Related papers: metaSPAdes: a new versatile de novo metagenomics a…

High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…

In recent years hypergraphs have emerged as a powerful tool to study systems with multi-body interactions which cannot be trivially reduced to pairs. While highly structured methods to generate synthetic data have proved fundamental for the…

Metamaterials are artificial materials designed to exhibit effective material parameters that go beyond those found in nature. Composed of unit cells with rich designability that are assembled into multiscale systems, they hold great…

Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic…

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…

Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…

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…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…

Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms.…

Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…

Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…

Disassembly is fundamental to binary analysis and rewriting. We present a novel disassembly technique that takes a stripped binary and produces reassembleable assembly code. The resulting assembly code has accurate symbolic information,…

While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is only viable when variants are relatively rare and the bubbles…

Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…

Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…

Metainformation is a common companion to biomedical images. However, this potentially powerful additional source of signal from image acquisition has had limited use in deep learning methods, for semantic segmentation in particular. Here,…

Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their…

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…

Heterogeneous graphs are ubiquitous data structures that can inherently capture multi-type and multi-modal interactions between objects. In recent years, research on encoding heterogeneous graph into latent representations have enjoyed a…