Related papers: Multiple Comparative Metagenomics using Multiset k…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…
The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
Modern high throughput sequencing technologies like metagenomic sequencing generate millions of sequences which have to be classified based on their taxonomic rank. Modern approaches either apply local alignment and comparison to existing…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…
Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in…
Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These…