wrap-up of the orthology, paralogy, and function symposium at SMBE 2012

I promised some people to write a short summary of the symposium that Matthew Hahn, Marc Robinson-Rechavi, Iddo Friedberg, and I co-organized at SMBE 2012. I particularly enjoyed the symposium and the room was pretty full all the time, despite running in parallel to other interesting topics. I will just write an overall summary without going into too much details of each of the talks, and at the end I would list a number of papers that were commented on the various talks. I have to clarify that this informal wrap-up only contains my own views and has not been consensuated among the organizers. I invite any of the attendants to add comments to highlight some important aspects that I may have missed.

I’ll start by providing a summary of how all this started... which is a rather unusual way, I believe. Indeed the idea of the symposium was born in the blogosphere, in the popular Jonathan Eisen’s Tree of Life blog, where he invited Matthew Hahn to write a special guest post on the “history behind” his paper on testing the orthology conjecture. One of the conclusions from that paper was that paralogous sequences were more similar in function (and in expression patterns) than paralogs, which contradicted one of the major expectations (and assumptions) behind the theories of duplication-driven functional divergence and the strategies for inferring functions from orthologous sequences. That paper had already caused a bit of a turmoil in the orthology community (I remember this was a hot discussion during the last Quest for Orthologs meeting, at Cambridge), and several concerns were being raised about the suitability of comparisons of functional annotations from different species, and the conclusions derived within the paper. Rather rapidly, several people commented on Matt’s post and a lively discussion started (more than 40 comments in total!). The discussion was so interesting that Marc Robinson-Rechavi suggested we should bring this scientific debate in the form of a symposium in one of the upcoming conference, and so is how some of us started to work on this idea.To me it was the first time that I met the other organizers in person.

The symposium started with Eugene Koonin, who nicely introduced the topic of what conjectures could be implied by the definition of orthology, a purely evolutionary one as introduced by Walter Fitch in 1970. He then showed results from his lab that indicate that conjectures tend to hold, but that there may be exception. For instance, the conjecture that orthologs should be best reciprocal hits can be broken by an accelerated evolution in one of the true orthologs, he then showed work from other groups (Sali, Sonnhammer) on the higher conservation of structure and domain architecture in orthologs as compared to paralogs. He criticized the use of GO terms by Hahn and others and argued that one should at variety of data on function to test the conjecture. He presented results from his own group which show higher conservation of expression across species. He concluded that the functional conjecture still holds, although he observed that differences may not be spectacular.  Catherina Gushanski was next talking on changes in gene expression following segmental duplications in mammals. They have produced an impressive dataset of expression from  different tissues in various mammal species. She used that set to ask the question whether duplication was contributing more to divergence than time alone and showed that levels of expression were decreasing in younger duplicates, changes were different across different tissues. She observed no differences between one-to-one orthologs or old duplicate pairs, she also found no differences in terms of tissue specificity in orthologs vs paralogs.  Next on stage was Nicholas Furnham who presented new implementations in FUNTREE that would allow exploring functional evolution on trees. He warned that EC classification is not univocal and that can also have problems for functional comparisons. They have developed “EC-Blast” which directly measures distances between enzymatic reaction based on the molecular structures of substrates and products. Christophe Dessimoz presented results from his recent paper in which they show important biases in GO term annotations, genes from the same species and families tend to be annotated with more similar terms because of experimental biases and author biases. When correcting for this biases, the conjecture still holds. However he admitted that differences were not very big, but still significant. Romain Studer came next. He measured selection and changes in structural stability in orthologs and duplicated genes. He showed that selected sites in paralogs tend to be more clustered in the structure than in orthologs, however he observed no differences in the evolution of stability between orthologs and paralogues. He concluded that differences between paralogues may be smaller than previously thought.

