metagenomics

TestNet-PA: Sampling-Zero-Aware Inference of Microbial Presence-Absence Networks

TestNet-PA addresses sampling zeros in microbial presence-absence networks by modeling them as structural or sampling zeros, improving FDR control and sensitivity compared to Fisher's exact test.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

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

Hybrid RY-mers increase aDNA alignment sensitivity

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: an AI powered update

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

Material context and TGF-β blockade timing determine retained matrix in patient-derived bioprinted keratoconus stroma

This study shows that timing of TGF-β blockade and material context affect matrix retention in bioprinted keratoconus stroma, with optimal regimens improving collagen retention and reducing contractile gene expression.

Interspecific social contacts spread gut microbiota in wild rodent communities

This study shows that social interactions between different rodent species can spread gut microbiota, with stronger transmission from wood mice to yellow-necked mice.

Continental scale genetic diversity supports geo-clustered ecoregions connectivity

The paper examines genetic diversity and connectivity between ecoregions, finding a divide between eastern and western regions with restricted gene flow in the west.

Global homeostatic forces shape the composition of a hyperdiverse tropical insect fauna

The paper estimates Madagascar's insect fauna contains at least 250,000 species, most unrecorded, and finds global homeostatic forces, not lineage composition, shape its ecological similarity to temperate forests.

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

Application of metagenomic sequencing to improve sessile serrated lesion detection using the faecal immunochemical test

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

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

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

Integrative identification of Tetratostichococcus sp. CCAH0201 (Trebouxiophyceae, Chlorophyta) from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam

The paper identifies a microalgal strain from mangrove leaves using molecular markers and phylogenetic analysis, placing it closely related to Tetratostichococcus jenerensis.

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

The paper uses metatranscriptomics to analyze viral diversity in freshwater and marine environments, identifying new RNA viruses associated with microalgae and proposing a new genus within Marnaviridae.

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

High reproducibility demonstrated in a direct-to-consumer microbiome testing workflow under real-world conditions using fecal reference material

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

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

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.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.

Wild wood mouse gut microbiota are influenced by captivity and cross-fostering

This study examines how captivity and cross-fostering affect gut microbiota in wood mice, finding that microbial diversity and functional potential shift with host history and environment.

Genetic Variation in Photosynthetic Maintenance and Post-Chill Recovery for Early Season Maize Plantings

This study evaluates genetic variation in maize's response to chilling stress and recovery, identifying heritable traits linked to cold resilience.

Hidden infections: Linking parasite ecology, fish health and stakeholder perceptions in Nile tilapia aquaculture in central Kenya

The paper investigates parasite infections in Nile tilapia aquaculture, finding that monopisthocotylan parasites are prevalent and linked to gill lesions, while stakeholders rarely identify parasites as a health cause.

Long-read shotgun metagenomics identifies distinct urogenital microbial community states associated with functional potential and urinary tract infection during pregnancy

This study uses long-read shotgun metagenomics to identify distinct urogenital microbial community states in pregnant women, linking them to functional potential and UTI risk.

Higher-order metabolic interactions among oral commensals gate pathobiont expansion through succinate-driven pH modulation

The paper identifies succinate as a mediator of interbacterial antagonism in the oral microbiome, showing how metabolic interactions among commensals regulate pathobiont expansion through pH modulation.

Polymerase and primer biases in eukaryote ultra-long-read metabarcoding

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.

A new Serratia taxon found in a trombidiform mite shows genomic evidence of host adaptation but is phylogenetically distinct from Serratia symbiotica

The paper identifies a new Serratia taxon in mites with genomic signs of host adaptation but phylogenetically distinct from S. symbiotica.

Unprecedented urban freshwater microviral survey highlights shift from sewage to river water communities

The paper surveys microviruses in urban freshwater environments, finding shifts in community composition from sewage to river water, with wastewater treatment plants acting as filters.

XRN1 couples RNA granule remodelling to global mRNA decay triggered by the activity of a viral endoribonuclease

The paper investigates how XRN1 links RNA granule remodeling to global mRNA decay triggered by the viral endoribonuclease vhs, revealing a sequential model of translational arrest and degradation.

MicrobeRT: A Framework and Suite of Fine-tuned Language Models for Genomic Sequences

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

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

COSMOS integrates vector-pathogen metagenomics to monitor mosquito-borne diseases, detecting pathogens and mosquito communities in field samples with high accuracy.

SedaDNA metabarcoding reveals hidden histories of within-species sequence variation

This study uses sedaDNA metabarcoding to analyze historical within-species sequence variation across multiple taxa and time periods.