Abstract. The idea that sex-differences in selection drive the evolution of suppressed recombination between sex chromosomes is well-developed in populatio

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple...

In this Review, Smith et al. describe DNA methylation landscapes that emerge over mammalian development and within key disease states, as well as how different methyltransferases interface w...

Martyn and Montgomery et al. present Variant-EFFECTS, a high-throughput technology developed to precisely measure the effects of CRISPR-mediated edits on gene expression. Variant-EFFECTS is reproducib...

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

This Perspective discusses strategies and challenges for the Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Consortium as it aims to catalogue the molecular and cellular phenotypes associated...

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into re...

Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...

In rare diseases, rare mutations have long been thought of as the only contributor. Genetic analyses of people with such conditions now suggest that the effects of common genetic variants can stack up and contribute to disease risk. Assessing the influence of common mutations on rare disease risk.

Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score tha...

Abstract. Speciation is a complex process that can unfold in many different ways. Speciation researchers sometimes simplify core principles in their writin

When nature evolves a gene over eons at scale, it produces a diversity of homologous sequences with patterns of conservation and change that contain rich structural, functional, and historical informa...

A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci ...

Li et al. thoroughly analyzed RNA splicing junctions in 34,775 samples and identified 29,051 tumor-specific transcripts that may serve as cancer driver genes, neoantigens, and circulating biomarkers.

Somatic stem cells are characterized by their low overall protein synthesis rates, a feature implica

Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increase...

Discover more about the ERGA Assembly Report – a comprehensive, community-driven Genome assembly Quality Control Document.

Background Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the ...

Nature Methods - This work introduces a k-mer-based approach to customizing a pangenome reference, making it more relevant to a new sample of interest. This method enhances the accuracy of...

Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to…

AbstractMotivation. A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approach

AbstractSummary. Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of ba

Metabuli enhances metagenomic read classification by jointly analyzing DNA and amino acid sequences for specificity and sensitivity, respectively.

Rodriguez-Algarra et al. present an analysis of rDNA copy number (CN) variation in the UK Biobank (UKB), revealing associations with altered counts of specific blood cell subtypes, such as neutrophils...