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The HPN-DREAM community challenge assessed the ability of computational methods to infer causal molecular networks, focusing specifically on the task of inferring causal protein signaling networks in cancer cell lines.

Epigenetic changes associated with post-natal differentiation have been characterized. Here the authors generate epigenomic and transcriptional profiles from primary human breast cells, providing insights into the transcriptional and epigenetic events that define post-natal cell differentiation in vivo.

Rare genetic variants can contribute to complex traits but this contribution is not well understood. Here, the authors analyse deep whole genome sequencing data across 1457 individuals from an isolated Greek population and find association of rare variant burdens with cardiometabolic traits.

A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.

Alterations of locus coeruleus signal intensity have been associated with functional changes in health and disease. Here, the authors tested a pre-registered hypothesis on a large number of subjects as part of the Cam-CAN consortium.

Authors of the March WHO report into how COVID-19 emerged warn that further delay makes crucial inquiry biologically difficult.

Open collaboration on biomedical discoveries requires a fundamental shift in the traditional roles and rewards for both investigators and participants in research.

The ability to remain true to cellular identity and function is lost during aging and carcinogenesis when DNA damage triggers inflammation that progressively erodes homeostatic cues. Shalabi et al. show that these losses are accelerated in patients with germline cancer mutations in DNA repair genes and are independent of chronological age.

This Registered Report presents evidence from 87 countries and regions showing that brief emotion-regulation interventions consistently reduced negative emotions and increased positive emotions during the COVID-19 pandemic.

Many COPD patients are deficient in vitamin D, a condition that can lead to bone problems as well as difficulty breathing. Can dietary supplements be of help?

The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

This paper examines the main approaches for studying gene expression evolution, tests their inherent biases and discusses open questions about the evolution of the transcriptome.

Decline in sensorimotor skills with age may be due to an overreliance on the prediction of the sensory consequences of one’s actions. Here the authors show that sensorimotor attenuation increases with age, and that this is associated with structural and functional changes in frontostriatal circuits.

Executive functions are affected by ageing but it is unclear how. Kievit et al.use brain imaging and modelling approaches to show how multifactorial explanations outperform single-factor models when relating age-related differences in grey and white matter to differences in fluid intelligence and multitasking.

The transcription factor GATA-3 is necessary for the formation of a mammary gland and the maintenance of mammary-cell differentiation. The loss of GATA-3 function in a fully formed mammary gland generates oestrogen receptor-negative, proliferating cells that lack expression of myoepithelial markers. Cells with similar characteristics in breast cancer are associated with poor prognosis.

In this Expert Recommendation, Faupel-Badger and colleagues present a conceptual framework to define precancer and advance our understanding of the earliest changes that occur in the progression to overt cancer, providing novel opportunities to intervene to prevent or treat their emergence.

Cognitive abilities change with age, but why some decline and some do not is not clear. Here, the authors use data from the Cam-CAN cohort to show that distributed, multi-component brain responsivity and default-mode deactivation supports and characterizes preserved cognition across the adult lifespan.

A new study shows that decreased cystatin A synthesis in aged epidermis mediates age-related bone loss, whereas topical treatment that restores cystatin A mitigates this loss. This report demonstrates that skin aging has systemic consequences by showing that signals originating in skin can control bone function.

In this DREAM challenge, 75 methods for the identification of disease-relevant modules from molecular networks are compared and validated with GWAS data. The authors provide practical guidelines for users and establish benchmarks for network analysis.

Combined analysis of proton-proton collision data from the Large Hadron Collider at CERN by the CMS and LHCb collaborations leads to the observation of the extremely rare decay of the strange B meson into muons; the result is compatible with the standard model of particle physics, and does not show any signs of new physics, such as supersymmetry.

Climate change mitigation strategies based on biochar generation—and its application to agricultural soils—can effectively sequester carbon, although biogeochemical and economic trade-offs must be considered.

Centromere identity is thought to be epigenetically propagated by stable inheritance of nucleosomes containing the histone variant CENP-A; the authors propose a different model here in which germline transcription defines the genomic regions that exclude CENP-A incorporation during embryogenesis in the holocentric worm Caenorhabditis elegans.

Considerable resources are required to gain maximal insights into the diverse big data sets in biomedicine. In this Review, the authors discuss how crowdsourcing, in the form of collaborative competitions (known as Challenges), can engage the scientific community to provide the diverse expertise and methodological approaches that can robustly address some of the most pressing questions in genetics, genomics and biomedical sciences.

In outbreak situations involving a novel pathogen timely and coordinated response is crucial. The WHO Scientific Advisory Group for the Origins of Novel Pathogens recently released a global framework to guide future scientific investigations into the origin of emerging pathogens.

The first report of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge introduces the BAMSurgeon tool for accurate tumor simulation and reports the performance of 248 submissions in calling single-nucleotide variants from three pairs of synthetic tumor–normal genome benchmarks.

William Dobyns and colleagues report de novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA in the sporadic overgrowth syndromes megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) and megalencephaly-capillary malformation (MCAP).

Large-scale metagenomic analyses are vastly increasing the rate of discovery of variation within species but they are also leading to scientific and semantic challenges. Bork and colleagues highlight the advances and challenges that are resulting from the use of metagenomic data to study within-species diversity.

This Consensus Statement highlights the importance of cancer-associated fibroblasts in cancer biology and progression, and issues a call to action for all cancer researchers to standardize assays and report metadata in studies of cancer-associated fibroblasts to advance our understanding of this important cell type in the tumour microenvironment.

The responses of freshwater stream biodiversity and biomass to temperature in Arctic regions varies with biogeography.

A plan to 'genomicize' epigenomics research and pave the way for breakthroughs in the prevention, diagnosis and treatment of human disease.