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Showing 1–50 of 535 results
Advanced filters: Author: Nicole K. Zhang Clear advanced filters
  • Despite improving therapeutic options, the prognosis for patients with metastatic castration-resistance prostate cancer (mCRPC) remains poor. Here, the authors identify MCL1 copy number alterations as a prognostic and predictive biomarker, demonstrating its therapeutic potential as a drug target, either alone or in combination, in patients with mCRPC.

    • Juan M. Jiménez-Vacas
    • Daniel Westaby
    • Adam Sharp
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-22
  • A study of several longitudinal birth cohorts and cross-sectional cohorts finds only moderate overlap in genetic variants between autism that is diagnosed earlier and that diagnosed later, so they may represent aetiologically different conditions.

    • Xinhe Zhang
    • Jakob Grove
    • Varun Warrier
    ResearchOpen Access
    Nature
    P: 1-12
  • The development of broadly neutralizing monoclonal antibodies is crucial in the fight against viral infections. Here, using combinatorial library technology, the authors identify 3D1, a monoclonal antibody with potential pan-inhibitory activity against a range of viral families, and provide structural analysis to reveal the basis of the broad cross-reactivity.

    • Lei Yan
    • Fulian Wang
    • Guang Yang
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14
  • A post-translational backbone extension acyl rearrangement (BEAR) reaction has now been developed that converts a ribosomal protein product into a new product containing a β-peptide, γ-peptide or δ-peptide backbone. BEAR reactions represent a general strategy to install extended backbones into genetically encoded proteins and peptides expressed in cells.

    • Leah T. Roe
    • Isabel M. Piper
    • Alanna Schepartz
    Research
    Nature Chemical Biology
    Volume: 21, P: 1621-1630
  • Pharmacologic inhibition of dihydroorotate dehydrogenase (DHODH) shows limited efficacy in pancreatic ductal adenocarcinoma (PDAC) models. Here the authors find that targeting the anti-apoptotic protein BCL-XL synergizes with DHODH inhibition in promoting apoptosis in PDAC cells, patient-derived organoids, and PDAC mouse models.

    • Huan Zhang
    • Naiara Santana-Codina
    • Joseph D. Mancias
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18
  • SARS-CoV-2 variant-specific neutralizing antibodies (nAbs) mediate protection against infection by the cognate variant to distinct extents, while the majority of protection elicited by natural infection is not mediated by nAbs.

    • Kaiyuan Sun
    • Jinal N. Bhiman
    • Nicole Wolter
    Research
    Nature Medicine
    Volume: 30, P: 2805-2812
  • 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
  • Hematopoietic stem cells (HSCs) differentiate into multiple lineages, with such capacity impacted by aging. Here the authors identify Kitlo HSCs as a functionally distinct population that exhibits distinct lymphoid-primed chromatin landscapes, which drive enhanced lymphoid reconstitution capacity, and is altered in aged hosts.

    • Harold K. Elias
    • Sneha Mitra
    • Marcel R. M. van den Brink
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20
  • 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
  • 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
  • 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
  • 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
  • A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

    • Mari E. K. Niemi
    • Juha Karjalainen
    • Chloe Donohue
    ResearchOpen Access
    Nature
    Volume: 600, P: 472-477
  • 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
  • Passive immunisation for respiratory syncytial virus for infants is recommended by the World Health Organization but products currently available have limited duration of protection. Here, the authors investigate the age distribution of infant hospitalisation for respiratory syncytial virus to inform optimal timing of immunisation.

    • Ling Guo
    • Sebastien Kenmoe
    • Eva Molero
    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
  • 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
  • A single-cell sequencing study using more than 30,000 tumour genomes from human ovarian cancers shows that whole-genome doubling is an ongoing mutational process that drives tumour evolution and disrupts immunity.

    • Andrew McPherson
    • Ignacio Vázquez-García
    • Sohrab P. Shah
    ResearchOpen Access
    Nature
    Volume: 644, P: 1078-1087
  • 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
  • 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
  • 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
  • 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
  • In two independent studies, Song et al. and Jiang, Dalgarno et al. present computational frameworks, perturbation-response score and Mixscale, respectively, to determine individual cellular variation in response to perturbation.

    • Bicna Song
    • Dingyu Liu
    • Wei Li
    ResearchOpen Access
    Nature Cell Biology
    Volume: 27, P: 493-504
  • Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.

    • M. Carola Zillikens
    • Serkalem Demissie
    • Douglas P. Kiel
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-13
  • 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
  • Sea-level rise poses a substantial risk to coastal communities and economies, thus accurate predictions are needed to enable planning and adaptation. This Perspective provides an overview of uncertainties in model projections of sea-level rise, and how observations can be used to reduce these.

    • Denis Felikson
    • David R. Rounce
    • Matthew Weathers
    Reviews
    Nature Climate Change
    Volume: 15, P: 1039-1051
  • The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

    • Federico Abascal
    • Reyes Acosta
    • Zhiping Weng
    ResearchOpen Access
    Nature
    Volume: 583, P: 699-710
  • 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
  • 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
  • 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
  • RNA modifications are key regulators of RNA functions. Here, the authors identify METTL8 as the enzyme installing m3C32 in mitochondrial tRNAThr/Ser(UCN). Lack of these modifications affects tRNA structure and impairs mitochondrial translation.

    • Nicole Kleiber
    • Nicolas Lemus-Diaz
    • Markus T. Bohnsack
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-19
  • Combination radiotherapy (RT) + αPD-L1 enhances tumor control via a tumor-draining lymph node (TdLN)-derived CD8+ PD-1+ TCF-1+ T cells. RT + αPD-L1 induces a novel LY6A+ subset in the TdLN that migrates to the tumor and differentiates into effectors.

    • Yang Shen
    • Erin Connolly
    • Zachary S. Buchwald
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15