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Although pathogen whole genome sequencing is becoming more common, for many pathogens far more partial sequences are available. In this study, the authors develop a phylogenetic pipeline to efficiently combine whole and partial viral genome sequences and demonstrate its application using rabies virus sequences.

Large-effect variants in autism remain elusive. Here, the authors use long-read sequencing to assemble phased genomes for 189 individuals, identifying pathogenic variants in TBL1XR1, MECP2, and SYNGAP1, plus nine candidate structural variants missed by short-read methods.

Single layers of carbon atoms are now well known for their useful properties, but a combination of two sheets can also exhibit some unusual electronic characteristics. Here, the authors identify two distinct electron states in bilayer graphene that result from spontaneous symmetry breaking.

Despite the potential of free electrons for quantum technological applications, these are still limited by the weak electron-photon interactions. To address this challenge, the authors introduce electron-light couplers that produce high-photon-number state generation, enabling quantum sensing and metrology with unprecedented precision.

The CMS Collaboration reports the measurement of the spin, parity, and charge conjugation properties of all-charm tetraquarks, exotic fleeting particles formed in proton–proton collisions at the Large Hadron Collider.

External Control Arm methods for clinical trials were developed to compare the efficacy of a treatment to a control group that is built with data from external sources. Here, the authors present FedECA, a privacy-enhancing method for analyzing treatment effects across institutions, streamlining multi-centric trial design and thereby accelerating drug development while minimizing patient data exposure.

In this work, the authors show that the essential Mycoplasma pneumoniae protein P116 enables cholesterol acquisition from lipoproteins and various cell types. An antibody against its C-terminal domain inhibits lipid acquisition, growth, and plaque binding, linking M. pneumoniae to atherosclerotic lipid-rich tissue.

Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.

Riccardo Velasco and colleagues report the genome sequence of the 'Golden Delicious' domesticated apple. These data shed new insight into the genomic events that preceded the origin of this crop.

The quark structure of the f₀(980) hadron is still unknown after 50 years of its discovery. Here, the CMS Collaboration reports a measurement of the elliptic flow of the f₀(980) state in proton-lead collisions at a nucleon-nucleon centre-of-mass energy of 8.16 TeV, providing strong evidence that the state is an ordinary meson.

Cerebral organoids can be used to gain insights into neuropsychiatric disorders. Here the authors carry out RNAseq characterization from organoids derived from donors with autism spectrum disorder to identify associated cell type specific driver genes.

The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genus, as the cultivated strawberry (Fragaria × ananassa) is an octoploid where F. vesca is predicted to be a subgenome donor.

The accuracy of melanoma diagnosis can vary considerably among clinicians, impacting both patient outcomes and the performance of related AI tools. Here, the authors systematically assess interrater variability among expert pathologists reviewing histopathological images and clinical metadata of melanoma-suspicious lesions collected at eight German hospitals.

Immunodeficiency-centromeric instability-facial anomalies syndrome is a life threatening autosomal recessive disorder caused by mutations in DNMT3B and ZBTB24. Here Thijssen et al. identify mutations in CDCA7 and HELLSin previously unexplained cases.

Many-body interactions typically involve spontaneous symmetry breaking and the breakdown of simple single-particle models. Lee et al. now show that trilayer-graphene devices are a tunable platform for investigating the transition between these two regimes.

Why are some species widespread while others are found only in small, isolated areas? This study shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, poor dispersers, and have evolved relatively recently.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Urothelial cancer is a challenging disease and an emerging field for targeted therapies. Here, the authors optimize clinical proteomics to provide proteome-level data on tumor specificity and identify robust prognostic subtypes with predictive information for repurposed drug candidates.

Here, the authors identify four novel regulators of the 2-cell-like state, and thus totipotency, via unbiased CRISPR knockout screens and Dazl re-expression as a readout. They show that these factors act upstream of DPPA2 and DUX, and independently of p53.

Copy number deletions in 2p16.3 locus (NRXN1) in individuals significantly increase risk for schizophrenia. Here, authors show, at single cell level, genetic background-specific effects that culminate in synaptic dysfunction using iPSC-derived brain organoid model.

