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This study identifies genetic factors influencing repeat abundance variation in Arabidopsis thaliana genomes using resequencing and genome-wide association analyses.

ReMeDy identifies differentially methylated regions by jointly modeling mean and variance changes in DNA methylation data, improving statistical power and biological interpretation.

The paper identifies biological features that influence cross-species predictability of regulatory occupancy and provides a framework to estimate predictability probabilities.

The paper analyzes epigenomic data from twelve human cell lines to reveal how transposable elements evolve in response to host defense mechanisms across different chromatin states.

This study analyzes ancient DNA from three European sites to assess the genomic impact of the second plague pandemic, finding no strong positive selection but evidence of reduced long-range immigration post-pandemic.

This study identifies fusion-driven oncogenic programs in translocation renal cell carcinoma (tRCC) that shape an immunosuppressive tumor microenvironment, explaining its reduced immunotherapy response.

TEDDY reconstructs and characterizes TE-dependent isoforms across biological contexts, revealing regulatory networks and identifying novel regulators like Arid3a with clinical relevance in cancer.

This paper introduces Spatial Hi-C-RNA, a spatial multi-omics technology that co-maps chromatin conformation and transcriptome in tissue, revealing spatially coherent domains and new insights into gene regulation.

The paper introduces a novel dual-spike-in normalization method for ChIP-seq, demonstrating its ability to clarify the relationship between RNA polymerase II activity and histone modifications.

The paper develops cell type-specific chromatin accessibility clocks using snATAC-seq data to predict age and detect aging-related changes in the brain.

The paper shows PAX7 acts in two chromatin compartments, with distinct mechanisms and biological outcomes during pituitary development.

The paper maps and interprets low-affinity transcription factor motifs in mESCs, showing they enhance chromatin accessibility and regulatory potential through cooperative interactions.

The paper investigates sex-specific molecular responses to early-life toxicant exposures in mice across multiple life stages using transcriptomic and epigenomic data.

This study shows early-life stress alters the transcriptome and chromatin accessibility of mouse spermatogonial cells, with molecular signatures persisting into adulthood.

The paper compares the genomes of two Hydra species, finding that the immortal species lacks anti-aging genes and has a distinct metabolic signature.

The paper examines how transcription factor co-occupancy and chromatin structure influence somatic mutation rates in liver cancer regulatory regions.

This study presents the first annotated nuclear and mitochondrial genomes of Agarikon, revealing biosynthetic pathways and phylogenetic placement, and provides a foundation for future research on its medicinal properties.

The paper presents chromosome-level genome assemblies for four Amaranthus species, revealing conserved sex chromosome inversions and providing resources for evolutionary and agronomic research.

This study uses machine learning to predict avian influenza zoonosis risk based on viral genome sequence features, finding that a multi-model approach outperforms individual models.

The paper identifies cell-type-specific epigenetic signatures linked to neuronal vulnerability and longevity across placental mammals using epigenomics and AI.