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The paper fine-tunes the Enformer model using synthetic regulatory sequences to improve its predictive performance on non-reference sequences.

This study shows that long-term composted organic waste application improves vineyard soil health and multifunctionality, with lasting effects on microbial communities and soil properties.

The paper introduces Micro-C-ChIP, a method for high-resolution chromatin organization analysis, and applies it to mouse and human cells to reveal promoter-promoter networks and bivalent promoter architecture.

The paper presents a near telomere-to-telomere genome assembly of the Chilean jack mackerel using PacBio and Hi-C data, achieving high completeness and enabling comparative genomics analyses.

This study identifies high blanchability donors, candidate genes, and molecular markers in groundnut using GWAS and SNP validation.

The paper presents a de novo whole genome assembly of the green shore crab using long-read sequencing and provides a DNA extraction protocol for brachyuran crabs.

The paper examines DNA methylation changes in children and adolescents with ADHD, finding distinct patterns between remitted and persistent ADHD outcomes.

The paper develops a long-read Hi-C method to study 3D interactions between integrated HBV DNA and host genomes, improving sensitivity and specificity for analyzing these interactions.

CrisprBuildr is a web-based tool for designing CRISPR constructs in Drosophila to delete genes or insert fluorescent tags, streamlining genome engineering workflows.

This study identifies LET-418 as a regulator of intracellular pathogen response in C. elegans intestine by analyzing its target genes and functional effects on immune response genes.

The paper quantifies how genetic mutations affect enhancer activity and gene expression using a novel method and identifies TF-specific regulatory programs and enhancer-gene relationships.

The paper identifies non-DNA-contacting residues that determine mono- versus bispecific DNA binding in forkhead transcription factors using protein binding microarrays.

This study identifies APOBEC3B depletion as a driver of L1 element derepression and increased DNA damage in senescent cells through high-throughput sequencing and Ribo-seq analysis.

The paper introduces PReCIS-seq, a nascent RNA assay, to study lineage-specific Pol II activity in mouse skin, revealing mechanisms of gene regulation in adult homeostasis.

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

This study identifies non-consensus XRE (NC-XRE) motifs as functional AHR binding sites in mouse liver, showing their role in regulating gene expression through direct transcriptional control.

This paper presents a second high-quality Denisovan genome from a 200,000-year-old molar, revealing genetic contributions from multiple Denisovan groups and refining the Denisovan genetic lineage.

The paper introduces TF-MAPS, a platform to map functional and allosteric sites of DNA-binding proteins, showing distance-dependent allostery and druggable pockets in three human TFs.

This study uses bulk RNA-seq to analyze transcriptional changes in the middle temporal gyrus across Alzheimer's disease and aging, identifying distinct gene expression patterns and pathways associated with each condition.

The paper identifies two SAP11-homologous effectors in a poinsettia-associated phytoplasma that independently induce branching in plants.