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Showing 1–50 of 342 results
Advanced filters: Author: Jean Fan Clear advanced filters
  • 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.

    • Matthew H. Bailey
    • William U. Meyerson
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-27
  • An analysis of annelid genomes reveals massive reshuffling of chromosomes in the ancestral lineage leading to clitellates, a clade composed of non-marine annelids, with potential implications for the adaptation of clitellates to freshwater and terrestrial environments.

    • Carlos Vargas-Chávez
    • Lisandra Benítez-Álvarez
    • Rosa Fernández
    Research
    Nature Ecology & Evolution
    Volume: 9, P: 1263-1279
  • Surface plasmon resonance sensing enables the label-free detection of molecular interactions at metal surfaces and highly sensitive measurements of film thickness. Refractive index changes caused by changes in the environment around a metal–dielectric interface cause variations in the interface optical response, which enable highly sensitive and time-resolved measurements.

    • Maryam Hojjat Jodaylami
    • Jean-François Masson
    • Antonella Badia
    Reviews
    Nature Reviews Methods Primers
    Volume: 5, P: 1-25
  • The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

    • Marek Cmero
    • Ke Yuan
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-15
  • Li et al. introduced tract-geometry coupling (TGC) to quantify the coupling between white matter tracts and cortical geometry in the human brain, shedding light on how the brain’s wiring and shape evolve together and its support for behavior and growth.

    • Deying Li
    • Andrew Zalesky
    • Lingzhong Fan
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18
  • Insight into the singlet–triplet energy gap and molecular structure relationship in polycyclic heteroaromatic molecules enables organic light-emitting diodes based on multiresonance thermally activated delayed fluorescence, with improved efficiency and roll-off.

    • Rajat Walia
    • Xin Xiong
    • Xiao-Hong Zhang
    Research
    Nature Materials
    Volume: 24, P: 1576-1583
  • 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.

    • Lauri A. Aaltonen
    • Federico Abascal
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 82-93
  • Sudden bursts of charged particles emitted from the surface of the Sun can disrupt the satellites orbiting Earth. However, the mechanisms that drive these so-called coronal mass ejections remain unclear. An advanced computer model now establishes a link between the onset of an ejection and the emergence of magnetic flux into the solar atmosphere.

    • Ilia I. Roussev
    • Klaus Galsgaard
    • Jun Lin
    Research
    Nature Physics
    Volume: 8, P: 845-849
  • The Enriquillo–Plantain Garden fault zone is the primary plate-bounding fault system in Haiti and was initially thought to be responsible for the 2010 earthquake. Palaeoseismic analyses of the fault system indicate that it ruptured during a large earthquake in either 1750 or 1770, but did not rupture during the 2010 earthquake.

    • C. S. Prentice
    • P. Mann
    • P. Jean
    Research
    Nature Geoscience
    Volume: 3, P: 789-793
  • Carbon loss from forests occurs through deforestation or the degradation of existing forest. The loss of forest area in the Brazilian Amazon was higher in 2019 than following drought and an El Niño event in 2015, yet degradation drove three times more biomass loss than deforestation from 2010 to 2019.

    • Yuanwei Qin
    • Xiangming Xiao
    • Berrien Moore III
    Research
    Nature Climate Change
    Volume: 11, P: 442-448
  • 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.

    • Claudia Calabrese
    • Natalie R. Davidson
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 129-136
  • 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.

    • Moritz Gerstung
    • Clemency Jolly
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 122-128
  • Two BCMA-targeted CAR T products, idecabtagene vicleucel (ide-cel) and ciltacabtagene autoleucel (cilta-cel), have been approved for the treatment of multiple myeloma (MM). Here the authors report distinct expansion, phenotype, function, and toxicity of cilta-cel vs. ide-cel CAR T cells in a realworld cohort of patients with MM.

