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This study reveals the 3D genome architecture of Zymoseptoria tritici, showing how chromatin structure and function are interconnected through nuclear organization and gene regulation.

The paper presents the first reference genome of the Black Redstart, assembled using PacBio HiFi sequencing and annotated with 18,609 genes, providing a resource for studying high-altitude adaptation in passerines.

The paper examines genomic diversity and adaptation in Apennine brown bears, finding unique genetic signatures linked to reduced aggressiveness, possibly due to human-induced selection.

This study uses deep learning to show that shorter and multiple U2-type introns improve splice site prediction in Arabidopsis thaliana.

This study benchmarks five DNA foundation models across genomic tasks, finding that mean token embeddings improve classification performance and specialized models outperform general ones in gene expression and QTL prediction.

The paper maps the transcriptional regulatory network of Cryptococcus neoformans by analyzing TF deletions and identifies functionally orthologous TF pairs across species.

This study uses long-read sequencing and genome graphs to analyze structural variation in Mycobacterium tuberculosis, identifying SVs linked to drug resistance and virulence.

This study reveals that deep-learning-based RNA splicing models have confounders and blind spots, leading to poor performance on non-reference sequences.

The paper compares gene expression and chromatin accessibility of ohnologues and single-copy genes in two arachnids, one with a history of whole genome duplication, to assess subfunctionalization.

The paper re-analyzes a lncRNA screen using Cas13d and finds that off-target effects caused many false-positive results, undermining the study's conclusions.

This paper presents a high-quality genome assembly and annotation for the bumble bee wax moth, Aphomia sociella, using long-read sequencing, and places it phylogenetically within the Lepidoptera order.

GPTAnno provides a hierarchical cell type annotation method using GPT models and ontology trees, improving accuracy across species and tissues by integrating clustering with ontology constraints.

This paper presents a chromosome-level genome assembly for Mozambique tilapia using PacBio HiFi and Omni-C sequencing, providing a resource for conservation and aquaculture.

This study uses multi-omic profiling to trace molecular changes in skin cells during carcinogenesis, identifying key mutations and spatial gene expression patterns in keratinocytes, actinic keratoses, and squamous cell carcinomas.

The paper presents the chromosome-level genome assembly of Androsace saussurei, a plant adapted to extreme alpine environments.

The paper integrates tissue-specific epigenetic annotations into genomic predictions of gene expression in three pig breeds, improving eQTL mapping interpretability but facing challenges in cross-breed predictions.

This paper compares DNA shotgun read measurements and cytometric genome size estimates across species, finding discrepancies and highlighting the need for better measurement controls.

SomaMutDB 2.0 is a database that catalogs 8.9 million somatic mutations from 10,852 samples and provides functional annotations to assess their impact in normal human tissues.

The paper presents a telomere-to-telomere diploid reference genome for the Chinese Quartet, improving centromere structure annotation and enabling population-specific structural variant analysis.

The paper quantifies introgression in tinamou species, showing asymmetric patterns linked to chromosomal features and resolving their species tree through genome-architecture-aware phylogenomics.