After the coffee break Jianzhi Zhang told us about his work towards probing the orthology conjecture. After giving a try, he gave up of using GO terms because of the many inconsistencies, and the biases observed. He thus reverted to interrogate for conservation of protein-protein interactions using experimentally determined interactions in various yeast species. Unfortunately the many interactions to test experimentally in duplicated proteins prevented him to show a comparison of orthologs and paralogs in this talk. Nevertheless he found that all PPIs tested for orthologs were conserved, even those that seemed not to be, were caused by possible errors in previous large-scale Yeast 2 Hybrid experiments. Alex Nguyen also showed results on the budding yeast gene duplications. They focused on a more specific aspect of function: the presence of short-conserved linear motifs in protein. They found that these were more likely to disappear/diverge after the duplication event, consistent with neo- or sub-functionalization models. We moved to Drosophila with our next speaker, Lev Yamplosky who exploited expression and genomic data from the 12 Drosophila genomes. They showed larger differences in paralogs, as compared to orthologs in rates of divergence, which were also more asymmetrical. They also found that these differences varied for fast- or slow-evolving families. Finally they could also find larger differences in paralogs in terms of expression. Then it was my turn, and I mainly showed our results on comparison of expression patterns in human and mouse. Our experimental design is different from others in that we use topological dating (not sequence divergence) to establish orthologs and paralogs of a similar age, and, second, we compared always orthologs to inter-species paralogs to get rid of species-specific biases in the comparisons. Our results support a larger divergence of paralogues as compared to orthologs in tissue pattern expression. Thanks to our experimental design we could also assess that most of the differences between paralogs were gained shortly after the duplication, linking the duplication event to a big fraction of the divergence. Our last speaker was Paul Thomas who gave an overview of what can you expect and what can you not expect from GO annotations. He also showed progress on how the consortium is trying to model functional evolution through gene families, and how these models can help in the study of the relationship between orthology, paralogy and gene function.

Thus we had a diverse set of talks, most of them focusing on the comparison of different aspects of functional evolution (GO annotations, expression, functional motifs, interactions, divergence, structure) and also using varying experimental designs and species. I would say one of the main conclusion is that GO (and even EC numbers) annotation can be misleading in our ascertainment of functional evolution. My personal view is that most talks showed results consistent with the conjecture, although the level of differences between paralogs and orthologs was sometimes small. Function can be described at multiple levels, and I would expect that functional divergence after duplications may affect only one or few of these. Thus if one experimental design focuses on one of such levels it may be expected to miss divergence in the other ones. In addition those designs that average over all levels will inevitably dilute small but important aspects of functional divergence. In conclusion this is an exciting topic and with the number and variety of groups that are now interested in the topic, I am sure that we will be closer and closer to understanding the complex relationships between orthology, paralogy and functional divergence.

Some links and  papers mentioned during the symposium (I probably miss some):

Abstracts from oral presentations in SMBE, including our symposium http://imgpublic.mci-group.com/ie/PCO/OralAbstracts_Final.pdf

The blog post that initiated this:  http://phylogenomics.blogspot.com.es/2011/09/special-guest-post-discussion.html

Another post on the orthology conjecture 

Announcement of our symposiyum 

Altenhoff et. al. Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

FunTree: a resource for exploring the functional evolution of
structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA,
Orengo CA, Thornton JM.
Nucleic Acids Res. 2012 Jan;40(Database issue):D776-82
http://nar.oxfordjournals.org/content/40/D1/D776.long

Brawand, D., et. al. The evolution of gene expression levels in mammalian organs. URL

 Forslund et. al. Domain conservation architecture in orthologs

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215765/

Huerta-Cepas. et. al. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

Huerta-Cepas and Gabaldón Assigning duplication events to relative temporal scales in genome-wide studies.

Nehrt et. al. Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002073

Nguyen et. al. Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions http://stke.sciencemag.org/cgi/content/abstract/sigtrans;5/215/rs1

 

Peterson et. al. Evolutionary constraints on structural similarity in orthologs and paralogs

http://onlinelibrary.wiley.com/doi/10.1002/pro.143/full

Thomas et. al. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report


Large-scale analysis of orthologs and paralogs under covarion-like and
constant-but-different models of amino acid evolution.
Studer RA, Robinson-Rechavi M.
Mol Biol Evol. 2010 Nov;27(11):2618-27.
http://mbe.oxfordjournals.org/content/27/11/2618.short

How confident can we be that orthologs are similar, but paralogs differ?
Studer RA, Robinson-Rechavi M.
Trends Genet. 2009 May;25(5):210-6.
http://www.sciencedirect.com/science/article/pii/S0168952509000559

Pervasive positive selection on duplicated and nonduplicated vertebrate
protein coding genes.
Studer RA, Penel S, Duret L, Robinson-Rechavi M.
Genome Res. 2008 Sep;18(9):1393-402.
http://genome.cshlp.org/content/18/9/1393.short
 

Interview with Nick Lane

As I reported in an earlier post, I had the opportunity to meet Nick Lane during the Spanish Evolutionary Society meeting. We had a very interesting discussion over a couple of beers around mitochondrial endosymbiosis and the origin of eukaryotes. Some days after the meeiing, Andrés Moya, the President of the society, suggested to me to interview him for the Society's  Bulletin eVolución.  You can find this interview translated to Spanish in the current issue of eVolution 7(1), however I think the interview might be of interest for a broader audience and thus I paste here the original, English version. 

