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Biomedical image analysis challenges have increased in the last ten years, but common practices have not been established yet. Here the authors analyze 150 recent challenges and demonstrate that outcome varies based on the metrics used and that limited information reporting hampers reproducibility.

Here the authors apply machine learning approaches to Alzheimer’s genetics, confirm known associations and suggest novel risk loci. These methods demonstrate predictive power comparable to traditional approaches, while also offering potential new insights beyond standard genetic analyses.

Phylogenomic analysis of 7,923 angiosperm species using a standardized set of 353 nuclear genes produced an angiosperm tree of life dated with 200 fossil calibrations, providing key insights into evolutionary relationships and diversification.

The authors present microwave emission measurements on a resistively shunted Josephson junction based on a HgTe quantum well. They demonstrate that, with significant spurious inductance in the shunt wiring, additional microwave emission peaks appear at half of the Josephson frequency, which can mimic the 4π-periodicity of topological Andreev states.

Medulloblastoma in children is a difficult cancer to treat and the immune response to this tumour is not fully understood. Here the authors characterise and validate T cell epitopes from these cancers using an immunopeptidomics approach, comparing different molecular subtypes.

A study presents archaeogenomic data for 131 individuals from 38 sites spanning 6,000 years, and details the demographic processes of the Caucasus and the surrounding steppe zone throughout the Bronze Age.

Gao and colleagues explore soluble biomarkers, immune cell subsets, viral antibody responses and plasma proteomics to better define and understand long COVID in two independent cohorts.

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

International challenges have become the de facto standard for comparative assessment of image analysis algorithms. Here, the authors present the results of a biomedical image segmentation challenge, showing that a method capable of performing well on multiple tasks will generalize well to a previously unseen task.

The BioDIGS project is a nationwide initiative involving students, researchers and educators across more than 40 research and teaching institutions. Participants lead sample collection, computational analysis and results interpretation to understand the relationships between the soil microbiome, environment and health.

In a real-world Swedish cohort of 28,017 women, screening for cervical cancer using a DNA methylation-based tool, the WID-qCIN test, either alone or in combination with HPV16/18 genotyping, showed better performance than cytology in triaging HPV-positive women.

Cancer-associated fibroblasts (CAFs) have different subtypes and play diverse roles in the tumour microenvironment. Here, the authors use single-cell RNA-seq and multiplex imaging mass cytometry data to propose a CAF classification scheme of nine subtypes across different cancer types.

Antibodies against SARS-CoV-2 can be used to treat infections but there is a risk of driving viral resistance to antibodies. Here the authors characterise SARS-CoV-2 escape mutants from an immunocompromised patient treated with anti-SARS-CoV-2 antibodies using mouse protection studies and structural prediction.

By increasing NAD⁺ consumption in various organelles, mitochondria are revealed to act as buffers that help maintain subcellular NAD⁺ levels. At the same time, cells are found to be particularly sensitive to a decline in NAD⁺ levels originating from mitochondria themselves.

Multisystem inflammatory syndrome following SARS-CoV-2 infection results from increased serum levels of TGFβ, which impairs the reactivation of virus-specific T cells.

Viromes, or viral communities, may evolve host-specificity. Here, the authors use 100 plant and insect viral sequences to find that plant-pollinator interactions and phenology shape the plant virus communities collected by bees, but insect viruses rarely replicate in multiple bee species.

Key measures of biodiversity were quantified and found to be affected by human pressures that shifted community composition and decreased local diversity across terrestrial, freshwater and marine ecosystems.

Schizophrenia exhibits significant variability in brain structures, traditionally viewed as static due to heterogeneous subgroups. Here the authors use magnetic resonance imaging data from 1,792 individuals with schizophrenia to reveal that gray matter volume variability is greater in early stages and decreases over time, highlighting dynamic brain alterations with implications for understanding disease progression.

Comprehensive pan-cancer analysis of loss of the Y chromosome (LOY) in benign and malignant cells establishes a new model linking LOY in circulating and tumour-infiltrating immune cells to LOY in malignant cells.

Certain peptides can boost viral infectivity. However, the requirements for their activity remain unclear. Here, the authors demonstrate that peptides are efficient viral enhancers if they form hydrophobic β-sheet-rich, positively charged μm-sized aggregates.

This large integrated analysis of the KRAS^G12C inhibitor sotorasib clinical efficacy biomarkers from the phase 2 CodeBreaK 100 and phase 3 CodeBreaK 200 trials shows that low expression of TTF-1 and high expression of NRF2 determine anti-tumor efficacy of sotorasib in non–small-cell lung cancer.

varVAMP is open-source software for designing primers for tiled-amplicon sequencing and qPCR. It simplifies primer design for viral pathogens with high genomic variability by including sequence variations into primer sequences.

Without targeted climate adaptation, impacts of climate change threaten achievement of all 169 SDG targets. Fuldauer et al. provide an actionable framework to assess these impacts and help systematically align national adaptation plans with the SDGs.

