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Showing 1–50 of 275 results
Advanced filters: Author: Alex L. Mitchell Clear advanced filters
  • High spatial resolution is essential for resolving cellular and subcellular organization in tissues. Here, authors present Seq-Scope-X, which integrates tissue expansion with Seq-Scope to achieve an order-of-magnitude improvement in resolution of spatial transcriptomics and proteomics.

    • Angelo Anacleto
    • Weiqiu Cheng
    • Jun Hee Lee
    ResearchOpen Access
    Nature Communications
    P: 1-20
  • Genome-wide association meta-analysis identifies 58 independent risk loci for major anxiety disorders among individuals of European ancestry and implicates GABAergic signaling as a potential mechanism underlying genetic risk for these disorders.

    • Nora I. Strom
    • Brad Verhulst
    • John M. Hettema
    ResearchOpen Access
    Nature Genetics
    Volume: 58, P: 275-288
  • Genomic analyses applied to 14 childhood- and adult-onset psychiatric disorders identifies five underlying genomic factors that explain the majority of the genetic variance of the individual disorders.

    • Andrew D. Grotzinger
    • Josefin Werme
    • Jordan W. Smoller
    ResearchOpen Access
    Nature
    Volume: 649, P: 406-415
  • The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitating the discovery of potential effects of genetic variants, including variants associated with disease, on genome structure and function.

    • Job Dekker
    • Betul Akgol Oksuz
    • Feng Yue
    ResearchOpen Access
    Nature
    Volume: 649, P: 759-776
  • 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
  • Mutational signature analysis of blood cells isolated from 23 chemotherapy-exposed samples and 9 nonexposed controls characterizes the effects of various drugs on mutational burden, signature exposure and cell types.

    • Emily Mitchell
    • My H. Pham
    • Michael R. Stratton
    ResearchOpen Access
    Nature Genetics
    Volume: 57, P: 1684-1694
  • 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
  • An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

    • Erola Pairo-Castineira
    • Konrad Rawlik
    • J. Kenneth Baillie
    ResearchOpen Access
    Nature
    Volume: 617, P: 764-768
  • Quantum computers may help to solve classically intractable problems, such as simulating non-equilibrium dissipative quantum systems. The critical dynamics of a dissipative quantum model has now been probed on a trapped-ion quantum computer.

    • Eli Chertkov
    • Zihan Cheng
    • Michael Foss-Feig
    Research
    Nature Physics
    Volume: 19, P: 1799-1804
  • A large genome-wide association study of more than 5 million individuals reveals that 12,111 single-nucleotide polymorphisms account for nearly all the heritability of height attributable to common genetic variants.

    • Loïc Yengo
    • Sailaja Vedantam
    • Joel N. Hirschhorn
    ResearchOpen Access
    Nature
    Volume: 610, P: 704-712
  • A high-resolution transcriptomic and epigenomic cell-type atlas of the developing mouse visual cortex from embryonic to postnatal development is presented, providing a real-time dynamic molecular map associated with individual cell types and specific developmental events.

    • Yuan Gao
    • Cindy T. J. van Velthoven
    • Hongkui Zeng
    ResearchOpen Access
    Nature
    Volume: 647, P: 127-142
  • Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD), underscoring the power of the presented analysis to minimize false assignments of disease risk.

    • Sanna Gudmundsson
    • Moriel Singer-Berk
    • Anne O’Donnell-Luria
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14
  • A genome-wide association meta-analysis study of blood lipid levels in roughly 1.6 million individuals demonstrates the gain of power attained when diverse ancestries are included to improve fine-mapping and polygenic score generation, with gains in locus discovery related to sample size.

    • Sarah E. Graham
    • Shoa L. Clarke
    • Cristen J. Willer
    Research
    Nature
    Volume: 600, P: 675-679
  • Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

    • Athanasios Kousathanas
    • Erola Pairo-Castineira
    • J. Kenneth Baillie
    ResearchOpen Access
    Nature
    Volume: 607, P: 97-103
  • 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
  • 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
  • Isolating and studying haematopoietic stem cells in young and aged mice demonstrates evolutionary processes related to blood production and provides a framework for interpreting future work using laboratory mice to study stem cell ageing.

    • Chiraag D. Kapadia
    • Nicholas Williams
    • Jyoti Nangalia
    ResearchOpen Access
    Nature
    Volume: 641, P: 681-689
  • Current understanding of Long COVID is limited, in part, due to lack of evidence from population-representative studies. Here, the authors analyse data from ten UK population-based studies and electronic health records, and find wide variation in the frequency of Long COVID between studies but some consistent risk factors.

    • Ellen J. Thompson
    • Dylan M. Williams
    • Claire J. Steves
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-11
  • A genome-wide study by the Long COVID Host Genetics Initiative identifies an association between the FOXP4 locus and long COVID, implicating altered lung function in its pathophysiology.

    • Vilma Lammi
    • Tomoko Nakanishi
    • Hanna M. Ollila
    ResearchOpen Access
    Nature Genetics
    Volume: 57, P: 1402-1417
  • Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development.

    • Cristian Pattaro
    • Alexander Teumer
    • Caroline S. Fox
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-19
  • 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
  • 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
  • Patients with metastatic cancers of unknown primary (CUP) are currently unable to gain access to drugs through standard of care or clinical trials. Here, the authors perform whole-genome and transcriptome sequencing (WGTS) on 72 patients with CUP and demonstrate the feasibility of using WGTS to determine the specific cancer types of CUP, thereby clinically benefiting patients with CUP.

    • Richard J. Rebello
    • Atara Posner
    • Richard W. Tothill
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15
  • 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 of more than 2,000 colorectal carcinoma samples provides a highly detailed view of the genomic landscape of this cancer and identifies new driver mutations.

    • Alex J. Cornish
    • Andreas J. Gruber
    • Richard S. Houlston
    ResearchOpen Access
    Nature
    Volume: 633, P: 127-136
  • 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
  • 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
  • Haematopoiesis has high clonal diversity up to about 65 years of age, after which diversity drops precipitously owing to positive selection acting on a handful of clones that expand exponentially throughout adulthood.

    • Emily Mitchell
    • Michael Spencer Chapman
    • Peter J. Campbell
    ResearchOpen Access
    Nature
    Volume: 606, P: 343-350
  • 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
  • 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
  • Data from over 700,000 individuals reveal the identity of 83 sequence variants that affect human height, implicating new candidate genes and pathways as being involved in growth.

    • Eirini Marouli
    • Mariaelisa Graff
    • Guillaume Lettre
    Research
    Nature
    Volume: 542, P: 186-190
  • 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
  • Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

    • Dinesh Aggarwal
    • Andrew J. Page
    • Ewan M. Harrison
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-13