XIth Spanish Symposium on Bioinformatics 2012
“Computational Biology of Molecular sequences”, day 2
Today, some more interesting talks at the “Computational Biology of Molecular sequences” X CRG Symposium taking place at the PRBB Conference Hall. I will focus on one talk of each of the sessions (genome regulation, RNA analysis and genome annotation), although all were very interesting!
Ron Shamir (Tel Aviv University) presented Amadeus, a software platform for genome-scale detection of known and novel motifs in DNA sequences, and explained some of the findings they have done with it. He also presented his new book “Bioinformatics for biologists”, which will surely be very useful for many biologists drowning in today’s sea of data and tools for analysing it.
Anna Tramontano (Sapienza University), the only female out of the 20 invited speakers (“it’s a man’s world…”?) and a very well-known figure in the protein world, gave her first RNA talk ever, as she presented it. She talked about a new method for controlling gene expression: a long ncRNA which contains 2 miRNAs within its sequence, and which competes with those miRNAs on binding to their target genes.
Tim Hubbard (Sanger Institute) gave so much information in 45 min that was hard to keep track of it all. He started with the catch 22 of reference genomes: we want it to be complete, but we don’t want it to change… the proposed solution: to keep the reference genome and to release patches with ‘novel’ information or with corrections (the ‘fix’ patches) whenever we get more information. Now, this means that alignment algorithms will need to be aware of patches, he warned the audience.
He then moved on to the costs of sequencing a human genome (5000 pounds, as per October 2011) and said that every 2-4 years the cost drops by 10 times! With this ever-lowing costs, he said, in the UK there has been quite a lot of movement regarding future policies on genomic medicine. And the main question is: what is the health economic value on having all this information, of sequencing the whole population? Nobody knows that yet, but according to Hubbard, one day the cost of sequencing will go low enough and the usefulness of the information will grow enough so that they will both meet and make it viable.
He finally presented the ITFoM (IT Future of medicine) project, one of the six funded by the Future and Emerging Technologies (FET) flagship programme of the EU – which has the goal of “encouraging visionary, “mission-oriented” research with the potential to deliver breakthroughs in information technology with major benefits for European society and industry”. The ITFoM project is expected to run for at least 10 years and will receive funding of up to € 100 million per year. Not bad, eh? But considering what they aim to do - integrating all available biological data to construct computational models of the biological processes that occur in every individual human – they will certainly need that much money… Just consider this fact: to cover all the ‘cancer genomes’ appearing every day, we would need to sequence a new genome every 2 seconds!
So, that was my own pick of the day. Of course, much more happened at the meeting. You can find summaries of all talks and much more at the Symposium’s website http://2011symposium.crg.es/
And if you are interested in Computational Biology, don’t miss to upcoming events also at the PRBB:
- XIth Spanish Symposium on Bioinformatics 2012, 23-25 of January 2012 (#jbi2012)
- Recomb2012 16th Annual International Conference on Research in Computational Molecular Biology, 21-24 April 2012
At the end of the day…genome regulation
In the early afternoon, genome evolution was still the focus of the talks at the X CRG Annual Symposium. Why do we care about reconstructing ancestral genomes? Apart from the fact that it’s difficult and fun (reasons enough for most computer scientists), according to Mathieu Blanchette (McGill University) it can help us to study the mechanisms of genome evolution and also for the identification of functional regions, such as TFBS. Blanchette also showed how to turn multiple sequence realignment into a game with Phylo http://phylo.cs.mcgill.ca/
Following on into genome regulation, Philipp Bucher (Swiss Institute of Bioinformatics) explained the workings of the Chip-seq technology and talked about the computational promoter analysis in the era of ultra-high-throughput sequencing.
And to finish of the quite long day, Alfonso Valencia (CNIO) substituted Gene Myers (Janelia Farm), who regretfully couldn’t make it at the last minute. Valencia talked about open questions in the protein universe, such as: what proteins are in a cell? What protein complexes exist? How did protein families originated? And are we using the right tools and approaches to analyze pathways? Some may think that we know the answers to some of them, but Valencia showed otherwise…
More tomorrow! And remember to follow the talks by the videostreaming (see last entry)! You can also check the rest of the program here.
“Computational Biology of Molecular sequences”, morning of day 1
Shortly after 9am today, the PRBB Auditorium was nearly full and ready for the start of the X CRG Annual Symposium on “Computational Biology of Molecular sequences”. With nearly 400 people registered – coming from more than 14 different countries - and 20 top speakers, the success was guaranteed.
Temple Smith (Boston University) opened the symposium with his Homo sapiens-Neanderthal mystery, which nobody in the audience was able to solve.
Michele Vendruscolo (Cambridge) summarized very well the main question of the meeting: what information are we able to extract from a sequence? That’s, after all, what all the people in this room are working on, though at different levels.
Vendruscolo told us that proteins are expressed at their critical concentration, and that even a slight increase or decrease in solubility leads to aggregation. Since aggregation is at the core of many diseases such as Alzheimer’s or Parkinson, this means the line between health and disease is very very fine indeed. Going back to his original question, he showed how the aminoacid (Aa) sequence determines folding, aggregation or complex formation propensities, and that even the maximum levels of mRNA expression can be predicted from the Aa sequence.
Amos Bairoch (University of Geneva), the father of the Swiss-Prot database, told us about his newest adventure: neXtProt. This is a new resource that aims to integrate all the information available about all human proteins. It is based on the sequence information at UniProt/Swiss-Prot, but it integrates (only for Human proteins) in one same database information on protein sequence, protein expression, mRNA expression, chromosome location, exon mapping, protein-protein interaction, post-translational modifications, and others, including, in the future, a 3D visualization tool. An enormous effort that promises to be very useful.
By midday, the Auditorium was proper packed to hear Eugene Koonin (NCBI) talking about whether universal laws in evolutionary genomics do actually exist. His point is that yes, they do, and that “evolutionary genomics is not that different from physics or chemistry”.
And then, off to lunch!