TG- After your recent visit to Spain as an invited speaker to the III SESBE congress (Madrid, November 2011), what is your opinion about the field of Evolutionary Biology in Spain?
 

NL- Well, I thoroughly enjoyed the few talks I attended, but my Spanish is poor and I could hardly judge many of them; and unfortunately I missed much of the conference. But I liked the great range of themes that were being discussed. And in general I am impressed with a lot of evolutionary research going on in Spain. There is a tendency to consider comparative physiology in evolution more than there is in England, for example, and I find that a very insightful approach. One thing that has struck me over the years is that Spanish researchers are not cited as frequently as they ought to be. This does not reflect the quality of the research, but rather the US-dominated English-language citation bias.

TG- Your career has been quite unconventional. Can you summarize for our readers which have been the major steps in your career path?
 

NL- It sure has! I had a medical research background, and my PhD was on mitochondrial function and oxygen free radicals in transplanted organs. But I was getting nowhere with that, and couldn’t see a way of getting from there into what was really an interest for me: evolutionary biology. So I took to writing instead, for several independent agencies doing medical education for pharmaceutical companies. That was an eye opener, and I learnt to write clearly and quickly, but it was also a frustration. After quite a lot of hard work I finally got a contract to write Oxygen, which was initially conceived as a book about free radicals, mitochondria and medicine, but ended up reflecting my interests in evolutionary biology to a much greater extent. That was the beginning of a decade spent writing books on evolutionary biochemistry, drawing heavily on my background in bioenergetics but ranging widely over any material that interested me. It was fantastic fun but no way to make a living. And ultimately frustrating too, in that in writing on that scope, you can’t help but come up with new ideas, essentially a broad synthesis with gaps, that you sketch in with speculations, which can be reframed as testable hypotheses. That’s what drew me back into research – the frustrated desire to test some of these hypotheses.

3) Thus, you have been active as a science writer, a researcher, and now you seem to combine both aspects. Do these two tasks reinforce or rather interfere with each other?

 
Both. I think I’ve benefited tremendously as a researcher from the decade I spent thinking and writing. I now have a coherent set of hypotheses that are testable in one way or another – experimentally or by some kind of mathematical modeling, or just by empirical analysis of existing data. So I’m drawing heavily on this ‘credit’ now. At the same time it is hard to think synthetically or to write books while in research, there are so many demands on time. So on a daily basis, writing and research interfere with each other, but I think if you are able to focus on one or the other for periods then they can, and should, reinforce each other. The trick is to balance each so that they reinforce each other over time. I’m not sure I’ve mastered that trick yet, but it is my long term goal: for me, it is the best way to understand the most interesting evolutionary questions, and that is what I want to do.

4) In your view, where lies the main responsibility of communicating science to the general society (e.g scientists, funding agencies, scientific societies etc, science journalists)?

 
Good question. There is certainly a responsibility, but being responsible counts for nothing if nobody listens to what you have to say: as a writer, you must be interesting to be noticed at all. And society is rarely interested in responsible but boring views. So there is a balance that you have to wrestle with every sentence, between interest and accuracy. That’s another reason I’m happy to be back in research: to write accurately (in precise scientific language) is at least as much pleasure for me as to write interestingly. Frankly it is the questions themselves that interest me. I think that the real challenge in writing for the public is to find ways of phrasing questions in an interesting way, which draws attention to the problem, without sacrificing the accuracy. That is the ideal: responsible (boring) and interesting at the same time.

With respect to which group has the responsability, I don't think that one group alone can be considered responsible communicating science to general society. Each group can address different needs, and each has its own responsibility. Scientists are responsible for sculpting new ideas, for conveying the excitement and intellectual thrust of science. The best ideas in science are still driven by individuals with passion, insight and ingenuity, and there is nobody better to convey this intensity to the general reader, although it is rare. Journalists are responsible for balanced reporting, explaining ideas clearly and intelligibly, providing context for the reader, ideally some commentary from other scientists. It is unusual for journalists to drive the scientific agenda, but serious journalists have a broader perspective and can sometimes see things that scientists can't.

