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Showing 51–100 of 581 results
Advanced filters: Author: Xing Du Clear advanced filters
  • 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
  • This study presents LoopID, which profiles proteins at targeted interacting enhancer–promoter (E-P) pairs, identifying the histone demethylase JMJD2 as a regulator of E-P interactions through biomolecular condensate formation independent of its catalytic activity.

    • Shaoshuai Jiang
    • Xinyi Liu
    • Junjun Ding
    Research
    Nature Genetics
    Volume: 58, P: 593-606
  • SFTS is an emerging tick-borne disease with high mortality rates caused by the SFTS virus. Here, the authors identify LRP1 as an entry factor for SFTSV, show that SFTSV glycoprotein Gn interacts with LRP1 and that blocking LRP1 reduces viral infection and improves survival in lethal mouse models.

    • Chen Xing
    • Cong Zhang
    • Yan Liu
    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
  • 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
  • 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
  • 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 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
  • A deep learning algorithm shows promising performance in predicting progression to diabetic retinopathy in patients, up to 5 years in advance, potentially providing support for medical treatment decisions and indications for personalized screening frequency in a real-world cohort.

    • Ling Dai
    • Bin Sheng
    • Weiping Jia
    ResearchOpen Access
    Nature Medicine
    Volume: 30, P: 584-594
  • 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
  • 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
  • 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
  • Designing bio-inspired artificial neurons within a single device is challenging. Here, the authors demonstrate a spintronic neuron with leaky-integrate-fire and self-reset characteristics and corroborate a new trajectory of all-spin neuromorphic computing hardware holistic implementation.

    • Di Wang
    • Ruifeng Tang
    • Guozhong Xing
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-12
  • Liang and colleagues show that the ORF45 protein from the Kaposi’s sarcoma-associated herpesvirus activates NLRP1 by binding to its Linker1 region through a mechanism distinct from the previously described, host protease DPP9-dependent mechanism of NLRP1 activation.

    • Xing Yang
    • Jingfan Zhou
    • Qiming Liang
    Research
    Nature Immunology
    Volume: 23, P: 916-926
  • Lipid droplets (LDs) and endosomes play crucial roles in cellular processes, yet their interplay is poorly understood. Here, the authors develop an LD-specific probe, AP1-coumarin, and reveal dynamic interactions between LDs and endosomes, regulating lipid homeostasis.

    • Wang Peng
    • Shu Chen
    • Jianbo Yue
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-16
  • Human guanylate kinase (GMPK) is the sole enzyme for GDP biosynthesis contributing to antiviral prodrug activation and tumorigenesis. Here, authors profile the ligand-specific conformations of human GMPK along with the reversible catalytic pathway.

    • Lei Wang
    • Zihuan Li
    • Ke Ruan
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12
  • Plasma cell differentiation is governed by a gene expression program, for which transcriptional regulators are mostly known but other regulatory elements, such as RNA-binding proteins remain lesser explored. Here authors show that an RNA-binding protein complex, Csde1-Strap, regulates the window of Bach2 expression, a transcription factor necessary for the transient expansion of B cells preceding plasma cell differentiation, via coupling its translation to its decay.

    • Pengda Chen
    • Lianghua Lin
    • Changchun Xiao
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-24
  • Setaria pan-genome constructed using genome assemblies of 110 representative accessions and variation analyses provides insights into foxtail millet domestication and the genetic basis for crop improvement.

    • Qiang He
    • Sha Tang
    • Xianmin Diao
    ResearchOpen Access
    Nature Genetics
    Volume: 55, P: 1232-1242
  • Here, the authors introduce a single-cell Hi-C method to study mammalian sperm, suggesting chromatin compartments but absent topological domains (TADs) or loops. It clarifies the unique 3D nuclear architecture of sperm and offers a foundation for investigating structural anomalies associated with male infertility.

    • Heming Xu
    • Yi Chi
    • Dong Xing
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14
  • Whilst superconductivity is understood to emerge when electronic pairing allows for conduction without resistance, the mechanism at work in Fe-based superconductors is unclear. Here, the authors address the details of Fermi surfaces and associated gaps as well as the pairing mechanism of (Li1−xFex)OHFeSe via scanning tunnelling methods.

    • Zengyi Du
    • Xiong Yang
    • Hai-Hu Wen
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-8
  • Heart failure is a complex syndrome that is associated with many different underlying risk factors. Here, to increase power, the authors jointly analyse cases of heart failure of different aetiologies in a genome-wide association study and identify 11 loci of which ten had not been previously reported.

    • Sonia Shah
    • Albert Henry
    • R. Thomas Lumbers
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • Vaccination provides protection from COVID-19, but optimization in design and route is an ever-ongoing process. Here the authors pursue an open-label, multi-arm phase I clinical trial to report the safety of a multi-valent, aerosol vaccine administered via inhalation, as well as superior mucosal immunity induced by ChAd over HuAd vectors.

    • Mangalakumari Jeyanathan
    • Sam Afkhami
    • Zhou Xing
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-21
  • Atomically dispersed Rh on N-doped carbon exhibits 28- and 67-fold enhancements compared with state-of-the-art Pd/C and Pt/C, despite the low activity of Rh/C. The Rh single atoms exhibit high tolerance to CO poisoning compared to Rh nanoparticles.

    • Yu Xiong
    • Juncai Dong
    • Yadong Li
    Research
    Nature Nanotechnology
    Volume: 15, P: 390-397
  • A meta-analysis of genome-wide association studies of type 2 diabetes (T2D) identifies more than 600 T2D-associated loci; integrating physiological trait and single-cell chromatin accessibility data at these loci sheds light on heterogeneity within the T2D phenotype.

    • Ken Suzuki
    • Konstantinos Hatzikotoulas
    • Eleftheria Zeggini
    ResearchOpen Access
    Nature
    Volume: 627, P: 347-357
  • Here they identify a selective PRC1.1 inhibitor, iBP, that treats bone loss by improving osteoblast function. iBP releases repression of Wnt/β-catenin signaling, enhancing bone formation and repair in aging, trauma, and disease models.

    • Liangyu Xing
    • Jinxin Xu
    • Xudong Wu
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18