相关论文: Accurate identification of bacteriophages from met…
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new…
Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…
Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers…
Motivation: As viruses that mainly infect bacteria, phages are key players across a wide range of ecosystems. Analyzing phage proteins is indispensable for understanding phages' functions and roles in microbiomes. High-throughput sequencing…
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…
Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major…
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields…
Metagenomic disease prediction commonly relies on species abundance tables derived from large, incomplete reference catalogs, constraining resolution and discarding valuable information contained in DNA reads. To overcome these limitations,…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits…
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…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
We present a new method for detecting and identifying bacteria by measuring impedance fluctuations (impedance noise) caused by ion release by the bacteria during phage infestation. This new method significantly increases the measured signal…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Filamentous phage, such as fd used in this study, are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. We constructed libraries of random peptides fused to all…
We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs.…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…