    • Djordje Atanackovic
    • Tim Luetkens
    • Mehmet H. Kocoglu
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12
  • The persistence of dendritic drainage patterns implies that rivers reorganize after a tectonic perturbation, preserving no long-term record of that tectonic event. Numerical simulations of the evolution of drainage patterns in the Southern Alps, New Zealand, however, reveal rivers that resist reorganization and thus preserve a record of plate tectonic strain over 10 million years.

    • Sébastien Castelltort
    • Liran Goren
    • Jean Braun
    Research
    Nature Geoscience
    Volume: 5, P: 744-748
  • Natural products have historically made a major contribution to pharmacotherapy, but also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization. This Review discusses recent technological developments — including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances — that are enabling a revitalization of natural product-based drug discovery.

    • Atanas G. Atanasov
    • Sergey B. Zotchev
    • Claudiu T. Supuran
    Reviews
    Nature Reviews Drug Discovery
    Volume: 20, P: 200-216
  • The annotation of the visual signs of emotions can be important for psychological studies and even human–computer interactions. Instead of only ascribing discrete emotions, Toisoul and colleagues use a single neural network that predicts emotional labels on a spectrum of valence and arousal without separate face-alignment steps.

    • Antoine Toisoul
    • Jean Kossaifi
    • Maja Pantic
    Research
    Nature Machine Intelligence
    Volume: 3, P: 42-50
  • Marine records indicate a greenhouse to icehouse climate transition at ~34 million years ago, but how the climate changed within continental interiors at this time is less well known. Here, the authors show an orbital climate response shift with aridification on the northeastern Tibetan Plateau during this time.

    • Hong Ao
    • Guillaume Dupont-Nivet
    • Zhisheng An
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-11
  • The control of turbulent flows is crucial for improving efficiency in engineering systems. Here, authors show in a numerical simulation that using deep reinforcement learning to control surface actuators can successfully mitigate turbulent flow separation, paving the way for new advancements in turbulence control.

    • Bernat Font
    • Francisco Alcántara-Ávila
    • Oriol Lehmkuhl
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-13
  • 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.

    • Matthew A. Reyna
    • David Haan
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-17
  • 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.

    • Constance H. Li
    • Stephenie D. Prokopec
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-24
  • 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.

    • Esther Rheinbay
    • Morten Muhlig Nielsen
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 102-111
  • 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.

    • Lina Sieverling
    • Chen Hong
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-13
  • 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.

    • Yilong Li
    • Nicola D. Roberts
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 112-121
  • 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.

    • Marc Zapatka
    • Ivan Borozan
    • Christian von Mering
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 320-330
  • 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.

    • Shimin Shuai
    • Federico Abascal
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • 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.

    • Wei Jiao
    • Gurnit Atwal
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • 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.

    • Vinayak Bhandari
    • Constance H. Li
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-10
  • 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.

    • Marta Paczkowska
    • Jonathan Barenboim
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-16
  • 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.

    • Ludmil B. Alexandrov
    • Jaegil Kim
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 94-101
  • 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.

    • Yiqun Zhang
    • Fengju Chen
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14
  • 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.

    • Yulia Rubanova
    • Ruian Shi
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • Carbon sequestration by Siberian forests has been low over the past decade due to disturbances that have decreased live biomass and increased dead wood, according to passive microwave observations.

    • Lei Fan
    • Jean-Pierre Wigneron
    • Rasmus Fensholt
    Research
    Nature Geoscience
    Volume: 16, P: 56-62
  • Authors introduce CRAWDAD, an R package for quantifying cell-type spatial relationships across length scales in tissues using spatial omics data, enabling the identification of consistent as well as sample-specific celltype spatial relationships across multiple spatial omics datasets.

    • Rafael dos Santos Peixoto
    • Brendan F. Miller
    • Jean Fan
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14
    • Jean-Paul Concordat
    • Philip Ingham
    News & Views
    Nature
    Volume: 375, P: 279-280