相关论文: Detecting gene innovations for phenotypic diversit…

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…

In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…

Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…

Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…

In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…

In creative design, where aesthetics play a crucial role in determining the quality of outcomes, there are often multiple worthwhile possibilities, rather than a single ``best'' design. This challenge is compounded in the use of…

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and…

Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…

The integration of advanced technologies, such as Artificial Intelligence (AI), into manufacturing processes is attracting significant attention, paving the way for the development of intelligent systems that enhance efficiency and…

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…

With recent progress in deep generative models, the problem of identifying synthetic data and comparing their underlying generative processes has become an imperative task for various reasons, including fighting visual misinformation and…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…