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BoNTax: a curated genome-based framework for taxonomic classification and characterization of Clostridium botulinum Group I and Clostridium sporogenes

BoNTax is a genomic framework for classifying and characterizing Clostridium botulinum Group I and C. sporogenes, resolving species relationships and providing toxin information.

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

Exploring protein duplication across Archaea genomes

The paper analyzes protein duplication across 1,829 archaeal genomes to assess how gene duplication scales with genome size and identifies lineage-specific patterns and functional enrichments.

From APTs to advanced persistent biological threats (APBTs): a taxonomy and large-scale metadata audit of genomic surveillance infrastructure

The paper audits metadata vulnerabilities in genomic repositories, identifying structural weaknesses that could enable malicious metadata poisoning as part of an APBT operation.

Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae)

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

The paper develops a hiPSC-based framework to study ancestry-related phenotypic variation in the Japanese population, finding no hepatic triglyceride differences despite genetic associations.

An improved Trypanosoma vivax genome assembly confirms the distinct organisation of its variant antigen repertoire

The paper presents an improved T. vivax genome assembly, revealing distinct VSG gene organization and expression mechanisms compared to T. brucei.

Ayahuasca plant genomes reveal retrotransposon-derived centromeres and contrasting routes to DMT and β-carbolines

The paper presents the genomes of Ayahuasca source plants, revealing retrotransposon-derived centromeres and distinct biosynthetic pathways for DMT and beta-carbolines.

The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing

This study uses long-read sequencing to analyze structural variants in Aspergillus flavus, identifying homopolymer tracts and deletions that arise spontaneously.

Pooled progeny sequencing effectively estimates polyandry in species with large families

This paper develops a likelihood-based method to estimate polyandry using pooled progeny sequencing and applies it to Drosophila melanogaster, finding 57% of families were sired by a single male.

Reinterpreting Keratoconus Gene Expression in Light of Inherited Stromal Weakness

This paper reinterprets keratoconus gene expression by showing that expression direction depends on control choice and stromal state, not disease causation or intervention effectiveness.

Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp.

The paper investigates the genomic diversity and metabolic traits of Fructilactobacillus isolates from honeypot ant crop microbiomes and identifies factors contributing to their dominance.

Systematic benchmark of demultiplexing workflows for direct RNA sequencing

This study benchmarks two demultiplexing tools for direct RNA sequencing using IVT spike-ins and species identity, showing their performance differences and the need for calibration.

A chromosome-level genome assembly of the chilli thrips Scirtothrips dorsalis Hood (Thysanoptera: Thripidae)

The paper presents a chromosome-level genome assembly for the chilli thrips Scirtothrips dorsalis, providing genomic resources for studying its biology and pest status.

Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley

The paper compares two viral sequencing pipelines from wastewater influent and solids, finding that solids capture more DNA viruses while influent captures more RNA viruses, with probe-capture enrichment providing comparable results across fractions.

The adaptive architecture of tRNA dependencies across physiological tumor environments

The paper maps tRNA dependencies in cancer cells across different environments, finding that tRNA dependencies are environmentally sensitive while some dependencies are shared across cell lines.

Random mtDNA mutagenesis maps genotype-phenotype associations across metabolic contexts and lineages

The paper introduces mtDIVE, a random mtDNA mutagenesis platform, to study genotype-phenotype associations in metabolic contexts and lineages, revealing lineage-specific effects and mutation-specific impacts.

Unveiling the Hidden Rules: Enhancing NMD Prediction for Protein-Truncating Variants

The paper develops a model to predict NMD outcomes for protein-truncating variants using RNA-seq data, achieving ~78% ROC-AUC and identifying non-canonical determinants.

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

The paper evaluates integration methods and parameters on cattle embryos to assess their impact on biological insights, finding that parameter choices affect cell type classification and functional interpretation.

DNA 6mA marks transcriptionally active chromatin in malaria parasites

The paper identifies 6mA methylation in Plasmodium falciparum, showing it is associated with active chromatin and transcription, and identifies a methyltransferase involved in this modification.