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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.

Bodenmiller and colleagues pair imaging mass cytometry with data from the METABRIC cohort to define single-cell phenotypic and genomic features of breast cancer with spatial context, finding associations with breast cancer subtypes and prognosis.

Connecting genomics and proteomics allows the development of more efficient and specific treatments for cancer. Here, the authors develop proteogenomic methods to defining cancer signaling in-vivo starting from core needle biopsies and with application to a HER2 breast cancer focused clinical trial.

Cultured adult cardiac tissue undergoes rapid dedifferentiation, which hinders chronic in vitro studies. Here the authors investigate biomimetic electromechanical stimulation of adult myocardial slices applying different preload conditions, identifying the optimum sarcomere length for prolonged culturing, and investigating transcriptional profiles associated with functional preservation.

Single-cell whole-genome sequencing shows that 'foreground' cell-to-cell structural variation and alterations in copy number are associated with genomic diversity and evolution in triple-negative breast and high-grade serous ovarian cancers.

The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

Genome-wide association studies have identified regions which confer risk of high-grade serous epithelial ovarian cancer. Here the authors use expression quantitative train locus analysis to identify candidate genes and functionally characterise them, identifying a role for HOXD9 in ovarian cancer.

Rheumatoid arthritis patients respond differently to anti-TNF treatment. Using community-based challenge, the authors show that currently available data does not reveal meaningful genetic predictors of response to anti-TNF therapy, thus confirming clinical observations.

Observations of TOI-849b reveal a radius smaller than Neptune’s but a large mass of about 40 Earth masses, indicating that the planet is the remnant core of a gas giant.

Physicists look past graphene for atom-thick layers that could be switches in circuits.

Several technology companies offer platforms for users without coding experience to develop deep learning algorithms. This Analysis compares the performance of six ‘code-free deep learning’ platforms (from Amazon, Apple, Clarifai, Google, MedicMind and Microsoft) in creating medical image classification models.

Whole-genome sequencing of human cancer cells in patient-derived mouse xenograft models indicates a key role for TP53 in determining the fitness landscape of polyclonal cancer cell populations.

Primary triple-negative breast cancers are shown to vary widely and continuously in the degree of clonal evolution and mutational content at the time of diagnosis, with implications for future studies of the disease.

An integrated subnational environmental and nutritional optimization approach indicates that, with a transition from current production and consumption patterns, India has the capacity to achieve national food self-sufficiency goals while reducing regional cropland use, water demand and GHG emissions.

Resistance to first line treatment is a major hurdle in cancer treatment, that can be overcome with drug combinations. Here, the authors provide a large drug combination screen across cancer cell lines to benchmark crowdsourced methods and to computationally predict drug synergies.

Certain point defects in crystals can be used as optically addressable quantum bits, much like atoms trapped in vacuum. Ivády et al. show that embedding such artificial atoms in stacking faults can actually improve their optical properties, making them function even more like true atoms.

Wordle, Minecraft and Scrabble are played online by millions. Gamifying experiments can make behavioural research more inclusive, rigorous and reproducible — if it’s done right.

Although the two B-family human DNA polymerases, pol δ and pol ε, are responsible for the bulk of nuclear genome replication, at least 14 additional polymerases have roles in nuclear DNA repair and replication. In this issue, newly reported crystal structures of two specialized A-family polymerases, pol ν and pol θ, expose these enzymes' strategies for handling aberrant DNA ends.

A modular architecture for managing and sharing electrophysiology, behavior, colony management and other data has been built to support individual laboratories or large consortia.

Typhoid fever is caused by Salmonella enterica serovar Typhi (S. Typhi). This study examines ∼2,000 clinical isolates of S. Typhi to show highly structured/geographically restricted genomes except rapidly disseminating H58 subclade, and design a genotyping framework for tracking the disease.

An integrated transcriptome, genome, methylome and proteome analysis of over 200 lung adenocarcinomas reveals high rates of somatic mutations, 18 statistically significantly mutated genes including RIT1 and MGA, splicing changes, and alterations in MAPK and PI(3)K pathway activity.

The authors pooled resources to identify best practices and develop a new standardized protocol for estimating functional connectivity in rats with magnetic resonance imaging.

Marco Marra and colleagues identify somatic mutations in EZH2 in diffuse large B-cell lymphomas and follicular lymphomas. EZH2 is a histone methyltransferase that participates in trimethylation of H3 Lys27 (H3K27) as part of the PRC2 complex. The mutations alter a single tyrosine residue in the SET domain of EZH2 and reduce the ability of PRC2 to trimethylate H3K27 in vitro.

LTT 9779 b is Neptune-sized planet rotating around its star with a period of 0.79 days and an equilibrium temperature of 2,000 K. It is not clear how it retained its atmospheric envelope, which contains ~10% of H/He, as it should have been photoevaporated by now.

A single dose of the ChAdOx1 nCoV-19 vaccine elicits antibodies and cytokine-producing T cells that might help control or prevent SARS-CoV-2 infection.

A community of researchers report the lessons learned from applying 44 algorithms to predict drug sensitivity in cancer cell lines using genomic, epigenetic and proteomic datasets

This Perspective considers the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.

The hypoxic deep inflow water in the Gulf of St. Lawrence spreads inland at 0.5 cm s-1 and the bulk of the inflow water will reach the estuary after about 4.5 years, according to the results from a Deep Tracer Release Experiment combined with analysis of Swish float data.

Crowdsourcing analysis improves computational prediction of cytotoxic responses in humans.

Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression.