Good luck, Julio!

June 14, 2010 § 1 Comment

This month, we say a tearful goodbye to Julio Saez-Rodriguez.  Julio is setting up his own group at the European Bioinformatics Institute (EBI) in Hinxton, near Cambridge UK, starting on July 1.  EBI is a great fit for him, with its focus on developing computational tools to serve the whole biological community.  There’s an added bonus in that he will be about 3,000 miles closer to his home town in Spain.

Julio came to the Department when the Sorger lab joined us from MIT.  He’s been a major driver of the Sorger lab’s efforts to develop logical models that represent real cellular pathways.  Much of the time, our view of a biological pathway is a kind of average, created by combining the lists of interactions identified in dozens or hundreds of cell lines.  But the pathway doesn’t have to be the same in every cell type — the differences in behavior between cells have to come from somewhere, and by now we know that there are not enough genes in the human genome to allow each cell type to have whole pathways that are different from other cell types.  When Julio looked at liver cells, for example (with Leo Alexopoulos), he started with a consensus model assembled from the literature of the pathways controlling the response to seven different cytokines.  Using an extensive dataset of signal/response measurements taken exclusively from HepG2 cells, he asked how well the literature model could predict actual cell behavior.  What he found was that in order to make the consensus pathway work, he had to drop several “proven” interactions in the network — and add several that had indeed been observed in one cell type or another, but were not sufficiently consistently observed to get into the consensus model.

One day, the signaling community will realize that Julio has done them a huge favor.  Instead of fighting over who’s right and who’s wrong, everyone can be right — as long as you’re studying different cell types, or (if you get desperate) different variants of the same cell types.  Studying one cell type instead of another is like entering an alternate universe: anything can happen somewhere.

Julio plans to continue to work on developing models to help us understand the logic, and the cell specificity, of signaling pathways.   He’s hiring post-docs, and he’s also interested in collaborators and short-term visitors; you still have a week or so to chat to him about the possibilities.  (The UK is warmer than Boston in the winter, although it has to be said that it is also grey and drizzly.)

Good luck, Julio, and keep in touch!

Where Am I?

You are currently browsing entries tagged with cue-signal-response; pathway analysis; cell type specificity; EBI at It Takes 30.