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Seed banks are reservoirs of plant diversity. This study shows that nutrient addition decreases diversity of grassland seed banks, increases their similarity to aboveground communities and interacts with aboveground herbivory to affect their abundance.

As the financial system is increasingly important in catalysing the green transition, it is critical to assess the impediments it may face. This study shows that existing financial regulations may impair the shift of financial resources from high-carbon to low-carbon assets.

An assessment at the scale of the Democratic Republic of the Congo shows that urban gullies are a growing problem, with 118,600 people displaced between 2004 and 2023.

Atmospheric concentration measurements at remote sites around the world reveal an accelerated decline in the global mean CFC-11 concentration during 2018 and 2019, reversing recent trends and building confidence in the timely recovery of the stratospheric ozone layer.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

Down syndrome causes extensive Alzheimer’s disease pathology in all individuals and has been instrumental in development of the amyloid hypothesis in AD. Here, the authors use proteomics on Down syndrome spinal fluid and brain tissues to illustrate the common and unique changes in DSAD compared to other genetic forms of AD and the more common late-onset form of the disease.

Kersting’s groundnut is an underutilised crop that is locally important, tolerant to drought and critical to food security. Here, the authors report its genome assembly, population genetics analyses, and candidate genes for seed coat colour.

Neuropixels 1.0 NHP is a 45-mm, high-density silicon probe capable of recording large numbers of neurons with single-neuron resolution from most areas in a macaque’s brain.

Adenosine-to-inosine editing is a form of RNA modification observed in the human brain transcriptome. Here the authors question the accuracy of utilizing postmortem samples to reflect the RNA biology of living brains. This is due to significant differences in adenosine-to-inosine editing between living and postmortem brain tissues, with most sites exhibiting higher editing levels postmortem.

A qualitative and quantitative analysis of 186 biodiversity-related policies in Colombia is used to describe how biodiversity has been integrated into policy domains, which policy instruments are most prevalent and how the policy mix has changed over six decades.

Current model-based financial regulations favour carbon-intensive investments. This is likely to disincentivize banks from investing in new low-carbon assets, impairing the transition to net zero. Financial regulators and policymakers should consider how this bias may impact financial system stability and broader societal objectives.

DREDge is a software tool for motion correction of high-density electrophysiology recordings. It can handle action potential or local field potential data and is demonstrated on a variety of acute or chronic recordings from humans, nonhuman primates and mice.

Analyzing clinical records from a cohort of 3,042 donors in the Netherlands Brain Bank, natural language processing models unveil the symptomatology and potential misdiagnoses of a broad range of neurodegenerative disorders.

For medical use, human stool should be considered a tissue, not a drug, argue Mark B. Smith, Colleen Kelly and Eric J. Alm.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Key measures of biodiversity were quantified and found to be affected by human pressures that shifted community composition and decreased local diversity across terrestrial, freshwater and marine ecosystems.

The size and shape of alluvial river channels control and adjust to the flow of water and sediment, with consequences for flooding and ecological habitat. This Perspective examines how the sediment entrainment threshold constrains the size, shape and dynamics of alluvial rivers.

Here the authors identify TNIP1 as a risk factor for a fatal neurodegenerative disorder and discover specific genetic loci associated with the three main subtypes of this disorder. The findings highlight distinct disease mechanisms, emphasizing the roles of immunity and the notch signaling pathway.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

A neural network platform that incorporates photonic components can be used to predict optical fibre nonlinearities and improve the signal quality of submarine fibre communications.

An expert-elicitation process identifies current methodological barriers for monitoring terrestrial biodiversity, and how technological and procedural development of robotic and autonomous systems may contribute to overcoming these challenges.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

The CommonMind Consortium sequenced RNA from dorsolateral prefrontal cortex of subjects with schizophrenia (N = 258) and control subjects (N = 279), creating a resource of gene expression and its genetic regulation. Using this resource, they found that ∼20% of schizophrenia loci have variants that may contribute to altered gene expression and liability.

PTSD has been associated with DNA methylation of specific loci in the genome, but studies have been limited by small sample sizes. Here, the authors perform a meta-analysis of DNA methylation data from 10 different cohorts and identify CpGs in AHRR that are associated with PTSD.

Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.

APOE is the major genetic risk factor for Alzheimer’s disease. In a large number of neuropathologically confirmed cases and controls, the impact of different APOE genotypes on Alzheimer’s dementia risk was greater than previously thought and APOE2 homozygotes had an exceptionally low risk.

Online matching platforms are increasingly used for applications with positive social impact such as matching blood donors with recipients, where matching algorithms need to balance fairness with an efficiency objective. The authors demonstrate, both in computational simulations and using real data from the Facebook Blood Donations tool, that introducing a simple online matching policy can substantially increase the likelihood of donor action.

A large empirical assessment of sequence-resolved structural variants from 14,891 genomes across diverse global populations in the Genome Aggregation Database (gnomAD) provides a reference map for disease-association studies, population genetics, and diagnostic screening.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Cortex morphology varies with age, cognitive function, and in neurological and psychiatric diseases. Here the authors report 160 genome-wide significant associations with thickness, surface area and volume of the total cortex and 34 cortical regions from a GWAS meta-analysis in 22,824 adults.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.