A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data

Phylogenetic Convolutional Neural Networks in Metagenomics

Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architecture for the classification of metagenomics data based on the Convolutional Neural Networks, with the patristic distance defined on the phylogenetic tree being used as the proximity measure. The patristic distance between variables is used together with a sparsified version of MultiDimensional Scaling to embed the phylogenetic tree in a Euclidean spa…

PGLasso: Microbial Community Detection through Phylogenetic Graphical Lasso

Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form functional communities can provide a solid foundation to understand microbiome related diseases; this can serve as a key step towards precision medicine. In order to understand how microbes form communities, we propose a two step approach: First, we infer the microbial co-occurrence network by integrating a graph inference algorithm with phylogenetic information …

从基因组和宏基因组数据推断微生物与其环境的相互作用

Inferring microbial interactions with their environment from genomic and metagenomic data

针对现有基因组规模微生物建模依赖模拟、结论易受参数影响的问题，研究团队开发了MetConSIN工具，可基于基因组规模代谢模型推断特定环境下微生物与代谢物的情境化相互作用网络。

Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees based on Subsets of Chloroplastic Core Genes

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 chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of…

Phylogenetic Profiles as a Unified Framework for Measuring Protein Structure, Function and Evolution

The sequence of amino acids in a protein is believed to determine its native state structure, which in turn is related to the functionality of the protein. In addition, information pertaining to evolutionary relationships is contained in homologous sequences. One powerful method for inferring these sequence attributes is through comparison of a query sequence with reference sequences that contain significant homology and whose structure, function, and/or evolutionary relationships are already known. In spite of decades of concerted work, there is no simple framework for deducing structure, fun…

Quantifying Reticulation in Phylogenetic Complexes Using Homology

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show cases where reticulate evolution can fail to be detected. We introduce an extension of the standard framework and define the median complex as a construction to recover signal of the frequency and scale o…