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The paper maps immune responses of ten eudicot species to 72 Botrytis cinerea isolates, revealing conserved physiological outcomes and lineage-specific regulatory programs.

This study uses multi-omics approaches to analyze how M. bovis infection reprograms the epigenome of bovine alveolar macrophages, identifying key genes and pathways involved in the host response.

This study assesses genetic health in two vulture cohorts using genomic data, finding signs of reduced population size, isolation, and inbreeding, with elevated polygenic deleterious burden in one cohort.

UniversalEPI predicts cell type-specific and differential chromatin interactions using DNA sequence and ATAC-seq data, showing robust performance across cell types and conditions.

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

DiffuST denoises spatial transcriptomics data by integrating spatial features and pathology images, improving downstream analysis and biological insights.

The paper generates near telomere-to-telomere genomes for Linum species to study chromosome evolution, finding lineage-specific DNA transposon expansion linked to pericentromeric restructuring.

The paper introduces a framework for validating somatic mutation burden assays using relative validation and secondary metrics, implemented in SomaticCODEC with strong linearity and precision in human samples.

The paper analyzes mitochondrial genomes of Camellia species to show short repeats drive genome expansion and reveals hybridization signatures through phylogenomic conflicts.

The paper presents a haplotype-resolved genome assembly of autotetraploid alfalfa, revealing extensive structural variation and resistance gene dynamics.

The paper investigates cohesin-mediated chromatin loop extrusion in human cells, revealing two dynamic modes of extrusion and showing that CTCF depletion increases extrusion activity.

This paper introduces improved genomic language models that balance long-range context with single-nucleotide resolution, achieving better performance and efficiency than prior methods.

BiGER is a Bayesian rank aggregation method for meta-analysis of gene lists, handling mixed rankings and missing data with high accuracy.

The paper identifies a novel sense-to-sense codon reassignment in Acidimicrobiales bacteria where ACA specifies aspartate instead of threonine.

This study presents the first telomere-to-telomere genome assemblies for Histoplasma ohiense and identifies genome plasticity, including translocations and transposon activity, in clinical isolates.

This paper introduces a standards framework for integrating single-cell and spatial omics data into brain cell atlases, enabling interoperable and reusable knowledge-ready resources.

The paper tracks H3K27 methylation dynamics in human cells using CUT&Tag, showing that tri-methylation is maintained stepwise after DNA replication and di-methylation occurs at inactive genes post-replication.

This paper develops a method to identify molecular sex and mitochondrial haplotypes from environmental DNA samples, achieving high concordance with tissue samples and resolving lineage-level genetic diversity.

The paper introduces a probabilistic framework to define chromatin accessibility in single-cell snATAC-seq data, avoiding arbitrary thresholds and providing a dynamic understanding of accessible regions.

The paper compiles a dataset of 9,511 horizontally transferred genes in eukaryotes, annotated with certainty levels based on reporting methods.