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Showing 1–50 of 1274 results
Advanced filters: Author: Joshua R. York Clear advanced filters
  • Here the authors develop a novel statistical method for quantifying mutation burden from whole genome sequencing data and use it to discover the genetic, genomic, and phenotypic correlates of clonal hematopoiesis without known driver genetic lesions.

    • Joshua S. Weinstock
    • Sharjeel A. Chaudhry
    • Marios Arvanitis
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15
  • Electronic health records are a rich source of clinical data but identifying associations with outcomes is complex. Here, the authors propose a modelling framework ‘InfEHR’ that identifies patient trajectories in electronic health records and generates a likelihood for clinical phenotypes.

    • Justin Kauffman
    • Emma Holmes
    • Girish N. Nadkarni
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-21
  • 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
  • Head motion is an artifact in structural and functional MRI signals, and some traits or groups are more strongly correlated with motion than others. Here the authors describe a method to attribute a motion impact score to specific trait-functional connectivity relationships.

    • Benjamin P. Kay
    • David F. Montez
    • Nico U. F. Dosenbach
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15
  • EchoNext, a deep learning model for electrocardiograms trained and validated in diverse health systems, successfully detects many forms of structural heart disease, supporting the potential of artificial intelligence to expand access to heart disease screening at scale.

    • Timothy J. Poterucha
    • Linyuan Jing
    • Pierre Elias
    ResearchOpen Access
    Nature
    Volume: 644, P: 221-230
  • A 1,024-channel microelectrode array is delivered to the brain cortex via a minimally invasive incision in the skull and dura, and allows recording, stimulation and neural decoding across large portions of the brain in porcine models and human neurosurgical patients.

    • Mark Hettick
    • Elton Ho
    • Benjamin I. Rapoport
    ResearchOpen Access
    Nature Biomedical Engineering
    P: 1-16
  • Resolution of G4s has been suggested to be required for efficient DNA replication. Here, the authors show that the nuclease DNA2 and the DNA repair complex MutSα (MSH2-MSH6) are required to remove G4 stabilized by environmental compounds to allow efficient telomere replication.

    • Anthony Fernandez
    • Tingting Zhou
    • Binghui Shen
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15
  • Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

    • Joshua S. Weinstock
    • Jayakrishnan Gopakumar
    • Siddhartha Jaiswal
    Research
    Nature
    Volume: 616, P: 755-763
  • 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
  • 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
  • There are no vaccines or antivirals available against enterovirus D68. Here, the authors report Jun6504 as a 2C inhibitor and show that it provides broad-spectrum antiviral activity against EV-D68, EV-A71, and CVB3 and potent antiviral efficacy in a neonatal neurological mouse model of EV-D68 infection.

    • Kan Li
    • Michael J. Rudy
    • Jun Wang
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18
  • 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
  • Between April and June 1946, Joshua Lederberg and Edward L. Tatum carried out a series of experiments that proved that bacteria can exchange their genes by sexual crossings. The experiments were reported in Nature just 40 years ago1. In the following pair of articles, Joshua Lederberg first provides a personal reminiscence of the circumstances of the discovery and then, together with Harriet Zuckerman, considers it as a possible case of ‘postmature’ scientific discovery.

    • Joshua Lederberg
    Comments & Opinion
    Nature
    Volume: 324, P: 627-628
  • Federated learning (FL) algorithms have emerged as a promising solution to train models for healthcare imaging across institutions while preserving privacy. Here, the authors describe the Federated Tumor Segmentation (FeTS) challenge for the decentralised benchmarking of FL algorithms and evaluation of Healthcare AI algorithm generalizability in real-world cancer imaging datasets.

    • Maximilian Zenk
    • Ujjwal Baid
    • Spyridon Bakas
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20
  • Meta-analysis of genome-wide association studies on Alzheimer’s disease and related dementias identifies new loci and enables generation of a new genetic risk score associated with the risk of future Alzheimer’s disease and dementia.

    • Céline Bellenguez
    • Fahri Küçükali
    • Jean-Charles Lambert
    ResearchOpen Access
    Nature Genetics
    Volume: 54, P: 412-436
  • Karcher et al. use data from the Adolescent Brain Cognitive Development Study to explore how changes in cognition and brain structure influence the relationship between risk factors and persistent distressing psychotic-like experiences in children aged 9–13 years.

    • Nicole R. Karcher
    • Fanghong Dong
    • Deanna M. Barch
    Research
    Nature Mental Health
    Volume: 3, P: 1012-1019
  • Deep learning-based generative tools are used to design protein building blocks with well-defined directional bonding interactions, allowing the generation of a variety of scalable protein assemblies from a small set of reusable subunits.

    • Shunzhi Wang
    • Andrew Favor
    • David Baker
    ResearchOpen Access
    Nature Materials
    Volume: 24, P: 1644-1652
  • Circulating tumor cell (CTC) clusters are much more likely to produce viable metastasis than single CTCs. Here the authors find that the transmembrane protein Plexin-B2 (PLXNB2) mediates homotypic and heterotypic CTC cluster formation, driving lung metastasis in breast cancer mouse models.

    • Emma Schuster
    • Nurmaa K. Dashzeveg
    • Huiping Liu
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20
  • 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
  • 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 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
  • 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
  • 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 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
  • 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
  • A computational model called Centaur, developed by fine-tuning a language model on a huge dataset called Psych-101, can predict and simulate human nature in experiments expressible in natural language, even in previously unseen situations.

    • Marcel Binz
    • Elif Akata
    • Eric Schulz
    ResearchOpen Access
    Nature
    Volume: 644, P: 1002-1009
  • The relationship between single-neuron activity and theta oscillations in the human brain remains unclear. Here, the authors demonstrate that human theta-phase locking is influenced by various properties of the local field potential and characterize its dynamics during spatial memory encoding and retrieval.

    • Tim A. Guth
    • Armin Brandt
    • Lukas Kunz
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20
  • 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
  • Craniofacial malformations have been linked to congenital heart defects, as in 22q11.2 deletion syndrome, but the mechanisms linking these lineages remain unknown. Here they show that zebrafish nxk2.7 is expressed in cardiopharyngeal progenitors and has roles in craniofacial development that cannot be compensated for by nkx2.5.

    • Caitlin Ford
    • Carmen de Sena-Tomás
    • Kimara L. Targoff
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-19
  • A long-period radio transient with coincident radio and X-ray emission and observational properties unlike any known Galactic object has been observed by the Australian Square Kilometre Array Pathfinder.

    • Ziteng Wang
    • Nanda Rea
    • Nithyanandan Thyagarajan
    Research
    Nature
    Volume: 642, P: 583-586
  • 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