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Showing 1–50 of 197 results
Advanced filters: Author: Chad Liu Clear advanced filters
  • 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
  • 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
  • Ziwen Liu et al. report Cytoland, an approach to train robust models to virtually stain landmark organelles of cells and address the generalization gap of current models. The training pipeline, models and datasets are shared under open-source permissive licences.

    • Ziwen Liu
    • Eduardo Hirata-Miyasaki
    • Shalin B. Mehta
    ResearchOpen Access
    Nature Machine Intelligence
    Volume: 7, P: 901-915
  • 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
  • Synthetic routes to aminoglycosides are often long and rely upon the coupling of semisynthetically produced fragments. Now, an enantioselective, copper-catalysed hydroamination of benzene has been developed to enable access to the aminoglycoside antibiotic ribostamycin. This bottom-up strategy provides modular and expedient entry into the aminocyclitol class.

    • Chad N. Ungarean
    • Petra Galer
    • David Sarlah
    Research
    Nature Synthesis
    Volume: 1, P: 542-547
  • The Cancer Genome Atlas Research Network reports an integrative analysis of more than 400 samples of clear cell renal cell carcinoma based on genomic, DNA methylation, RNA and proteomic characterisation; frequent mutations were identified in the PI(3)K/AKT pathway, suggesting this pathway might be a potential therapeutic target, among the findings is also a demonstration of metabolic remodelling which correlates with tumour stage and severity.

    • Chad J. Creighton
    • Margaret Morgan
    • Heidi J. Sofia.
    ResearchOpen Access
    Nature
    Volume: 499, P: 43-49
  • The development of a desktop nanofabrication tool allowing high-resolution patterning and high-throughput synthesis is a long-standing goal in many nanoscience fields. Here, the authors report a system that can write arbitrary patterns composed of diffraction-unlimited features over square centimetre areas.

    • Xing Liao
    • Keith A. Brown
    • Chad A. Mirkin
    Research
    Nature Communications
    Volume: 4, P: 1-7
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Pneumocystis jirovecii is a fungus that can cause life-threatening pneumonia in immunocompromised patients. Here, the authors sequence the genomes of P. jirovecii and two other Pneumocystisspecies, and show the unexpected absence of chitin (a near universal fungal cell wall component).

    • Liang Ma
    • Zehua Chen
    • Joseph A. Kovacs
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-14
  • 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.

    • Yuan Yuan
    • Young Seok Ju
    • Christian von Mering
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 342-352
  • The accumulation of alpha-synuclein fibrils within neurons is the defining feature of Lewy body dementia (LBD). Here the authors report a method to produce large quantities of alpha-synuclein fibrils that reproduce the complex structure of the fibrils that accumulate in LBD brain tissue.

    • Dhruva D. Dhavale
    • Alexander M. Barclay
    • Paul T. Kotzbauer
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-18
  • The ability of BCG vaccination to prevent pulmonary tuberculosis could be improved by targeting mucosal immunity within the lung. Here the authors compare latent Mtb-infected donors with intradermal or oral BCG vaccine recipients to show distinct systemic and pulmonary immune responses are induced by differing routes of natural infection or vaccination.

    • Richard F. Silver
    • Mei Xia
    • Daniel F. Hoft
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-17
  • The underlying mechanism of acquired resistance to targeted therapy in cancer remains to be explored. Here, the authors show that upregulation of the FOSL1 transcription factor restores YAP/TEAD occupancy on chromatin to drive resistance to GNE-7883, an allosteric TEAD inhibitor.

    • Sayantanee Paul
    • Thijs J. Hagenbeek
    • Anwesha Dey
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-21
  • Sun et al. report human lifespan changes in the brain’s functional connectome in 33,250 individuals, which highlights critical growth milestones and distinct maturation patterns and offers a normative reference for development, aging and diseases.

    • Lianglong Sun
    • Tengda Zhao
    • Yong He
    Research
    Nature Neuroscience
    Volume: 28, P: 891-901
  • Combinatorial Optimization problems can be solved by investigating the ground states of particular Ising models. Here, the authors developed a neuromorphic architecture to ensure asymptotic convergence to the ground state of an Ising problem and to consistently produce high-quality solutions.

    • Zihao Chen
    • Zhili Xiao
    • Shantanu Chakrabartty
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-13
  • Targeted sequencing panels such as MSK-IMPACT have been successfully used to profile solid tumours in clinical settings. Here, the authors develop and implement the MSK-IMPACT Heme sequencing panel and platform to profile haematologic malignancies using paired tumor and normal tissues.

    • Ryan N. Ptashkin
    • Mark D. Ewalt
    • Maria E. Arcila
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-16
  • Alterations in the tumour suppressor genes STK11 and/or KEAP1 can identify patients with advanced non-small-cell lung cancer who are likely to benefit from combinations of PD-(L)1 and CTLA4 immune checkpoint inhibitors added to chemotherapy.

    • Ferdinandos Skoulidis
    • Haniel A. Araujo
    • John V. Heymach
    ResearchOpen Access
    Nature
    Volume: 635, P: 462-471
  • Currently, gold recovery from waste materials requires inorganic cyanides and more environmentally benign methods are required. Here, the authors report that host–guest interactions between α-cyclodextrin and gold lead to the precipitation of one-dimensional superstructures, offering a selective and green alternative.

    • Zhichang Liu
    • Marco Frasconi
    • J. Fraser Stoddart
    ResearchOpen Access
    Nature Communications
    Volume: 4, P: 1-9
  • LKB1 is frequently mutated in lung squamous cell carcinomas. Here, the authors show that sole LKB1 depletion is sufficient to drive the development of this cancer, where downstream defective MKK7-JNK1/2 signalling activates the ∆Np63/p63 pathway to induce subsequent epithelial cells transformation and tumour progression.

    • Jian Liu
    • Tianyuan Wang
    • Francesco J. DeMayo
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-16
  • There is growing interest in designing electrolytes to enable Li-metal batteries. Here the authors show that asymmetric solvents improve lithium redox kinetics and achieve long cycle life in anode-free cells under electric vertical take-off and landing conditions, demonstrating potential for future high-power applications.

    • Il Rok Choi
    • Yuelang Chen
    • Zhenan Bao
    Research
    Nature Energy
    Volume: 10, P: 365-379
  • The dysregulation of the m6A epitranscriptomic networks have been reported to contribute to the development of gliomas. Here, the authors utilize induced pluripotent stem cell-derived astrocytes with a p53 mutation and demonstrate that mutant p53 upregulates the m6A reader YTHDF2, resulting in the initiation of gliomas.

    • An Xu
    • Mo Liu
    • Dung-Fang Lee
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-19
  • A large-scale field intervention experiment on 23,377 US Facebook users during the 2020 presidential election shows that reducing exposure to content from like-minded social media sources has no measurable effect on political polarization or other political attitudes and beliefs.

    • Brendan Nyhan
    • Jaime Settle
    • Joshua A. Tucker
    ResearchOpen Access
    Nature
    Volume: 620, P: 137-144
  • Although continuous monitoring of tissue oxygenation is critically important after tissue/organ graft procedures, current technologies have key limitations. Here, the authors develop a miniaturized, minimally invasive, self-anchoring optical probe and demonstrate continuous monitoring of oxygenation in porcine flap and organ models.

    • Hexia Guo
    • Wubin Bai
    • John A. Rogers
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-12