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Lake Tanganyika’s cichlid radiation is the main source of East African cichlid diversity. Irisarri et al. resolve its phylogenetic backbone using anchored phylogenomics and identify trans-lineage hybridization prior to major speciation bursts and adaptive loci underlying ecological innovations.

The structure of many natural products can often only be confirmed by comparison with a synthetic sample. Here, scanning probe microscopy techniques allow the ultimate discrimination between structures suggested by the standard range of analytical techniques, proving the power of single-molecule imaging for molecular structure determination.

Ferrimagnets possess multiple spin sub-lattices resulting in a complex magnon band structure and subtle spin transport across interfaces. Here, the authors show how the spin Seebeck effect, the thermal generation of pure spin current, may be an effective tool to study these magnetic excitations.

Detection and manipulation of single charges in molecules are fundamental cornerstones in molecular electronics. Here, Steurer et al. demonstrate a technique with the use of an atomic force microscope that is able to resolve charge states and single electron charge transfer between molecules.

Endothermy facilitated mammalian species radiation, but the events leading to sustained thermogenesis are not clear. Here, the authors report functional brown adipose tissue in a protoendothermic mammal, linking nonshivering thermogenesis directly to the roots of eutherian endothermic evolution.

Indeno[1,2-b]fluorene (IF) is an extremely reactive polycyclic conjugated hydrocarbon with antiaromatic character, thus it has not been detected to date. Here, the authors present the successful generation and characterisation of IF both on-surface and in-solution.

The Bergman cyclization is a fascinating rearrangement reaction with implications beyond organic chemistry. It has now been shown that a reversible Bergman cyclization reaction in a single molecule sitting on an ultrathin NaCl film can be triggered and directly imaged using atomic force microscopy. The interconverted diradical and diyne products are shown to have distinct chemical and physical properties.

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.

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.

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.

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.

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.

Multinucleated giant cells (MGCs) are important in the pathogenesis of various diseases. Here, the authors demonstrate that extracellular presence of the amino acid arginine is required for MGC formation and metabolism, suggesting a translational impact for strategies utilizing systemic arginine depletion in MGC-mediated diseases.

miRNAs have been involved in tumour development and progression. Here the authors uncover a double feedback loop between miR-1199-5p and the Zeb1, potentially coordinating a protein involved in epithelial mesenchymal transition and tumour metastasis.

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.

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.

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.

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.

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.

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.

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.

Hydrogen bonding is a central concept in (bio)chemistry and has been intensively studied in the prototypical complex H₂O-H₂O. In this joint experimental/theoretical study, the authors find hydrogen bonding in H₂S-H₂S to be distinctly different.

Ruggeri et al. find in a study of 61 countries that temporal discounting patterns are globally generalizable. Worse financial environments, greater inequality and high inflation are associated with extreme or inconsistent long-term decisions.

Analysis of genotyping-by-sequencing data for more than 20,000 barley accessions from a German genebank provides a framework for genomics-assisted genebank management and analysis of large germplasm collections for important crops.

Phylogenetic distribution and phenotypic traits of livestock and crops reveal that domesticated species explore a reduced portion of the phenotypic space occupied by their wild counterparts and have particular traits in common.

In this largest whole-exome sequencing study of epilepsies to date, the Epi25 Collaborative identified extremely rare variants that confer risk for diverse epilepsy subtypes, highlighting roles in synaptic transmission and neuronal excitability.

Genome-wide association meta-analyses identify 26 risk loci for epilepsy, including 19 loci specific to genetic generalized epilepsy. Prioritized candidate genes implicate synaptic processes and overlap with targets of antiseizure medications.

Here, the authors perform a meta-analysis in 26,699 people with seizures and 492,324 controls to identify 25 genome-wide significant copy-number variants. The discovered loci point to known disease genes and associations with clinical annotations.

Genomic data from over 100 populations of Timema stick insects are used to show the transition from an early phase of speciation involving localized genetic regions to later stages involving genome-wide differentiation.

Proteasomal degradation of EZH2 in AML patients in response to therapy triggers the expression of stem cell markers and has been identified as an epigenetic pathway leading to acquired drug resistance. Treatments aimed to restore EZH2 expression in relapsed AML patients have shown clinical efficacy and constitute a viable approach to re-sensitize tumors to chemotherapy.

Long non-coding RNAs (lncRNAs) can contribute to cancers that are driven by Sonic hedgehog (SHH) signaling. Here the authors report that lncRNA HHIP-AS1 stabilises the mRNA of dynein complex 1, thereby, promoting the pro-mitotic effects of SHH-driven tumors.

In acute myeloid leukemia, hypomethylating agents decitabine and azacytidine are used interchangeably. Here, the authors show that the major metabolite of decitabine, but not azacytidine, is subject to SAMHD1 inactivation, highlighting SAMHD1 as a potential biomarker and therapeutic target

Analysing data from 39 grassland biodiversity experiments, the authors uncover the direct and indirect contributions to ecosystem stability of taxonomic, phylogenetic and functional trait diversity.

A combined scanning tunnelling and atomic force microscopy approach is used to generate and characterize triangulene on various surfaces.

A study of the electronic structure of molecular wires as a function of their length reveals strong coupling between electrons and molecular vibrations. The mechanism provides a means to coherently couple electronic levels by nuclear motion, and possibly to mechanically control electron transport in molecular electronics.

Kelvin probe force microscopy can reveal the distribution of charge within a single naphthalocyanine molecule.

Atomic manipulation was used to control the reductive rearrangement of 1,1-dibromo alkenes to acetylenes on a NaCl surface at 5 K, and the stages of the reaction were visualized with atomic resolution using AFM. Polyynes ranging from triyne to octayne were prepared in this way, and STM was used to map their frontier orbitals and determine their transport gaps.