Related papers: Weighted-Codon-Usage Based Phylogeny In Ectocarpal…
Biological systems evolve with minimum metabolic costs and use common components, and they represent guideposts toward a paradigm of manufacturing that is centered on minimum energy, local resources, and ecological integration. Here, a new…
The opportunistic fungal pathogen Candida albicans causes serious hematogenic hospital acquired candidiasis with worldwide impact on public health. Because of its importance as a nosocomial etiologic agent, C. albicans genome has been…
A first systematic study of the effects of the choice of the input scale in global determinations of parton distributions and QCD parameters is presented. It is shown that, although in principle the results should not depend on these…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
We consider a Gibbs distribution over all spanning trees of an undirected, edge weighted finite graph, where, up to normalization, the probability of each tree is given by the product of its edge weights. Defining the weighted degree of a…
The new parameterization of the generalized parton distributions t-dependence is proposed. It allows one to reproduce sufficiently well the electromagnetic form factors of the proton and neutron at small and large momentum transfer. The…
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Direct Coupling Analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to…
A critical appraisal is given of a recent analysis of the quark-mass and finite-size dependence of unquenched lattice QCD data for the nucleon mass. We use this forum to estimate the boundary of the chiral regime for nucleon properties.
Objective: To analyze the frequency and co-occurrence of dermoscopic patterns in BCC lesions and their relationship with histopathologic subtypes, using statistical analysis and Information Theory tools such as entropy, conditional entropy,…
In this paper we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of…
We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained…
Bacteriophages densely pack their long dsDNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of…
Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…
Cancer prognosis is often based on a set of omics covariates and a set of established clinical covariates such as age and tumor stage. Combining these two sets poses challenges. First, dimension difference: clinical covariates should be…
The Rosids is one of the largest groups of flowering plants, with 140 families and ~70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…