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Robustness checks and reproduction of analyses with existing and updated data based on 110 articles in economics and political science journals with data and code-sharing requirements found high levels of robustness and reproducibility and determined that robustness was not dependent on author characteristics or data availability.

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

Intense extreme UV and X-ray coherent sources are set to revolutionize numerous research areas, yet characterization of their polarization remains elusive. Here, Mazza et al.measure the polarization state of circularly polarized extreme UV light from a free-electron laser using circular dichroism.

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

Here, the authors show that cystatin C (CST3) regulates the activity of cathepsin B during pancreatitis in a pH dependent manner. Moreover, cathepsin B activity is inhibited by monomeric CST3 but activated by dimeric CST3.

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.

Strings of local excitations are interesting features of a strongly correlated topological quantum matter. Here, the authors show that Boltzmann-distributed strings of local excitations also describe the topological physics of the Santa Fe geometry of artificial spin ice, which is a classical thermal system.

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.

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 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.

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.

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.

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.

Bilayer graphene allows the realization of electron–hole double-quantum dots that exhibit near-perfect particle–hole symmetry, in which transport occurs via the creation and annihilation of single electron–hole pairs with opposite quantum numbers.

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.

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.

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.

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.

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.

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.

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.

Graphene quantum dots promise applications for spin and valley qubits; however a demonstration of phase coherent oscillations has been lacking. Here the authors report coherent charge oscillations and measurements of coherence times in highly tuneable double quantum dots in bilayer graphene.

The electrochemical reduction of CO₂ on organometallic catalysts is commonly limited to two-electron products. Now, an iron tetraphenylporphyrin catalyst immobilized onto a nickel electrode is shown to achieve a Faradaic efficiency for ethanol of 68% due to the strong electronic coupling between the catalyst and the support.

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.

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.

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.

Graphene has long been considered to be a promising host for spin qubits, however a demonstration of long spin relaxation times for a potential qubit has been lacking. Here, the authors report the electrical measurement of the single-electron spin relaxation time exceeding 200 μs in a bilayer graphene quantum dot.

A series of early-time, multiwavelength observations of an optical transient, AT2022cmc, indicate that it is a relativistic jet from a tidal disruption event originating from a supermassive black hole.

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1–2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.

There is interest in understanding the relaxation mechanisms of photoexcitation in atoms, molecules and other complex systems. Here the authors unravel the photoexcitation and ultrafast relaxation of superfluid helium nanodroplets using a pump-probe experiment with FEL pulses.

Cavitation bubbles show many nonlinear characteristics of liquid and gas phase. Here the authors demonstrate coherent diffractive imaging of cavitation bubble using infrared pump and XFEL probe and discuss the formation and evolution of the bubbles.

Moderately reducing the visibility of renewable energy infrastructure in Germany is found to have a negligible impact on energy system costs and design. Strict visibility restrictions, however, may reduce the system’s resilience and increase costs by 38% in 2045.

Radiocarbon dating of sediment cores and ice-penetrating radar observations are used to demonstrate that the West Antarctic Ice Sheet has not retreated progressively during the Holocene epoch, but has instead showed periods of retreat and re-advance.

Genome-wide association analyses of DNA methylation in peripheral blood from 3,799 Europeans and 3,195 South Asians identify unique SNP–CpG associations (meQTL), providing insights into molecular mechanisms and the potential links to phenotypic variation.

Fractional Chern insulators, topological insulators with partially filled bands, do not require large magnetic fields to form fractional quantum Hall states. Here, the authors investigate the correlation between the stability of such states and the bandgap to their creation on a variety of lattices.

A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.

Improved electron microscopy methods are used to map a mammalian retinal circuit of close to 1,000 neurons; the work reveals a new type of retinal bipolar neuron and suggests functional mechanisms for known visual computations.

The first operation of the European X-ray free-electron laser facility accelerator based on superconducting technology is reported. The maximum electron energy is 17.5 GeV. A laser average power of 6 W is achieved at a photon energy of 9.3 keV.

Understanding the interaction between spin and valley degrees of freedom in graphene-based quantum dots underpins their applications in electronics and quantum information. Here, the authors study the low-energy spectrum and resolve the spin-valley coupling in single-electron quantum dots in bilayer graphene.

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.

Cycles of electron capture and β⁻ decay involving neutron-rich nuclei at a typical depth of about 150 metres are found to cool the outer crust of a neutron star by emitting neutrinos while also thermally decoupling the surface layers from the deeper crust; this mechanism has been studied in other astrophysical environments, but has not hitherto been considered in neutron stars.

This directory was made possible by a unique international collaboration between the 633 scientists whose names appear below. It represents both the first published description of the complete sequence of most chromsomes from Saccharomyces cerevisiae, and the first published overview of the entire sequence. As such, the authors would like future papers referring to the entire sequence and/or its contents to cite this directory; future papers referring to the sequence of individual chromosomes should refer to the papers listed at the head of page 9. The authors’ affiliations appear in the papers describing the individual chromosomes.

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.