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This paper improves DNA CNNs' ability to predict indel effects on gene regulation by addressing technical variance through shift augmentation and introduces an interpretation technique validated with experimental data.

LeafCutter2 identifies and quantifies unproductive splicing events from RNA-seq data, revealing their role in gene regulation and disease, including Alzheimer's.

The paper identifies ESBL-producing Enterobacterales on vegetable plants in Madagascar, showing genetic links to human, animal, and environmental strains.

The paper shows that active enhancers recruit cohesin to form cell-specific chromatin domains, using the alpha globin cluster as a model.

This study identifies mutation patterns, TMB, HLA haplotypes, and LINE-1 activation as potential biomarkers for predicting ICI response in NSCLC and MIBC.

This study presents a chromosome-level genome assembly of Pinguicula gigantea and performs phylogenomic analysis to explore the evolution of carnivory in this species.

The paper identifies hominoid-specific transposable elements that regulate neural crest migration genes, showing their role in craniofacial evolution.

The paper presents gap-free genomes of three Fusarium oxysporum f. sp. niveum races, identifies race-specific effectors, and demonstrates one as a critical virulence factor.

This study identifies RAP1's role in alternative splicing, particularly intron retention, and links it to nonsense-mediated decay in yeast.

The paper reports the complete genome sequences of nine bacterial isolates from microplastics in the Bow River, revealing their potential for plastic biodegradation.

The paper identifies TF-sensitive chromatin regions as highly enriched for heritability of blood cell phenotypes, using a novel single-cell multi-omics approach.

This paper proposes a statistical framework using hierarchical mixed-effects models to analyze ctDNA dynamics in liquid biopsy data, finding that a hierarchical linear spline model best captures patient-level ctDNA evolution.

The paper investigates how GSK3B inhibition with tideglusib reverses ethanol-induced transcriptomic changes in mouse brains and links these findings to human genetic risk for alcohol dependence.

The paper shows BRCA1 correlates with proliferation in human neural progenitor cells and medulloblastoma, particularly in Group 3 and 4 tumors, and is linked to worse prognosis.

This study analyzes the gut microbiome of humpback whales during feeding and fasting periods, revealing significant taxonomic and functional changes associated with migration and fasting.

This study quantitatively analyzes E. coli moonlighting proteins to identify patterns in amino acid composition and structural-functional relationships.

CINner models chromosomal instability in cancer, showing how selection parameters and WGD influence tumor progression and heterogeneity.

The paper integrates single-cell transcriptomics and epigenomics to show how neural stem cells shift lineage bias and epigenetic states during mouse corticogenesis.

The paper analyzes whole-transcriptome data from BLV-infected cows to identify gene expression differences between high and low proviral load groups, finding immune response genes are downregulated in high proviral load cows.

This study constructs a haplotype-phased genome assembly for Haliotis gigantea and identifies non-syntenic homologous chromosomes with structural variations that may contribute to functional diversification.