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The paper uses population-level whole-genome sequencing to study colistin resistance evolution in diverse Pseudomonas aeruginosa lineages under increasing colistin pressure.

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

The paper introduces dreamlet, an R package for efficient differential expression analysis of large-scale single-cell transcriptomics data, showing improved speed and memory usage compared to existing methods.

The paper identifies 1,596 Consensus HAQERs by aligning T2T assemblies, showing they are rapidly evolved regions with mutation signatures, regulatory functions, and disease associations.

The paper investigates the invasion history of box tree moth in North America using genomic and morphological data, finding multiple introductions and genetic structuring.

The paper develops TEgment, a tool to analyze transposable element transcriptional modalities, showing that CDK9 inhibition leads to TE activation in AML through non-autonomous expression patterns.

The paper uses nanopore sequencing to analyze genomic and methylation differences between two MCF-7 sublines, finding substantial methylation divergence and associations with cancer-related genes.

This study examines how DNA methylation profiles change across three generations in quails exposed to genistein, finding that while methylation differences accumulate, genetic factors largely explain these changes.

This study uses a deep-learning model to analyze scRNA-seq data and identifies how folate deficiency disrupts metabolic transitions in developing mouse neural ectoderm, leading to morphological defects.

This study verifies nucleotide sequence reagents and cell line identities in circRNA papers and finds frequent errors in high-impact journals.

Stairway Plot v3 infers nonparametric effective population size trajectories from the site frequency spectrum at biobank scale, achieving high resolution with large samples.

This study shows that H3.3K27M mutation disrupts lamina-associated domain organization, leading to activation of neuronal gene programs in DIPG.

The paper identifies differentially expressed genes and gene modules in pig skeletal muscle and shows CCND2 promotes myogenic differentiation.

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

The paper identifies ancient whole-genome duplications in bryozoans using synteny-based methods, revealing genomic signatures and functional enrichment in cilia-related genes.

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

Fishash assigns perturbations to cells in Perturb-seq data using Fisher's Exact Test, improving accuracy and speed over existing methods.

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

This paper introduces Mikado, a method using sparse linear algebra to accelerate genotype representation graph computations, significantly improving speed over existing tools on large biobank datasets.

This study identifies genetic differentiation and directional selection in sympatric rockfish species, suggesting reinforcement maintains species boundaries.