Regulatory Genomics, Systems Biology and Dream3

These joint RECOMB Satellite conferences were held at the Broad Institute (Oct 29 – Nov 2, 2008). This was a somewhat grueling 5 day meeting … with half hour keynotes (17) and twelve minute talks (>75). As with previous conferences, there is FriendFeed coverage. The full length papers from the conference will be published in either Genome Research, the Journal of Computational Biology, or Molecular Systems Biology … available by the end of the calendar year. As is frequently the case at computational biology meetings, some of the best talks were about recently published work.

My Highlights from the meeting:

• Daphne Koller and Gal Chechik both spoke (Daphne as a keynote) on their recent work on identifying active motifs within networks (citation below).
• Uri Alon gave a beautiful keynote on how evolution for varying goals, when the goals share substructure, results in modularity.
• Aviv Bergman gave a nice keynote in a similar vein … on how evolution effects a network’s robustness, complexity, and the observed variance in the population.
• Moran Cabili gave a nice short talk on their recent publication on predicting tissue-specific metabolism (citation below).
• Amir Mitchell gave a nice talk on adaptive environmental conditioning.
• Todd Wasson gave a nice talk (and had a poster) on their model of competitive binding of DNA by nucleosomes and transcription factors. Tim Hughes, in the final keynote, presented a ton of data showing clear competition effects.
• There were four excellent talks on visualizing expression via imaging. Two were looking at the effects of enhacers (Eddy Rubin’s keynote and Jeffrey Chuang) and two focused on context-dependent expression in Drosophilia (Angela DePace and Erwin Frise).
• Robert Bradley had a very nice poster on his Fast Statistical Alignment (FSA) work. The ability to align multiple complete human genomes quickly and accurately.
• Michal Rabani had a poster on her recent work on identifying RNA motifs involved in post-transcriptional regulatory processes (citation below).

Gal Chechik, Eugene Oh, Oliver Rando, Jonathan Weissman, Aviv Regev, Daphne Koller (2008). Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network Nature Biotechnology DOI: 10.1038/nbt.1499

Tomer Shlomi, Moran N Cabili, Markus J Herrgård, Bernhard Ø Palsson, Eytan Ruppin (2008). Network-based prediction of human tissue-specific metabolism Nature Biotechnology, 26 (9), 1003-1010 DOI: 10.1038/nbt.1487

M. Rabani, M. Kertesz, E. Segal (2008). Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes Proceedings of the National Academy of Sciences, 105 (39), 14885-14890 DOI: 10.1073/pnas.0803169105