Archive by category | Genome-wide

Systems biology & global warming

Systems biology & global warming

Observations suggest that current climatic models may underestimate how quickly the climate system is changing (in particular for sea level), according to a report in Science a few weeks ago (Rahmstorf et al, 2007). Another Science paper published last week shows that the capacity of the Southern Ocean CO2 sink is weakening, which may result in increased atmospheric CO2 levels in the long run (Le Quere et al, 2007). I remember Hiroaki Kitano calling the systems biology community, in his talk at the ICSB meeting last October in Yokohama, for ideas on how system-level approaches could contribute to address the  … Read more

Open Source Biology

Open Source Biology

Novartis, The Broad Institute, and Lund University today announced the completion of a genome-wide map of genetic differences in humans and their relationship to type 2 diabetes and other metabolic disorders. All results of the analysis are being made accessible, free of charge on the internet to scientists around the world (Novartis Media Release, Feb 12, 2007) The results of this study are available at http://www.broad.mit.edu/diabetes/ Has the increasing complexity of genome-wide studies and other large-scale systems biology datasets reached a threshold that makes the open source option more attractive to the pharma industry?  Read more

Analyzing time-series expression data

Analyzing time-series expression data

Ziv Bar-Joseph and colleague describe their new method Dynamic Regulatory Events Miner (DREM) to analyze time-series gene expression data and combine them with static ChIP-chip experiments. The expression profiles are modeled using an extension of Hidden Markov Model that enforces a tree structure onto the expression profiles. The technique allows to deduce the condition-specific or time-dependent activity of transcription factors that explain the observed expression profiles.  Read more