The social exposome—lifelong social and economic adversity—can shape brain health and dementia risk. Here, the authors show that an adverse social exposome is linked to poorer clinical, cognitive, and brain changes in Latin American older adults.

Basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) of the salivary gland are rare tumours. Here the authors report that BCA and BCAC patients possess distinct genomic profiles despite histopathological similarities, and identify a recurrent FBXW11 missense mutation (p.F517S) which leads to accumulation of β-catenin in BCA and higher expression of Wnt/β-catenin targets.

DNAJC12 variants cause parkinsonism. Here, the authors show that DNAJC12 stabilizes tyrosine hydroxylase, a crucial enzyme in dopamine synthesis, and identify key structural motifs for this interaction, explaining the pathogenesis of truncated variants.

J-domain proteins (JDPs) regulate Hsp70 function and specificity. Here, authors combine functional assays and cryoEM to describe the structure of a dynamic tubular assembly of DNAJA2, a class A JDP, and its stabilizing interdomain interactions.

Overexpression of c-MYC regulates tumor metabolism in pancreatic ductal adenocarcinoma (PDAC). Here the authors identify ELOVL6, a fatty acid elongase regulated by c-MYC, as a potential therapeutic target of PDAC.

The selective CO₂ photoreduction in water mediated by earth-abundant photocatalysts remains highly challenging. Here the authors present the coordinative anchorage of molecular catalysts on a pyridine-armed covalent triazine framework for CO₂ photoreduction to CO in fully aqueous solutions.

A study reporting the results of a clinical trial co-administering the GDF-15-blocking antibody visugromab with the anti-PD-1 antibody nivolumab demonstrates that neutralizing GDF-15 can overcome resistance to immune checkpoint inhibition in cancer.

The CMS Collaboration reports evidence for off-shell Higgs boson contributions in the production of Z boson pairs, and measures the width of the Higgs boson, which is inversely related to its lifetime.

Chirality can be induced both by physical forces and by chemical induction processes. Here, a self-assembled system is reported in which chiral selection is controlled by the combined action of a chiral dopant and vortical stirring, which can act either constructively or destructively.

The most up-to-date combination of results on the properties of the Higgs boson is reported, which indicate that its properties are consistent with the standard model predictions, within the precision achieved to date.

Phylogenetics and population genetics analysis of ancient tiger genomes inform tiger evolution and suggest post-glaciation admixture of divergent tiger lineages in China.

AMBRA1-mediated degradation of cyclin D through CRL4–DDB1 regulates cell proliferation and prevents replication stress in neurodevelopment and cancer.

The PACAP-PAC1R neuropeptide system regulates neuroendocrine stress responses. Here the authors demonstrate a role for PACAP-PAC1R in ventromedial hypothalamus in modulating fear extinction.

B cell activation in the germinal centre (GC) is accompanied by metabolic adaptation, but the functions of mitochondria remodelling during this process is unclear. Here the authors find that B cell-specific deficiency of Tfam, a transcription factor modulating mitochondria remodelling, impacts GC responses and induces aged immune features in B cells.

Artificial intelligence has become popular as a cancer classification tool, but there is distrust of such systems due to their lack of transparency. Here, the authors develop an explainable AI system which produces text- and region-based explanations alongside its classifications which was assessed using clinicians’ diagnostic accuracy, diagnostic confidence, and their trust in the system.

The Tachykinin 2 (Tac2) pathway in the central amygdala is sufficient and necessary for modulating fear memory consolidation. The authors show that silencing Tac2 neurons in the amygdala of male mice reduces fear expression, while fear expression in female mice is increased when manipulations are made during proestrus.

The CMS Collaboration reports the study of three simultaneous hard interactions between quarks and gluons in proton–proton collisions. This manifests through the concurrent production of three J/ψ mesons, which consist of a charm-quark–antiquark pair.

Ultra-high-energy gamma-ray emission from the microquasar V4641 Sagittarii is reported, suggesting that large-scale jets from microquasars could be more common than previously thought and also could be a notable source of galactic cosmic rays.