Scientific societies can provide very helpful consensus statements on difficult issues, from global warming to the effectiveness of chemotherapy. It's not really for them to give a sense of the cut and thrust of science, more the strength of the conclusions that emerge from the uncertainty.

Finally, funding agencies. In my view, funding agencies have a duty to explain to the public and to politicians that research is open-ended and unpredictable. Research that appears to have little immediate societal impact can have immense and unimagined benefits in the future. Most major scientific breakthroughs, with the greatest economic benefits, came from unexpected quarters, and could not have been anticipated by either the scientists themselves or the funders. This perspective is being lost in a political drive to justify spending by societal impact. As with so much, short-term political cycles are trumping long term good sense. It is up to funding agencies to explain why research should be funded on its own merits, without constant recourse to some hoped-for and probably illusory impact.      
 TG- In one of you articles, to commemorate the 150 anniversary of “The Origin of species”, you discuss about what Darwin would love to know about the origin of the eye if he were still alive. Darwin is granted for being the first who used a “tree of life” to describe the evolutionary relationships of species and their shared ancestry. What do you think he would love to now in this respect if he were still alive?

 
NL- Well I think he’d love what’s going on in microbial genomics. The picture that has emerged over the last couple of decades of lateral gene transfer and endosymbiosis in microbes is radically different to the idea of gene sequence divergence between populations. Having said that, I see all this as a juxtaposition to standard Neodarwinian population genetics. He would have loved that too, although it is old hat to us now; but given that Darwin knew nothing about genes, he would have been thrilled by the Neodarwinian synthesis, and what amounted to a genetic basis for a tree of life. All of this means that variation is more complex than any of us imagined; and in this sense, Darwin’s coyness on the mechanisms of variation was well placed: it really is wild and fascinating.

  TG- In one of your last books, you mention 10 major transitions in the evolution of life on earth. Which one of them is, according to you, the most enigmatic or difficult to explain?
 

NL- Consciousness, without a doubt. Frequently the origin of life and consciousness are put forward as the twin pinnacles, the two big unanswered questions in biology. I think we’re actually quite close to understanding the origin of life in conceptual terms, but I personally can’t understand consciousness well at all. I read a lot on the subject and came to the conclusion that nobody really does. We still can’t answer the simple question: how does the depolarization of a neuron give rise to a feeling or sensation of anything at all? They are two different languages, and we don’t seem to have any kind of Rosetta stone at the moment.

  TG- Some of these transitions seem to have happened only once in the history of life. If they were so advantageous why they have been restricted to a single lineage?
 

NL- I think each transition has to be taken on its own terms. These are tremendously difficult questions and you will find diametrically opposed answers to each question from very insightful researchers. The answers reflect temperament more than anything else. Christian de Duve actually wrote a book called ‘Singularities’, and my reading of that is that there isn’t a single answer that would apply to the origin of life, the origin of photosynthesis, the origin of the eukaryotic cell, the origin of animals, and the origin of consciousness. Obviously for some reason, each was improbable or it would have happened more than once (like eyes), but the reasons for improbability differ and are very dependent on context. In the case of eukaryotes, I would say their unique origin was based on an improbable endosymbiosis between prokaryotes, followed by a problematic reconciliation of selfish interests between two entities that had to live in intimate union. There were no advantages at all until they had come out of that tight bottleneck; on the contrary, all the advantages were with the bacteria that just kept on doing their bacterial thing. From that point of view, the difficult question is why did it happen at all?

  TG- Some of your research interests concern very ancient events (e.g. the origin of eukaryotes, of life itself). This is a field in which different hypotheses are difficult to prove right or wrong given the difficulty of direct experimentation. What are the criteria used by scientists in your area to reach a consensus over which is the support for the different  scenarios?

