Using Evolutionary frameworks to Study Epigenetic Aging – the Epigenetic PaceMaker In multiple studies DNA methylation has proven to be an accurate biomarker of age. To develop these biomarkers, the methylation of multiple CpG sites is typically linearly combined to predict chronological age [1]. By contrast, in this study we apply the Universal PaceMaker (UPM) model to investigate changes in DNA methylation during aging. The UPM was initially developed by us in a separate project to study rate acceleration/deceleration during genome evolution. Here, rather than identifying which linear combinations of sites predicts age as in the traditional approach, the new framework, the Epigenetic PaceMaker (EPM) models the rates of change

Universal PaceMaker of Genome Evolution Here we are collaborating with the Evolutionary Genomics group of Eugene Koonin at the NIH. We were awarded the BSF grant on a project tackling prokaryotic evolution, but are now looking at another, somehow broader, more fundamental evolutionary phenomenon. This project concerns with correlation between evolutionary rates of the various genes in the genome and was originated from our other project  dealing with identifying HGT. Gene evolution is traditionally considered within the classical framework of the Molecular Clock (MC) model [1] according to which each gene is characterized by an approximately constant rate of evolution. However, in a recent comparative analysis of numerous gene histories (gene phylogenies)

MaxCut Supertree A quartet tree (or simply a quartet) is a tree over four taxa (species) that is the most basic phylogenetic building block – A tree can be decomposed into its defining quartets that uniquely define it. It is this fundamentality that confers the quartets their power. The converse however, is not true – it is rare that an arbitrary quartet set agrees on some tree. Hence, given a set of quartets, it is a common practice to look for a tree agreeing with the most of them. This seemingly simple and “clean” question lies at the heart of almost any specific, more complicated question in phylogenetics. Due to

Convex Recoloring of Trees and Networks Definition: Given a necklace of colored beads, we say that the string is convex if all beads of the same color are in one chunk. In graph theory terms, we can view the necklace as a path and the coloring C as function from V to the set of colors C . Then C is convex if every subset of vertices belonging to the same color class is connected . However, when the coloring is not convex, we would like to find the closest coloring C’ that is convex. This distance between the two colorings C’ and C depends on the model assumed. Under the simplest model this is just the number of vertices whose color is changed between C’ and C . It can be shown that under this model,

Statistical Analysis of Phylogenetic Trees and Networks The study of Evolution and understanding the history of life on Earth, has attracted scientists’ attention since the dawn of modern science. Phylogenetics, the reconstruction of this history, has expanded beyond its traditional role in evolutionary studies and with the advent of next generation sequencing is increasingly integrated into modern biological areas such as preventive medicine, epidemiology, and human migration. Maximum Likelihood (ML) is considered as the most accurate phylogenetic method. Our lab has developed expertise in analytical solutions to ML phylogenetic reconstruction. The novelty of our approach is the representation of the ML problem as a constraint optimization problem and using algebraic