Related papers: Predicting Horizontal Gene Transfers with Perfect …
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
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…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
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…
Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different…
Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…
Plant phenotyping (Guo et al. 2021; Pieruschka et al. 2019) focuses on studying the diverse traits of plants related to the plants' growth. To be more specific, by accurately measuring the plant's anatomical, ontogenetical, physiological…
Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…