 
NL- There is a consensus on quite a lot: cell structure, behavior (phagocytosis or sex) genome sequences (albeit with disputes over methodology), the existence of introns in certain positions and so on. Where consensus breaks down is when different methods give different answers. That happens all the time. I’m actually focusing a lot of my attention now on the origin of life itself, because this seems to me to be more experimentally tractable: we can ask specific experimental questions that involve chemistry and thermodynamics, which are much more reliable than biology and genes, so although the event was the most ancient of all, it is not necessarily the most inaccessible. I think we’re making progress on many questions, but in the case of the origin of eukaryotes a lot of the evidence is oblique and disputable. The reasoning is often equivalent to historical reconstruction in that you need to weigh the evidence: there’s no doubt that it happened, and there’s plenty of evidence, it’s just that some of it is unreliable and some is irrelevant, so there’s plenty of scope for argument still.

  TG- In this respect. What is the impact on your field of the ever-growing number of genome sequencing projects?. What are the species or environments you would like to be sampled in order to help answering important questions in the origin and evolution of complex life.

 
NL- Genome sequences have made a tremendous difference, the only trouble being that they tend to reflect pathogens or industrially interesting bugs, rather than those most relevant to, say, the origin of eukaryotes. I would love to see more genomes from anoxic or anaerobic deep ocean environments, or the deep hot biosphere. I’m especially interested in two questions: the variation in eukaryotic genomes, and the variation in mitochondrial genomes. There is a brilliant and bold hypothesis that the origin of the eukaryotic cell was an endosymbiosis between two prokaryotes, an archaeon host cell and an alpha-proteobacterium (or somesuch). The prediction is that all eukaryotes should have mitochondria or organelles derived from them like hydrogenosomes or mitosomes; and that in terms of mitochondrial genomes we should find more overlap between bacterial metabolic capacity and metabolically versatile mitochondria. This is a wonderful prediction because it is so easy to falsify, and yet all the genome sequencing so far has failed to disprove it. The places most likely to disprove – or prove – it are precisely those anaerobic environments that have been undersampled so far.

TG- Carbon has always been considered a hallmark of life on earth, but life (elsewhere) based on other molecules (e.g Silicium) has been speculated. You seem to favor the idea that oxygen was the molecule that enabled the appearance of complex life on earth, could you speculate on the theoretical possibility of other molecules playing a similar role in other forms of life.

 
NL- I think it is most likely that life elsewhere would be constrained by much the same issues that constrain life here. I doubt very much that there will be silicon based life forms. There are two important properties of carbon: it is much better than silicon at organic chemistry; but equally important, it is available in the form of a gaseous oxide, a Lego brick if you will. There are no gaseous silicon oxides, only sand, which is vast and unwieldy in comparison. You can’t build a house on sand and you can’t build an organism from sand. My feeling is that not only is carbon especially useful, it is also more abundant than silicon. Likewise, water is more abundant than methane and a much better solvent (you can’t dissolve carbon chains of more than about 5 carbon atoms in methane). And so on. On the basis of usefulness and abundance, I would argue that life would mostly be carbon based. I would go further to argue that it is likely to require proton gradients over membranes for thermodynamic reasons. When I say that oxygen is necessary for complex life, I mean large active animals. I doubt that anything else could do the job: nothing else could accumulate to the appropriate level in an atmosphere and at the same time be sufficiently reactive to provide the power needed. So I’d say that in terms of their broad biochemistry, alien life won’t be all that different. In terms of morphology or the specifics of their biochemistry, they could be very different, of course.

  TG- Are you already working on your next book?, can you advance something on what is it about?

 
NL- I’m not writing yet, but I do have a contract… and it will be about everything I have talked about here. The origin of complex life, and why it was a unique event here on Earth.

RECOMB 2012 (Barcelona): one week left for early registration

 As I reported in an earlier post, RECOMB 2012 will be held in Barcelona and CRG's Bioinformatics and Genomics program is part of the local organizing committee.
 This post is a reminder that the deadline for early registration with a reduced rate is approaching and will expire 31st of January. More information here.

 See you there!

SMBE 2012 early registration deadline and symposium on orthology

 For those who don't know, the deadline for abstract to the next Society for Molecular Biology and Evolution meeting (Dublin 23-26 June) is approaching. I am co-organizing a workshop on orthology/paralogy and function in collaboration with Marc Robinson-Rechavi, Matthew Hahn, and Iddo Friedberg. Find below an invitation to submit to SMBE2012 and more info on this workshop.

 Hope we can meet in Dublin. 

Dear colleague,

We invite you to submit an abstract to the symposium "The complex relationship between orthology, paralogy, and function" to take place at the meeting of the Society for Molecular Biology and Evolution in Dublin (23rd-26th June, 2012).

