metagenomics

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 study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

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.

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

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

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

The paper identifies a uORF, PHYRE, essential for phytochrome B translation and photomorphogenesis in Arabidopsis, showing its role in translational regulation.

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

This study identifies RBM3 as a host factor that promotes PEDV infection by stabilizing viral RNA and upregulating the entry factor HSPA5.

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

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

The paper compares immune profiles and microbiomes of breast milk from mothers with different farm exposures to identify associations with immune development and atopic disease.

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 shows that ROS1-induced DNA demethylation leads to distinct epigenetic changes in chromosome arms and pericentromeres during plant immune memory formation and erasure.

The paper investigates how a bacterial chaperone-usher pathway enables interkingdom protection of a fungus from antimicrobial compounds.

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 uses deep functional metagenomics to discover new streptothricin acetyltransferase genes in soil, revealing previously unknown resistance mechanisms.

This study shows that ESX-5 deletions in Mtb reduce cytokine secretion in macrophages via a post-transcriptional mechanism and alter heavy metal response genes.

This study uses multi-omics to uncover Gardnerella genomic features linked to biofilm formation and interspecies interactions in the vaginal microbiome, identifying potential therapeutic targets for bacterial vaginosis.

This study shows AP2-L is essential for Plasmodium liver-stage development by regulating PVM formation and host-cell interactions.

This study explores the eco-genomic diversity of Chrysophyceae algae, revealing their evolutionary adaptations and gene markers linked to trophic strategies and environmental responses.

The paper characterizes the seasonal dynamics of cell-associated viral communities in Big Turkey Lake, identifies their functional roles through auxiliary metabolic genes, and reconstructs viral genomes.

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

This study shows that bacterial fermentation, not respiration, dominates in upland soils during hypoxia, challenging the assumption that respiration is the primary metabolic strategy.

The paper investigates the genetic basis of blue floral pigmentation in orchids, finding an unexpected pathway involving duplicated genes and regulatory changes rather than the expected CYP75A pathway.

Akkermansia expansion reduces short-chain fatty acid-producing Firmicutes in human-flora uveitis mice, raising Th1 responses and disease; a Verrucomicrobia/Firmicutes ratio is elevated in uveitis, MS and Crohn's patients.

The paper introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

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