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This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

Ribosomal translation is coupled to cotranslational protein folding, process assisted by dedicated chaperones. Here, authors present structures of the ribosome-bound yeast Hsp70 chaperone Ssb, identifying its ribosomal binding site and revealing its interactions with a model nascent chain.

The impact of tumour heterogeneity on metastatic potential in prostate cancer remains poorly understood. Here, the analysis of single nuclei RNA sequencing and whole-genome sequencing from samples from five patients suggests an interplay between clonal evolution and cellular plasticity driving metastatic seeding.

Yin and colleagues propose that diffraction-limited fluorescence videos contain hidden binding-type information. The authors present a deep learning model, T2C CNN, which exploits that hidden information to classify molecular interactions with high accuracy using a single dye in seconds.

Caspase 8 protein expression is largely absent in small cell lung cancer (SCLC) patients. Here, the authors generate a caspase 8 deletion SCLC mouse model and show that it promotes a neuronal progenitor-like cell state and pre-tumoral immunosuppression triggered by necroptosis that promotes metastasis.

The ability to tune spin-orbit interaction is crucial for spintronic and quantum devices. Alarab and colleagues use soft X-ray ARPES to show that this interaction in MoSe₂ can be strengthened by a proximity induced spin-orbit field transfer from a Pb layer deposited onto the MoSe₂ surface.

RNA base editing represents an exciting modality in precision genetic medicine. Here the authors develop short, metabolically stable RNA oligonucleotides (RESTORE 2.0) that enable precise and efficient RNA base editing, demonstrating successful in-vivo correction of a disease-causing human mutation.

This study explores the use of quantum computing to address multi-objective optimization challenges. By using a low-depth quantum approximate optimization algorithm to approximate the optimal Pareto front of multi-objective weighted max-cut problems, the authors demonstrate promising results—both in simulation and on IBM Quantum hardware—surpassing classical approaches.

Polygenic scores for body mass index and obesity constructed using data from 5 million people with different ancestries were associated with distinct weight gain trajectories from early childhood to adulthood.

Sagar et al. show that human sniff behaviour is sensitive to the perceptual characteristics of the odour being detected.

This protocol details in vitro and in vivo approaches for labeling tumor cells with secreted luciferases to enable precise, longitudinal monitoring of tumor growth in mice, through the analysis of small blood samples.

Cell-surface receptors form the front line of plant immunity. Here, the authors show that the RLP co-receptors SOBIR1 and BAK1 directly phosphorylate each other, leading to activation of the immune receptor complex in which RLCKs are differentially required for production of reactive oxygen species that play a role in resistance against Phytophthora palmivora.

African ancestry is a known risk factor for prostate cancer development, but the genetic determinants of this are incompletely understood. Here, the authors identify 172 potentially pathogenic variants which are enriched in an African population.

Small cell lung cancer cells form functional synapses with glutamatergic neurons, receiving synaptic transmissions and deriving a proliferative advantage from these interactions.

Dynamic control of components is required for large-scale quantum photonic networks. Here, Kapfingeret al. show dynamic control of the interaction between two coupled photonic crystal nanocavities forming a photonic molecule. Tuning is achieved by using an electrically generated radio frequency surface acoustic wave.

Optical nanoantennas can be used for spectroscopic investigations at previously unattainable dimensions. Schumacheret al.describe time-resolved antenna-enhanced ultrafast nonlinear optical spectroscopy and determine the transient absorption signal of a single gold nanoparticle.

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.

Using G•U wobble base pairs at specific loci increases RNA base-editing precision and efficiency.

A major Chilean earthquake shows how two physical processes cohesively make intermediate-depth quakes bigger. This allows ruptures to extend into previously assumed stable rocks, posing a greater destructive potential than previously understood.

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

Analysis of northern elephant seal populations shows no evidence of inbreeding depression, probably because a recent extreme bottleneck purged much of the genetic load.

Pathology-oriented multiplexing (PathoPlex) represents a framework for widespread access to multiplexed imaging and computational image analysis of clinical specimens at a relatively high throughput and subcellular resolution.

The transport measurements of an interacting fermionic quantum gas in an optical lattice provide a direct experimental realization of the Hubbard model—one of the central models for interacting electrons in solids—and give insights into the transport properties of many-body phases in condensed-matter physics.

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.

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.

Mapping DNA methylomes in single cells is challenging, and thus studies using bulk samples remain common. Here, authors develop a transformer-based method for methylation pattern analysis to enhance bulk methylome deconvolution and cancer detection.

All chondrites are shown to have Ru isotopic compositions that are more different from that of the Earth’s mantle the further from the Sun they formed; this means the Earth’s late veneer cannot derive from volatile-rich material formed in the outer Solar System.

Findings on solar activity in the first millennium CE confirm four Grand Solar Minima and indicate two patterns of weakening-then-strengthening in the Schwabe cycle, providing insights into solar dynamo behavior, according to analysis of Δ14C data from tree rings.

Allogenic haematopoietic stem cell transplantation (allo-HSCT) can induce bone marrow fibrosis regression in patients with myelofibrosis (MF) however, the effect on the skeleton is unclear. Here, the authors perform in-depth, longitudinal evaluation of skeletal homeostasis following allo-HSCT in patients with MF using high-resolution imaging and bone biopsy analysis.

A large genome-wide association study of more than 5 million individuals reveals that 12,111 single-nucleotide polymorphisms account for nearly all the heritability of height attributable to common genetic variants.

CLPP-deficiency-driven mitochondrial dysfunction in brown adipose tissue leads to the accumulation of d-2-hydroxyglutarate, in turn promoting lipid-droplet enlargement by altering gene expression and epigenetically regulating nuclear stiffness.

Huber and colleagues utilize a multi-omic analytical pipeline to define an axis of proliferative drive involving mTOR, MYC and OXPHOS metabolic activity that is associated with disease heterogeneity and outcome in clinical cohorts of CLL.

In patients with newly diagnosed, transplant-ineligible multiple myeloma, addition of weekly bortzomib to isatuximab, lenalidomide and dexamethasone leads to increased minimal residual disease negativity compared with isatuximab, lenalidomide and dexamethasone.

Chromothripsis (CT) is a type of genome instability which is prevalent in medulloblastoma with germline TP53 mutations (Li-Fraumeni syndrome, LFS). Here the authors combine single-cell genomic and transcriptomic analyses to reveal the clonal heterogeneity and functional consequences of CT in LFS medulloblastoma.

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.

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.

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.

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.

Long non-coding RNAs (lncRNA) are known immune regulators, yet a systemic understanding of their regulatory crosstalk is still elusive. Here the authors establish a platform integrating RNA-binding proteome analyses and protein interactomes to map the lncRNA target network in human primary macrophages to build a searchable atlas of lncRNA.

Laboratory performance tests provide the gold standard for running performance but do not reflect real running conditions. Here the authors use a large, real world dataset obtained from wearable exercise trackers to extract parameters that accurately predict race times and correlate with training.

Grasses have evolved a wide variety of inflorescence architectures. Here Vardanega et. al show how the barley CLV1 receptor and FCP1 peptide signal interact to control meristem shape, organ formation and determinacy thus shaping barley spike morphology.

A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

RNA base editing enables a precise, reversible and doseable change of genetic information. Here, authors propose base editing as a method to control post-translational modifications via removal of regulatory phosphorylation and acetylation sites, applying the approach to modulation of the JAK/STAT pathway via editing of wildtype alleles.

The role of the hippocampus in shaping dopaminergic prediction errors is unclear. Here, the authors show that without a functional hippocampus, dopaminergic neurons fail to properly encode prediction errors, particularly during changes in upper-level states.