The deadline to submit an abstract is the 27th of January 2012, for more details please visit:

http://www.smbe2012.org/scientific-content/call-for-abstracts.html


Symposium "The complex relationship between orthology, paralogy, and function"

Orthology and paralogy have been central concepts in molecular evolution since the distinction was first proposed by Fitch in 1970. A long standing interpretation of this distinction has been that orthologs would be more similar in function than paralogs. Until recently, this interpretation was rarely tested, and in fact rarely explicitly articulated in a testable manner. Yet it has been widely used, from undergraduate teaching, to the practical application of orthology searches for genome annotation. There has been a recent increase of research, seeking to define and test this "ortholog conjecture". Notably, a recent paper (Nehrt et al. 2011, PloS Comput. Biol.) has reported a higher functional similarity of paralogs than of orthologs. This paper has generated much attention and debate, while at the same time recent work on orthologs has shown the vitality and importance of this field to a broad range of applications and questions. Our symposium will feature speakers addressing the fundamental relationships between molecular evolution and biological function, focusing especially on the role of orthology and paralogy in modulating such relationships.

Confirmed speakers: Eugene V. Koonin, Jianzhi Zhang

If you have any question regarding this symposium please do not hesitate to contact us:

Toni Gabaldon , Matthew Hahn , Iddo Friedberg, Marc Robinson-Rechavi

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 10^th CRG Annual Symposium on Computational Biology of Molecular Sequences, celebrated last 10^th and 11^th 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 10^th CRG Annual Symposium web.

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. 

XI Jornadas de Bioinformatica in Barcelona (23-25 January)

  A short note to spread the word on the joint Spanish and Portuguese Meeting on Bioinformatics.  This is a yearly meeting that is gaining momentum every year, and it is a great opportunity to meet most groups doing bioinformatics in the region. Talks are in English and everybody is welcome to attend.

 As other years, this meeting has associated a regional (Spain, Portugal and North Africa) ISCB student symposium. This year this symposium is co-organized by, Salvador Capella-Gutierrez, one of the members of my lab. 

 If you plan to submit a communication, there is time till the end of November.

 See you there.

ALPHY 2012: French-Spanish meeting on Bioinformatics and Evolutionary Genomics (March 19 -21, Banyuls-sur-Mer)

 I am glad to announce ALPHY 2012, which for the first time is jointly co-organized by French and Spanish researchers. I was very glad to be invited by my French colleagues to sit at the organizing committe. I think it is a great opportunity to join two communities with ample experience in phylogenetics-related research.

ALPHY is an annual meeting, organized in France since 1995, dedicated to the field of Bioinformatics and Comparative Genomics (ALPHY = ALignments and PHYlogeny). The main goal of this meeting is to promote informal exchanges in this highly multidisciplinary field, and to encourage young scientists to present their work. The official invitation follows, plus a very tempting picture of the location.

This year, ALPHY is co-organized by Spanish and French scientists, in the nice city of Banyuls. There will be two invited speakers (Henrik Kaessmann and Jose Castresana), and the program will be open to contributions for 20’ talks.
The registration to the meeting is free, but mandatory. Please use the link (top left of this page) to register. If you wish to present your work, submit your abstract in the registration form.
Important dates:

• Deadline for abstract submission: January 10 2012
• Deadline for registration : February 1st 2012

Hasta pronto – A bientôt – fins aviat - see you in Banyuls!

RECOMB 2012 (Barcelona)

 The next RECOMB meeting will be held at Barcelona. Our department is part of the local organizing committee and the list of confirmed speakers looks very promising.

 Submission opened in September, and you still have time to submit papers until the end of the week. Do not miss the deadline.

CRG Symposium: Computational Biology of Molecular Sequences. 10-11 November

Registration is open for the CRG symposium organized by our Bioinformatics and Genomics programme. This meeting will host internationally reknown scientists in the Bioinformatics field. Just to cite some: Smith, Tramontano, Ponting, Sankoff, Koonin, Bairoch, Brunak... Below you'll find the symposium overview and the complete list of speakers. 

