Here are some highlights from May’s PLOS Computational Biology
Convex Clustering: An Attractive Alternative to Hierarchical Clustering
The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. Despite the advantages of convex clustering, there are still obstacles that stand in its way of becoming a practical tool in bioinformatics: current algorithms are computationally intensive, and there is minimal guidance available on how to choose penalty weights. To address these issues, Gary K. Chen and colleagues describe a fast new algorithm and a corresponding software implementation, CONVEXCLUSTER (freely available at http://www.genetics.ucla.edu/software/).
Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer
Breast cancer survival is strongly correlated with genetic markers that are associated with increased resistance and invading skills of cancer cells, but it is poorly correlated with the amount of circulating tumour cells. To improve the understanding of the dynamic progression of the disease, Annalisa Occhipinti and colleagues develop a multi-compartment model which mimics the dynamics of tumoural cells in the mammary duct, in the circulatory system and in the bone.
Synaptic Restructuring Across the Sleep-Wake Cycle
Sleep is important for long-lasting memories. One existing theory posits that sleep weakens synapses, leading to the forgetting of all but the strongest memories. An alternative theory proposes that sleep promotes both weakening and strengthening of different connections, the latter through a process known as long-term potentiation (LTP). Sidarta Ribeiro and colleagues measure the levels of a protein related to LTP during the sleep cycle of rats, and use these data to build models of sleep-dependent synaptic plasticity. The results indicate that the current competing theories are not mutually exclusive; rather, each constitutes an important stage of memory consolidation.