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SARS-CoV-2 evolved into several sublineages harboring different mutations in spike. Here, the authors isolate and characterize nine SARS-CoV-2 variants and show that EG.5.1.3 has highest fitness in nasal epithelial cells, while JN.1 shows lower affinity to ACE2 and higher immune evasion compared to BA.2.86.1.

In this study, the authors estimate the effectiveness of the mRNA-1273 (Moderna) vaccine for Omicron subvariants using data from the USA on ~31,000 cases and ~92,000 matched controls. They find that effectiveness against infection waned rapidly after third and fourth doses, but effectiveness against hospitalization remained high.

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.

Release of the zero-COVID policy in China in late 2022 led to two large Omicron-driven waves of infection in 2023. Here, the authors analyze virus genomes and serology data from before and after the two waves and describe changes in virus lineage distribution and age-specific antibody responses.

Understanding collective behaviour is an important aspect of managing the pandemic response. Here the authors show in a large global study that participants that reported identifying more strongly with their nation reported greater engagement in public health behaviours and support for public health policies in the context of the pandemic.

The factors influencing risk of reinfection with SARS-CoV-2 are poorly understood. Here, the authors use data from the UK COVID-19 Infection Survey, a community based longitudinal study, to assess characteristics of ~45,000 reinfections compared to initial infections.

Monitoring of co-infections of SARS-CoV-2 variants is important to evaluate their clinical impact and the risk of emergence of recombinants. Here, the authors develop and validate a methodological pipeline to detect co-infections and apply it to samples from France in early 2022, when Delta and Omicron were co-circulating.

The duration and strength of protection against SARS-CoV-2 infection resulting from a booster vaccine dose or breakthrough infection are not well understood. This study uses data from the UK COVID-19 Infection Survey to investigate correlates of protection against Omicron BA.4/5 infection and assess antibody responses to booster vaccination and breakthrough infections.

Many SARS-CoV-2 infections may go undetected through conventional PCR or lateral flow tests. Here, the authors analyse the utility of analysing longitudinal nucleocapsid antibody trajectories to improve identification of prior SARS-CoV-2 infections using surveillance data from the UK.

Bivalent mRNA COVID-19 vaccines have been developed to provide broader protection against SARS-CoV-2 variants. In this cohort study based on electronic health records from the United States, the authors estimate the effectiveness of bivalent, compared to monovalent, vaccines and no vaccination against a range of COVID-19-related outcomes.

Bacterially produced bile acids inhibit T_H17 cell function, which may be relevant to the pathophysiology of inflammatory disorders such as inflammatory bowel disease.

In this work, the authors performed a single-cell genotyping and transcriptomics analysis, revealing cell-type-specific and nonautonomous effects of mTOR pathway mutations in mosaic focal cortical dysplasia.

Molecular ferroic materials receive considerable interest in view of field-induced switchable polar/magnetic orders. Here, the authors exploit metal-free antiferroelectrics in molecular solid solutions to assemble high-performance ferroic materials.

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.

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.

This study quantifies how the largest wildfire in New Mexico’s history altered runoff processes and generated water quality disturbances that propagated along hundreds of kilometers and over multiple months, affecting key aquatic ecosystem processes.

The authors observe the emergence of ferroelectricity in Sn-based perovskite [93.3 mol% (FA0.86Cs0.14)SnI3 and 6.7 mol% PEA2SnI4] semiconductor films doped with 2-methylbenzimidazole, ascribing to the hydrogen bond enhancement after imidazole molecular doping.

The human cortex displays an anterior-to-posterior asymmetry, identified via both post-mortem and in vivo microstructural measurements. Microstructural asymmetry is heritable, varies across cortical layers and between sexes, and relates to functional asymmetry and behavior.

Estimates of infection rates from the UK COVID-19 Infection Survey may have been biased by the characteristics of people who chose to take part. Here, the authors show that the survey population had unusually high vaccination rates and adjust infection estimates taking this into account.

Authors identify a genic male sterility gene, ZmENR1, in maize and report that it encodes an enoyl carrier protein reductase that forms heterodimers with ZmHAD1 to ensure maize pollen and anther development through regulating lipid and ROS metabolism.

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.

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.

Li et al. report large circular dichroism in 2D chiral perovskite single crystals, arises from the inorganic sublattice, instead of chiral ligands, driven by electron-hole exchange interactions. This is evidenced by both reflective circular dichroism spectroscopy and ab initio theory.

Antiferroelectric (AFE) materials are emerging as a remarkable candidate for efficient energy-storage applications. Here, the authors report on a high-temperature, lead-free, AFE perovskite, (CHMA)₂CsAgBiBr₇ (where CHMA is cyclohexylmethylammonium) with high fatigue endurance at a high electric breakdown field strength.

NADP can directly bind with FTO and enhance its m⁶A demethylase activity, thus affecting RNA m⁶A modification and adipogenesis.

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.

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.

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.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

A test-negative case–control analysis using data from a diverse population in California, USA, demonstrates that vaccine efficacy of a three-dose regimen of the mRNA-1273 COVID-19 vaccine is reduced against infection with the Omicron SARS-CoV-2 variant in comparison to Delta, but that efficacy against hospitalization remained high for both variants.

Tailored to provide diabetes management recommendations from large training and validation datasets, an artificial intelligence system integrating language and computer vision capabilities is shown to improve self-management of patients in a prospective implementation study.

RNA-cleaving DNA enzymes are catalytic DNA that can cleave RNA in a sequence-specific manner. Here, the authors report three crystal structures of the 8–17 DNAzyme that include the pre-catalytic state of the RNA cleavage reaction, providing insight into the catalytic mechanism and may guide the rational design of DNAzymes.

CCR5 is a co-receptor for many transmitted HIV strains. Here, the authors show that biweekly injection of the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges of a CCR5-tropic SHIV.

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.

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.

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.

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.

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.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Characterization of a biosynthetic pathway for the sulfonation of steroidal metabolites, such as cholesterol, by gut bacteria may have implications for immune cell trafficking and inflammatory bowel disease.