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I’ll describe our recent efforts to model protein evolution and amino-acid substitutions by (1) designing an easy to use pipeline to estimate amino-acid replacement matrices for specific protein groups, (2) using the knowledge of the protein structure, when available, (3) simplifying mixture models that have been proposed so far.

Originally it was thought that, at least in eukaryotes, gene order is random. However, in all well studied genomes genes of similar expression sit in close proximity to each other. Why is this? In this talk I'll present evidence that gene order is in part selected as it affects the noise level of genes. This explains operons organization in bacteria, clustering of essential genes and gene orientation in yeast

Is protein evolution just about protein function? In this talk I'll show that the processes involved in protein manufacture, rather than end-function, have a major role in determining rates of evolution and choice of both codons and amino acids. I'll examine in detail two issues, splicing and nucleosome occupancy

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Aging is an intrinsic feature of living organisms, which is partly genetically determined. In budding yeast, a mother cell can produce a limited number of daughter cells before it enters senescence. Over the last fifteen years, budding yeast has emerged as a compelling organism in which to investigate the genetic mechanisms that regulate longevity. Yet a precise and quantitative understanding of the transition to replicative senescence is still missing, in part because of the lack of techniques to monitor age-induced cellular processes over a long enough period of time. We have developed a new microfluidics technique to track the successive divisions of single yeast cells from birth to death under the microscope. Using this methodology, we have started to characterize the transition to replicative senescence in a quantitative manner using custom data analysis. Our data reveal that aging cells experience a large variability in cell cycle durations and undergo stochastic and partially…