database / resource

AOPTK automates toxicological literature analysis using AI, achieving high accuracy in identifying chemical-biological effect relationships.

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

PLATE provides a global resource of food metaplasmidomes, offering curated catalogs and annotations for studying plasmid diversity and function in food ecosystems.

This study uses ancient environmental DNA to show how whaling and climate change impacted Antarctic marine biodiversity over two centuries.

This study surveys the virome of migratory birds and ticks in Switzerland, detecting novel viruses and highlighting the role of birds in virus and tick dispersal.

The paper introduces PANIMaSTA, a method to construct minimally fragmented metagenomic pangenome graphs for highly diverse viral genomes, improving graph topology for comparative analysis.

ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

The paper integrates stool chemistry metrics with shotgun metagenomics in adults to identify distinct gut health profiles associated with microbial and inflammatory markers.

The paper introduces the SAR11 Genome Atlas, a resource integrating SAR11 genomes and functional data to support ecological and genomic analysis of oceanic bacteria.

This study identifies new antibiotic resistance gene-mobile genetic element associations using metagenomic long reads from diverse environments.

The paper identifies a novel Chilomastix lineage in wild Moroccan Barbary macaques using metagenomic sequencing, showing it is distinct from human-derived C. mesnili.

ArthroVerse compiles and annotates protein families from arthropod-associated microbiomes to explore functional diversity and host-microbe interactions.

The paper maps the global distribution of β-lactamases across environments and microbes, revealing their abundance and potential origins in plant and wastewater ecosystems.

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

TRUEDA identifies true pathogens in low-biomass disease-microbe associations by accounting for contamination, outperforming existing decontamination methods and correcting false associations.

The paper introduces TACTIC, a tool that combines denoising and clustering to improve 16S rRNA diversity estimates by reducing inflation caused by within-species sequence variation.

CPMsi is a computational pipeline that efficiently processes and integrates large-scale MSI data, enabling faster analysis and discovery of molecular patterns across tissue sections.

The paper identifies novel Alveolate parasites in lizard tissues using 18S rRNA metabarcoding and phylogenetic analysis, revealing sequences related to Stylocephalidae and Perkinsea not previously found in reptiles.

GlyEnzEA constructs enzyme-specific glycan sets from glycomics data and identifies significant changes in specific enzyme groups.

The paper identifies innate immune activation and CMV-specific antibody reactivity as early markers of preclinical NMOSD, preceding clinical onset by over 12 years.

This study isolates and identifies four known compounds from the flowers and three from the leaves of Munnozia hastifolia, reporting the first chemical composition analysis of the species.

EzHit retrieves enzyme-reaction associations efficiently, outperforming baselines and enabling large-scale metagenomic biocatalyst discovery.

The paper discovers a novel archaeal AP endonuclease from a salt marsh metagenome using cell-free functional metagenomics, showing its high salt tolerance and structural similarity to human APE1.

NeoOmni Atlas integrates proteogenomic data to catalog tumor neoantigens across 26 cancer types, identifying novel ligands and epitopes for immunotherapy.

The paper expands a bile acid and steroidal MS/MS spectral library across three repositories, capturing diverse structures and providing a resource for classifying unknown spectra.

This study uses dental calculus metagenomics to show that domestication affects oral microbiomes across three mammalian genera, with genus-specific variations observed.