Browse Articles

High-resolution mapping of promoter-anchored chromosomal contacts in type 3 innate lymphoid cells (ILC3s), coupled with GWAS effector gene prioritization and functional studies, identifies ILC3-linked genes as potential mediators of risk for several immune diseases.

Eukaryotes share many ancient histone post-translational modifications, but whether they use them in the same way remains unknown. By profiling some of these modifications across diverse eukaryotic lineages, we find that active chromatin states are deeply conserved, whereas repressive heterochromatin has diversified extensively.

scE2G is a family of models that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues.

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukaryotic species. Despite the conservation of hPTMs across eukaryotes, the functional chromatin states they define are not always conserved.

This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor binding and chromatin context.

The authors present INCOMMON, an open-source Bayesian inference tool that determines the multiplicity and copy number of driver mutations from tumor sequencing datasets.

During human development, the human kidney reproducibly generates approximately one million patterned nephrons. Using spatial transcriptomics and functional validation studies, we help identify how ligands and cell–cell interactions coordinate this complex process.

The spatial organization of human kidney development is explored using single-cell RNA sequencing and spatial transcriptomics, highlighting the crucial role of microenvironmental signals in guiding cell fate.

With the profound epithelial and stromal remodeling observed in inflammatory bowel disease, why does progression to cancer often take decades? Using a mouse model of early malignant lesions arising from colitis, we identify a close link between tissue repair and neoplasia, whereas immune-refractory cellular neighborhoods appear relatively protected.

Singapore’s National Precision Medicine program phase II establishes a multi-ancestry Asian population cohort, national-scale genetic testing and public–private partnerships, demonstrating how small countries can contribute to global genomics efforts.

Multi-ancestry genome-wide association analyses of Hashimoto’s thyroiditis identify new risk loci and highlight shared genetic architecture with other autoimmune diseases and pleiotropic effects on clinical outcomes.

This study uses a mouse model of inflammatory bowel disease to explore how mutations and cellular context combine to drive the transition to malignancy.

This Review surveys the current landscape of genomic artificial intelligence through the lens of sequence-to-function models, examining how architectural choices, training data, prediction tasks, model interpretation and evaluation strategies can shape their generalization.

Genome-wide analyses in up to 121,579 pregnant women from China identify genetic associations across 111 phenotypes, including gestation-specific effects and interactions with gestational timing.

This study reports genetic effects on mass spectrophotometry-based plasma proteomics in a cohort of ~1,400 British South Asians, accessing parts of the proteome missed by other proteomics platforms. The resulting protein quantitative trait loci are integrated with genome-wide association study data to find potential mechanisms of disease.

Intrinsically disordered regions impose regulatory restraints on gene-activating demethylases, limiting chromatin engagement and preserving genomic stability. This function is a key determinant of the distinct substrate preferences and regulatory activities of FTO and ALKBH5 in mammals and plants.