Related papers: Phylogenetic analysis of gene expression
Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts, and any other predictors of phenotype that are of interest. Second, describe fitness…
Observed differences in mean phenotypic values across human groups have attracted renewed interest with the rise of large-scale genomic studies and polygenic risk prediction. However, the genetic basis of these differences is far more…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which…
In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Phylogenetic methods have broad potential in linguistics beyond tree inference. Here, we show how a phylogenetic approach opens the possibility of gaining historical insights from entirely new kinds of linguistic data--in this instance,…
Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
This paper presents a high-level conceptual framework to help orient the discussion and implementation of open-endedness in evolutionary systems. Drawing upon earlier work by Banzhaf et al., three different kinds of open-endedness are…