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The paper develops TNSEEK, a pipeline for analyzing Tn-seq data across multiple bacterial strains, identifying conserved and strain-specific essential genes in Pectobacteriaceae.

This study links polygenic scores for QT interval to changes in Kv11.1 protein interactions in hiPSC-CMs, revealing connections between genetic variants and endocytic trafficking mechanisms.

This paper introduces an RNA-aware preservation method, RIPIN, that improves spatial transcriptomics data quality by inhibiting RNase activity across human and mouse tissues.

The paper investigates the evolutionary origins of protein novelty in Saccharomycotina yeasts, identifying two distinct modes of de novo and divergent gene evolution and their structural implications.

This paper benchmarks how reference genome choice affects human genome interpretation by comparing T2T references and finding ancestry-matched references provide more accurate variant discovery.

This paper presents the first nuclear genome assembly for the endangered huemul (Hippocamelus bisulcus), along with a mitochondrial genome, enabling conservation and evolutionary studies.

GenomeCompendium is a database that integrates repeat, assembly quality, and functional content data from complete prokaryotic genomes to improve genome annotations and analyze taxonomic coverage.

Digital Kennison maps Y-linked sequences to Drosophila melanogaster fertility regions using computational methods, achieving 97% precision and reducing time from weeks to minutes.

The paper reassesses the 'sexy' X hypothesis by analyzing X-linked gene expression and associations with male-specific reproductive disorders, finding male-biased enrichment in testicular cell types and monogenic disorders.

Apollo 3 is a new manual genome annotation tool that integrates with JBrowse 2, enabling multi-genome editing and synteny visualization.

This paper uses genomic and historical data to refine the timeline and origin of the Second Plague Pandemic in Western Eurasia.

This study shows that RNAPII and XPC remodel chromatin loops and domains during UV repair, enhancing lesion recognition and repair efficiency.

The paper uses deep mutational scanning to analyze structure-switching aptamers, identifying base requirements, base-pairing, and regions critical for sensitivity or specificity.

The paper uses single-nucleus RNA-seq and spatial transcriptomics to show how the maternal-fetal interface diverges in structure and function between the basal plate and chorionic membranes, identifying NID2 as an ancestry-associated regulator of trophoblast invasion.

The paper compares bulk and single-cell RNA-seq/ATAC-seq data and models to assess their impact on predicting causal genes from GWAS variants in TNFα-treated endothelial cells.

The paper creates a cellular atlas of gene expression in fed and starved C. elegans L1 larvae, revealing transcription in starved primordial germ cells and the role of aak-1/AMPK in chromatin compaction.

This study shows that acute LINE-1 overexpression in human fibroblasts causes widespread changes in transcriptome, proteome, and secretome, affecting cell cycle and interferon pathways, beyond retrotransposition.

The paper uses population genomics to analyze Schistosoma japonicum re-emergence in Sichuan, China, revealing a diverse parasite population maintained in reservoirs and a regional transmission network.

The paper uses single-cell RNA sequencing to analyze PDL cells from maxilla and mandible pairs, finding uniform mesenchymal populations with donor-specific substates and limited jaw-related transcriptional differences.