systematics, to evolutionary genomics and darwinian medicine. Thus, the meetings are very diverse and one can listen to the most diverse talks, always with the common ground of evolutionary theory as a framework of analysis.

Due to other commitments, I could only stay two days but it was worth and enjoyed most of the talks and, most of all, meeting colleagues around Spain. I would highlight here the talk of Nick Lane, on the evolution of eukaryotes and the role played by mitochondrial endosymbiosis. Nick, who is also a prolific writer of popular science books, gave a very nice talk that seduced the whole audience, including me. I had the opportunity to discuss with him, and it was nice to discuss again on big theories on the evolution of eukaryotes, a big theme that I am passionate.

This year, the SESBE elected a new board, in which I will stand as a secretary. Not that I am very keen on holding such a position, but I was asked and I think one should be prepared to contribute his two cents to noble causes, such as that of this society promoting the study of evolution and its transmission  to society in our country.