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Using single-cell transcriptomics and functional analyses, the authors identify a specialized neural network in the male schistosome gynecophoric canal and show that lsamp maintains its integrity, enabling intersex communication and female reproductive maturation.

This study defines tissue- and sex-specific N- and O-glycoproteomes of adult Schistosoma mansoni, uncovers novel and HexA-modified glycans, shows glycosylation is essential for parasite survival, and reveals vaccine candidates as glycoproteins.

Bronchiectasis and asthma can co-exist in the same patient, and the characteristics may be different from bronchiectasis alone. Here the authors characterise the function of ILC3 cells and how IL-17C potentiates IL-17A expression promoting a neutrophil dominated asthma endotype in mouse bronchiectasis-asthma models.

Most of the available fluorogenic RNA approaches emit visible fluorescence, and there is a need for tools working at longer wavelengths. Here, the authors identify and modulate red fluorescent protein-like fluorophores to bind the fluorogenic RNA Squash, thereby obtaining near-infrared fluorogenic RNA-based tools.

Mn dissolution is dominantly responsible for capacity fading of most Mn-rich cathodes. Here the authors reveal that soluble Mn²⁺ species significantly destabilizes solvent and anion via its unique solvation sheath structure, providing insight into the failure mechanism of related cathode chemistries.

A natural pathway in rice and in seven other major crop species degrades 57–89% of accumulated methylmercury and releases Hg into the air. The MeHg demethylation within rice mitigates Hg flux into human food webs, diminishing human cognitive damage and generating global economic benefits of US$30.7–84.2 billion.

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.

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

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.

Flux jumps can lead to premature quenching and irreversible damage of superconducting magnets. Here, authors developed a GPU-optimized algorithm aimed at tackling the complex intertwined effects of electromagnetism, heating, and strain acting concomitantly on real superconducting coils.

Litsea cubeba belongs to the Lauraceae family within the Magnoliids clade. Here, the authors assemble its genome and reveal divergence of inflorescence and sexual differentiation, the phylogenetic relationships across the Lauraceae and related species, and biosynthetic genes related to essential oil synthesis.

Evaluating the off-target effect is crucial for ensuring the safety of CRISPR–Cas9-based technologies. Duan, Gao and Zhang et al. developed TOPO-seq, a method to capture and evaluate DNA topology-regulated off-target activity of Cas9-based genome-editing tools.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

Circular RNAs are known to regulate cancer. Here, the authors show that the circular RNA circTP63 promotes lung squamous cell carcinoma by competing with endogenous RNA to upregulate FOXM1.

Histone acetylation influences the speed of seed germination. Here, Wang et al. show that loss of the SNL1/SNL2 histone deacetylase binding factors accelerates seed germination and provide evidence that they act by regulating the expression of AUX1which in turn influences cell division.

Stanene is a single sheet of tin atoms. Here, it is shown that a few stacked layers of stanene can be a superconductor. Changing the thickness of the substrate modifies the form of superconductivity and critical temperature.

In this study, the authors combine an anti-viral drug and immune system inducer to treat influenza A and B viral infections in vitro and in vivo. They show that the compound outperforms zanamivir alone as it is still able to clear infection three days post infection, and it can be administered via different routes without reduced efficacy.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

Qing Lan and colleagues report the results of a genome-wide association study of lung cancer in never-smoking women from Asia. They identify three new susceptibility loci and confirm three other previously reported associations.

Emerging SARS-CoV-2 variants with multiple mutations raise concerns on vaccine effectiveness. Here, Kang et al. report that a quadrivalent mosaic nanoparticle vaccine displaying spike proteins from the SARS-CoV-2 prototype and three different VOCs confer protection against SARS-CoV-2 variants in mice.

The gapless surface states of topological insulators could enable quantitatively different types of electronic device. A study of the topological insulating Bi₂Se₃ thin films finds that a gap in these states opens up in films below a certain thickness. This in turn suggests that in thicker films, gapless states exist on both upper and lower surfaces.

Growing demand for food is confronting constraints to its sustainable production. This study finds that intercropping increases grain yields and their stability and that yield benefits increase over time.

Estrogen receptor alpha (ERα)-negative cells, which are enriched during endocrine therapy, are associated with metastatic relapse of breast cancer. Here the authors show that ERα inhibits breast cancer metastasis and suggest that ERα suppresses the amoeboid-like migration of breast cancer cells by upregulating vinculin.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.

Efficient, large-scale genomic analysis is facilitated on the cloud by a computational tool with error-diagnosing and self-healing capabilities.