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The paper updates a yeast reference transcriptome using direct RNA sequencing to improve UTR annotation and provides a reusable pipeline for future updates.

This study shows insulin signaling links prenatal adversity to long-term brain and behavioral changes, with sex-specific effects in rats.

The paper introduces gmMAP, a framework that integrates metabolite GWAS with single-cell and spatial transcriptomes to map metabolic programs at cellular and spatial resolution, revealing associations between exogenous metabolites and cellular states.

This study uses spike-in normalization to analyze age-related changes in gene expression across mouse cell types, finding decreased mRNA content in non-immune cells and increased in immune cells, along with reduced gene expression and shared regulatory processes between ageing and proliferation arrest.

The paper identifies diverse mobile genetic elements in Xanthomonas species and their role in adaptive traits through comparative genomic analysis.

The paper introduces and benchmarks two droplet-based single-nucleus assays for chromatin accessibility and gene expression, showing they are cost-effective and produce high-quality data.

This study characterizes endogenous retroviruses in the slow loris, identifying active retroviral elements and their evolutionary dynamics across strepsirrhine primates.

The paper presents a high-quality genome assembly of Cercospora cf. flagellaris, identifying genes and pathways relevant to its pathogenicity and host interactions.

The paper maps H3K4me3 in T. cruzi and finds it correlates with transcriptional activity and genomic span of initiation regions.

The paper presents a high-quality reference genome for Hymenolepis diminuta using PacBio HiFi long-read sequencing, achieving high contiguity and completeness.

This study profiles allele-specific expression across 42 tissues and 34 pig breeds using an open-source pipeline, revealing widespread and tissue-specific allelic imbalance.

This study analyzes interspecies variation in the 45S rDNA locus across vertebrates, revealing lineage-specific differences in organization, copy number, and sequence evolution.

The paper presents a draft genome assembly of the slipper lobster and identifies an XX/XY sex-determination system, along with a diagnostic PCR marker for monosex aquaculture.

HiFiRe3 improves rare structural variant detection by reducing artifacts through error suppression and correction strategies across long and short-read sequencing platforms.

The paper integrates bulk RNA-seq data from multiple studies to identify reproducible matrix-immune gene expression signatures in IPF.

The paper corrects genome assemblies of two Lupinus species, revealing differential diploidization after a shared whole-genome duplication across six Lupinus species.

The paper examines transcriptomic responses to heat stress in coral recruits from thermally distinct broodstock, finding conserved stress-response pathways and limited genetic differentiation.

The paper shows processed pseudogenes are dynamic evolutionary elements, not inert, and links their abundance to life-history traits and cancer-related dynamics across vertebrates.

This paper introduces a method to improve long-read transposon-insertion sequencing by combining restriction-site-based enrichment with adaptive sampling, achieving high coverage and efficiency.

The paper identifies a cis-regulatory variant in the ASIP gene associated with gray coat color in donkeys through genome-wide analysis and functional validation.