 

Advances in methods to sequence nucleic acids, coupled with more general advances in automation, robotization, and multiplexing, have resulted in the capacity to survey the phenomena of life in a global manner and with unprecedented resolution. As a result, Biology, traditionally an analytic science in which the natural world is dissected in its elemental components in order to be comprehended, is becoming a synthetic science, in which the phenomena of life is approached in more systemic way. In parallel, Biology, a science in which human effort  been directed until very recently towards data acquisition, is increasingly becoming a discipline in which data is obtained with almost no human intervention, and the effort is being directed towards data analysis. Computational systems to store, analyze and model biological data have thus become an essential part of research in Biology. The connection between Biology and Computation, however, runs much deeper as we are coming to realize that the unfolding of the instructions in the genome is, stricto senso, a computation on the DNA sequence.  Biology, thus, cannot be understood without Computation. The two-day CRG symposium on “Computational Biology of Molecular Sequences” will bring together renowned Computational Biologists from around the world, including both pioneers in the field, as well as promising young scientists. Presentations, discussions and dialogue during the Symposium will contribute to survey the status of a discipline that, at the intersection of Biology and Computation, will have an enormous impact on the world of the XXIst century.

Confirmed Speakers
Amos BAIROCH Swiss Institute of Bioinformatics (SIB) and University Geneva, Geneva CH
Mathieu BLANCHETTE McGill University, Montréal CA
Søren BRUNAK Technical University of Denmark, Kongens Lyngby DK
Philipp BUCHER Swiss Institute for Experimental Cancer Research (ISREC), Lausanne CH
Brendan FREY University of Toronto, Toronto CA
Mark GERSTEIN Yale University, New Haven US
Nick GOLDMAN European Bioinformatics Institute, Hinxton UK
Tim HUBBARD Wellcome Trust Sanger Institute, Hinxton UK
Eugene V. KOONIN National Center for Biotechnology Information, Bethesda US
Gene MYERS Janelia Farm Research Campus, Ashburn US
Chris PONTING University of Oxford, Oxford UK
David SANKOFF University of Ottawa, Ottawa CA
Ron SHAMIR Tel-Aviv University, Tel-Aviv IL
Temple F. SMITH BioMolecular Engineering Resource Center, Boston US
Terry SPEED Walter & Eliza Hall Institute of Medical Research, Parkville AU
Peter STADLER Universität Leipzig, Leipzig DE
Gary STORMO Washington University School of Medicine, Saint Louis US
Ana TRAMONTANO Sapienza University, Rome IT
Michele VENDRUSCOLO University of Cambridge, Cambridge UK
Martin VINGRON Max Planck Institute for Molecular Genetics, Berlin DE

The best of....... SMBE2011

With this post I initiate a series that will highlight some talks or posters in (some of) the meetings I attend. I want to note from the very beginning that this is very subjective and is according to my own taste and interests. I hope, however, that these highlights may also be interesting for some of the readers of this blog.

 I came back recently from the last Society for Molecular Biology and Evolution meeting (SMBE 2011) in Kyoto, Japan. This meeting has been marked by the recent natural disaster of the 2011 earthquake that affected the nuclear power station of Fukushima and the attendance was significantly lower than recent SMBE meetings. (around 650 attendees as compared to 2000 in SMMBE2010 in Lyon). However, despite this, the quality of the meeting has been really high with plenty of interesting presentations in the form of posters or talks.

 The poster that most caught my attention was one presenting the "Centroid Wheel Tree" representation, who allows representing alternative topologies within the same phylogenetic tree.

Wheel Tree Representation

I still have to explore that possibility and how it differs from the more standard network representations, but it looks promising and fairly adequate to accomodate our interest in accounting for the topological variation within phylomes.  

Among the selected oral presentations, my favourite was that  from Shigehiro Kuraku (Konstanz University, Germany) on the debated positions of the two rounds of whole genome duplications in the early vertebrates.

 From the invited speakers I would choose the talk of Nancy Moran, which went through many fascinating examples of insect endosymbiotic bacteria showing extremely reduced genomes.

 And, finally, one of the interesting parts of the meeting was one special session organized to conmemorate Walter Fitch, who passed away earlier this year (see my previous post). It was iinteresting to hear of many annecdotes from Masatoshi Nei, who shared with him the efforts of initiating the Society for Molecular Biology and Evolution and the MBE journal.

Mashatoshi Nei commemorating Walter Fitch at SMBE 2011

 Of course these are just some very personal highlights from a very interesting meeting. I will most probably attend next SMBE 2012  meeting in Dublin.  

 PS- I just noted that my blog has surpassed the 1,000 visits, this is encouraging.