Wednesday, October 20, 2010

ICSB 2010 - From design principles to genome-wide and that persistent gap in-between

I am back from the 11th International Conference on Systems Biology (ICSB 2010) that was held in the lovely cite of Edinburgh. A full week of talks dedicated to systems biology (however you might define it). Speaking of definitions, it was refreshing to note that no speaker spent much time trying to define the field this time around. Aside from the keynote lectures, there were constantly four parallel sessions (see program) so you were always guaranteed to miss out on something interesting. With the help of a couple of attendees we took some notes of the conference in a FF room. There is lots of notes to go through if you are interested but here a few of my favorite highlights.

From all the keynotes the ones I enjoyed most were from Luis Serrano, Mike Tyers and Aldons Lusis. Unfortunately, Sydney Brenner was scheduled but canceled last minute.

Luis Serrano talked about his lab's work on characterizing a mycoplasma species (notes here) using a multi-omics approach. They are trying to use available technologies to build parts lists and models of all aspects of this species. They have learned a lot by taking such a systematic approach on a bug with so few genes but there is no plan that I could see on how to follow up on all this work. I can see that many computational biology labs will use this data but it would be a missed opportunity if more labs don't continue to go beyond the omics limitations.

The lecture by Tyers (notes here) was also very much about omics. He talked about their recent effort (Breitkreutz et al Science 2010) to search for kinase-protein interactions in yeast and how hard it is, in general, to study signalling pathways in this way (promiscuous interactions, complex systems etc). From kinases he moved to drug-gene interactions and chemogenomics. In particularly he briefly mention some unpublished work on evolution and prediction of drug-synergy. This is topic that I am really interested in as an applied side of evolutionary biology (more on that hopefully soon).

Another keynote I enjoyed was from Aldons Lusis (see notes). His presentation centered on a strategy for association studies in mice (Bennett et al. Genome Research 2010). This sort of work is out of my comfort zone but I really like all the examples he gave of using this strategy to find loci associated with clinical traits or protein/gene expression levels. Maybe I should be trying to read Nature Association Studies Genetics more often.

Parallel sessions
I went to the sessions of "Functional Genomics", "Cell signalling dynamics","Parameterizing proteomics" and "Biological noise and cell decision making".  In the Functional Genomics session, Lars Steinmetz talked about genome wide analysis of antisense non coding transcription and David Amberg's talk covered the use of genetic interactions to study actin mutants (an extension from Haarer et al. G&D 2007).
I really liked many of presentations from the Cell Signaling Dynamics session, including talks by Walter Kolch, Timothy Elston and Nils Bluthgen. It was interesting to note that many people presenting were following a similar approach of first enumerating different models that could achieve the function they were studying and then finding the most plausible by elimination.
From the proteomics session the highlight for me was the really cool work presented by Christian von Mering. They have essentially compiled a lot of mass-spec data and used corrected spectral counts to estimate protein abundance for many different species. The data can be found at and some reported results are published (Schrimpf et al., PLoS Biology 2009 and Weiss et al., Proteomics 2010). Overall the message appears to be that protein abundance is more conserved across species than gene expression.
Finally, from the session on noise and cell decision I particularly liked the talk of Roy Kishony, on his lab's work with antibiotic response, and James Locke's analysis of sigma b promoters (Elowitz lab).

Bridging the gap
Besides all the cool science I come back from this meeting with the feeling that we still have this huge gap between the -omics work and the detailed 'design principles' pathway analysis. There is even such a tension between people working in these two camps that it becomes almost a joke. Maybe this is why it is so hard to define systems biology, each "type" of researcher sees it differently. Some would say that it is not systems biology if it is not genome wide, while others will claim that we don't learn anything with omics (just a parts list). In this meeting there were great examples of both camps using established methods to attack new systems but there is still no clear attempt to bridge the gap. How do we go from genome-wide to quantitative mechanistic understanding ? Maybe next year in Heidelberg / Mannheim (ICSB 2011) we will see both camps, at least, acknowledging each other.