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The paper tests enhancer-promoter compatibility using improved assays, finding that promoter responsiveness, not enhancer rank order, determines activation sensitivity.

This study compares genomic and transcriptomic differences between highly and weakly parasitic Trichoderma atroviride strains to identify molecular mechanisms underlying mycoparasitic performance.

PhenoXtract extracts phenotypes from clinical descriptions using a hybrid approach of Large Language Models and Knowledge Graph embeddings, achieving high recall and precision.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

SMURF improves spatial transcriptomic analysis by accurately assigning mRNAs to cells and revealing gene-expression zonation in tissues.

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

The paper models the genetic architecture of cortical expansion using GWAS data and links it to neuropsychiatric disorders.

traceCB improves cell-type-specific eQTL mapping by integrating scRNA-seq and bulk data across ancestries, increasing eGene discovery and replication rates.

This paper presents a chromosome-level genome assembly for Podocoryna americana, revealing gene family expansions and contractions compared to other cnidarians.

fastder detects expressed regions from RNA-seq data without relying on annotations, achieving high accuracy and speed for large-scale analysis.

The paper develops a framework to correct cohesin positioning measurements in ChIP-seq by accounting for antibody background, revealing its impact on cohesin positioning estimates.

The paper uses ATAC-seq data and TF footprinting tools to identify novel cis-regulatory elements in Drosophila embryos, finding that many TF binding sites lie outside known enhancers.

This study identifies two distinct LAM subtypes and their microenvironmental interactions using multi-omics and spatial transcriptomics, revealing key regulatory networks and potential therapeutic targets.

kmerRRR improves analysis of repetitive genomic regions by using k-mer frequency analysis to enhance mappability and recover lost biological signals in chromatin and small RNA data.

Lorax enables real-time visualization of biobank-scale ancestral recombination graphs with integrated metadata and genomic information.

This study identifies 8-oxoguanine as a DNA modification in Plasmodium falciparum associated with transcriptionally active chromatin and elevated gene expression during its developmental cycle.

The paper assesses challenges in reusing scRNA-seq data from GEO, finding that only ~40% provide usable processed data and <10% include cell-type annotations.

The paper presents a spatial cell atlas comparing surface and cave-dwelling Mexican tetra fish brains, revealing transcriptional changes across cell types linked to cave adaptation.

ARGformer uses transformers to learn embeddings from ancestral recombination graphs, enabling population structure analysis and ancestry inference without genotype data.

This paper uses Visium HD spatial transcriptomics to create a high-resolution map of human liver cell types and spatial gene expression in adult and pediatric samples.