Pertussis toxin is used extensively for perturbing Gαi/o pathways in the study of physiology and disease, but an equivalent inhibitor of Gαq signalling is not currently available to the research community. Here the authors characterize FR900359 as a specific Gq inhibitor and demonstrate its utility to dissect GPCR signalling and its potential to inhibit melanoma cells.

Machine learning can be used to identify subtypes of psychiatric disease. Here the authors identified two neurostructural subgroups in schizophrenia, each showing reproducibility and generalizability across different collection locations and illness stages, using the SuStain algorithm.

Using cryo-electron microscopy, Schäfer et al. solved the structure of the yeast ceramide synthase complex, consisting of Lip1, Lag1 and Lac1 subunits. They found that fumonisin B1 binds competitively at a key site, suggesting a mechanism for ceramide synthesis.

The authors show that in a creative setting people make choices partially based on how empowering their choices are.

This study shows that the tRNA-modifying enzymes TRM1A/TRM1B are essential to attain the steady-state pool of tRNAs and reveals how they functionally cooperate with RNase P in vivo for the early steps of tRNA biogenesis in Arabidopsis.

Genomic analysis of Plasmodium DNA from 36 ancient individuals provides insight into the global distribution and spread of malaria-causing species during around 5,500 years of human history.

Analysis of HbA1c and FPG levels across 117 population-based studies demonstrates regional variation in prevalence of previously undiagnosed screen-detected diabetes using one or both measures and suggests that use of elevated FPG alone could underestimate diabetes prevalence in low- and middle-income countries.

Autoimmune Addison’s disease is a rare complex disease, which has not yet been characterized by non-biased genetic studies. Here, the authors perform the first GWAS for the disease, identifying nine loci including two coding variants in the gene Autoimmune Regulator (AIRE).

Here, the authors report the incidence of Clostridioides difficile infection (CDI) and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients of 50 years and above receiving newly initiated antibiotic treatment.

The endocardium lines the interior of the heart chambers and has been debated as a source of hematopoietic lineages. Here they show that the endocardium may act as a source of, and resident tissue for, hematopoietic stem and progenitor cells in zebrafish, providing evidence for diversity in origins and residences of hematopoietic cells.

This study shows that only those dual-targeting antibiotics limit resistance in Gram-negative pathogens that also target the membrane of the bacteria. This mechanism provides a basis for designing future antibiotics with reduced resistance potential.

The filamentous fungus expression system Thermothelomyces heterothallica (C1) is a protein expression system that may be useful for large scale antibody production. Here the authors characterise the production of a human monoclonal antibody that neutralises SARS-CoV-2 and compare functional properties in vitro and in animal models to antibodies produced using other methods.

How much the environment influences inherited adaptive traits is debated and challenging to demonstrate in mammals. Here the authors performed a multigeneration study that failed to morphologically replicate enhanced wound healing response following ancestral liver injury in rats. However, heritable transcriptional effects suggest transmission at the molecular level, albeit of unclear functional relevance.

A multi-omics approach reveals host–microbiome interactions in aging in mice.

A consensus cell type atlas for the fly brain provides both an intellectual framework and open-source toolchains for brain-scale comparative connectomics.

Nickelate superconductivity has so far been limited to thin films, raising questions about the role of the polar substrate–film interface. Here the authors utilize advanced characterization techniques to reveal the interfacial atomic structure and its relevance for superconductivity.

Here they use single nuclei RNA-seq to identify transcripts in skeletal muscle that maintain the neuromuscular junction, both under normal and denervated conditions, which allows them to characterize PDZRN4 as a novel MuSK interactor at the Golgi apparatus.

Vaccination with multiple doses has been proven effective against severe COVID-19, but protection levels widely vary among individuals. This study examines the serological and immunological profiles in recipients of multiple doses of Pfizer BNT162b2 vaccine for immune markers that correlate with protection against and susceptibility for SARS-CoV-2 infection.

The phase behavior of grain boundaries can influence the interfacial properties. Here the authors demonstrate nanoscale patterning of a grain boundary by two alternating phases in Cu that exhibit a congruent, diffusionless transition between the two phases.

COVID-19, similarly to systemic autoimmune diseases, is characterised by the presence of autoantibodies. Authors show here that the abundance and network signature of autoantibodies targeting G protein-coupled receptors and RAS-related proteins are altered in COVID-19 patients, and the level of disruption marks clinical severity.

Population-scale ancient genomics are used to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist, showing that Neolithic plague was widespread.

Amyloid fibrils grow through the recruitment of soluble monomer to the fibril end that propagates the fibril structure. Here the transition state, the rate-limiting conformation, of such a reaction has been characterized by Φ-value analysis. An energy landscape model has been developed and fibril growth rates predicted from first principles.

The impact of breakage fusion bridge (BFB) cycles on tumour heterogeneity and clinical outcomes remains poorly understood. Here, the authors develop OM2BFB, an algorithm to detect and reconstruct BFB amplifications using optical genome maps and use it to study BFB events across 2557 primary tumours and cancer cell lines.