metagenomics

This study evaluates genomic language models' ability to generate taxonomically informative embeddings of viral fragments, finding that some models outperform traditional methods on reference and novel datasets.

The paper develops SPARTA for in situ genetic reprogramming of native microbiomes and introduces ScRibe-seq to identify engineered taxa, demonstrating functionality across diverse environments.

This paper introduces GeneEmbedLLM, a framework using large language models to generate gene embeddings from multi-source textual annotations, achieving competitive performance in various downstream tasks.

This study shows that two decades of EU pesticide substitution have not reduced environmental harm to stream invertebrates, as toxic pressure and impairment remained stable over time.

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.

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

This study demonstrates high reproducibility in a DTC microbiome testing workflow using NIST fecal reference material across multiple processing steps and real-world conditions.

This study evaluates polymerase and primer biases in ultra-long-read metabarcoding for soil eukaryotes, finding that certain polymerases and primer pairs improve data quality and biodiversity recovery.

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

This paper introduces a model-agnostic decomposition method to analyze differences in mean response between groups, using game-theoretic attribution and optimal transport coupling.

HiFiTaxa is a Nextflow pipeline for analyzing PacBio HiFi reads of 16S rRNA and ITS amplicons, offering multiple classifiers and benchmarking their performance on mock communities and holdouts.

This study identifies spatio-temporal dynamics and ecological niche factors influencing Theileria equi infection in Portugal using field-surveillance data and environmental variables.

This paper introduces PGL, a Bayesian regression method for microbiome feature selection that uses phylogenetic trees to improve detection of exposure-associated ASVs.

This paper benchmarks confounder-aware differential abundance methods for microbiome studies, finding that covariate adjustment improves false discovery control but reduces sensitivity, with different strategies performing better under various conditions.

This study examines how different fitness statistics in high-throughput microbial experiments affect interpretations of mutant fitness and evolutionary dynamics.

The paper shows that the human gut microbiota recovers to an individual-specific state after antibiotics, not to a generic healthy state.

The paper uses graph neural networks to interpret microbial association patterns in IBD, showing that coordinated associations, not just abundance shifts, are predictive.

This study analyzes gut microbiota in Passalidae beetles to determine if host phylogeny or geography shapes microbiome composition, finding that phylogeny is the primary driver.

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

This paper develops a mathematical framework to model microbial communities optimizing growth rates through metabolic cooperation and resource allocation.

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 assesses biodiversity recovery on modular shellfish reefs using eDNA metabarcoding, showing rapid taxonomic richness gains but ongoing compositional shifts over time.

This paper evaluates autonomous eDNA metabarcoding for offshore biodiversity monitoring around an FPSO, finding that repeated sampling is needed to distinguish transient from persistent patterns.

The paper introduces taxon-in-context to capture individualized microbial context in the human gut microbiome, showing that microbes occupy different contexts across individuals and over time, improving recurrence prediction.

This study characterizes river biofilm viromes across a national network, revealing seasonal structure, host associations, and metabolic functions linked to environmental variables.

This study identifies core microbiota associated with postlarval survival in shrimp through a meta-analysis of 16S rRNA gene datasets.

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.