Related papers: Quantifying the common genetic variability of bact…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
Nosocomial infections have important consequences for patients and hospital staff: they worsen patient outcomes and their management stresses already overburdened health systems. Accurate judgements of whether an infection is nosocomial…
Identifying disease genes from human genome is an important and fundamental problem in biomedical research. Despite many publications of machine learning methods applied to discover new disease genes, it still remains a challenge because of…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
A rigorous methodology is proposed to study cell division data consisting in several observed genealogical trees of possibly different shapes. The procedure takes into account missing observations, data from different trees, as well as the…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
The broad sense genetic heritability, which quantifies the total proportion of phenotypic variation in a population due to genetic factors, is crucial for understanding trait inheritance. While many existing methods focus on estimating…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a…
The data we analyze derives from the observation of numerous cells of the bacterium Escherichia coli (E. coli) growing and dividing. Single cells grow and divide to give birth to two daughter cells, that in turn grow and divide. Thus, a…
This paper introduces a new measure of heritability which relaxes the classical assumption that the degree of heritability of a continuous trait can be summarized by a single number.This measure can be used in situations where the trait…
We describe the evolution of $E.coli$ populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…
We wish to formally test for changes in the taxonomic diversity of a community, especially in the presence of high latent diversity. Drawing on the meta-analysis literature, we construct a model for diversity that accounts for covariate…
Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in honey bees. Recently, 2 970 queens were genotyped to gather a reference population. For the…
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across different settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization,…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…