Related papers: A phylogenetic scan test on Dirichlet-tree multino…

Phylogenetic trait evolution models allow for the estimation of evolutionary correlations between a set of traits observed in a sample of related organisms. By directly modeling the evolution of the traits along an estimable phylogenetic…

Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…

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…

Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…

High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…

The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…

In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…

The Dirichlet-multinomial (DM) distribution plays a fundamental role in modern statistical methodology development and application. Recently, the DM distribution and its variants have been used extensively to model multivariate count data…

Healthcare data from patient or population cohorts are often characterized by sparsity, high missingness and relatively small sample sizes. In addition, being able to quantify uncertainty is often important in a medical context. To address…

We introduce a method to identify heritable microbiome communities when the input is a pairwise dissimilarity matrix among all samples. Current methods target each taxon individually and are unable to take advantage of their phylogenetic…

When analyzing data from multiple sources, it is often convenient to strike a careful balance between two goals: capturing the heterogeneity of the samples and sharing information across them. We introduce a novel framework to model a…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

A central part of population genomics consists of finding genomic regions implicated in local adaptation. Population genomic analyses are based on genotyping numerous molecular markers and looking for outlier loci in terms of patterns of…

Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the…

Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

Most data in genome-wide phylogenetic analysis (phylogenomics) is essentially multidimensional, posing a major challenge to human comprehension and computational analysis. Also, we can not directly apply statistical learning models in data…

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…