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Showing 1–9 of 9 results
Advanced filters: Author: Ka Ming Nip Clear advanced filters

  • Most existing long-read transcriptome assembly methods rely on reference genomes and transcript annotations, while reference-free methods remain scarce. Here, Nip et al. introduce RNA-Bloom2, a reference-free method that requires substantially less memory and runtime than other reference-free methods.

    • Ka Ming Nip
    • Saber Hafezqorani
    • Inanc Birol
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-14

  • Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. GoldRush departs from this paradigm, generating highly contiguous assemblies with linear time complexity and using an order of magnitude less RAM than state-of-the-art methods.

    • Johnathan Wong
    • Lauren Coombe
    • Inanç Birol
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-9

  • Medulloblastoma is the most common malignant brain tumour in children; having assembled over 1,000 samples the authors report that somatic copy number aberrations are common in medulloblastoma, in particular a tandem duplication of SNCAIP, a gene associated with Parkinson’s disease, which is restricted to subgroup 4α, and translocations of PVT1, which are restricted to Group 3.

    • Paul A. Northcott
    • David J. H. Shih
    • Michael D. Taylor
    ResearchOpen Access
    Nature
    Volume: 488, P: 49-56

  • Comprehensive analyses of 178 lung squamous cell carcinomas by The Cancer Genome Atlas project show that the tumour type is characterized by complex genomic alterations, with statistically recurrent mutations in 11 genes, including TP53 in nearly all samples; a potential therapeutic target is identified in most of the samples studied.

    • Peter S. Hammerman
    • Michael S. Lawrence
    • Matthew Meyerson
    ResearchOpen Access
    Nature
    Volume: 489, P: 519-525

  • Several genomic features have been found for acute myeloid leukaemia (AML) but targeted clinical genetic testing fails to predict prognosis. Here, the authors generate an AML prognostic score from RNA-seq data of patients, which successfully stratifies AML patients and which may provide guidance for therapeutic strategies.

    • T. Roderick Docking
    • Jeremy D. K. Parker
    • Aly Karsan
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-15

  • This Registered Report presents the results of the Long-read RNA-Seq Genome Annotation Assessment Project, which is a community effort for benchmarking long-read methods for transcriptome analyses, including transcript isoform detection, quantification and de novo transcript detection.

    • Francisco J. Pardo-Palacios
    • Dingjie Wang
    • Angela N. Brooks
    ResearchOpen Access
    Nature Methods
    Volume: 21, P: 1349-1363

  • The Cancer Genome Atlas reports on molecular evaluation of 295 primary gastric adenocarcinomas and proposes a new classification of gastric cancers into 4 subtypes, which should help with clinical assessment and trials of targeted therapies.

    • Adam J. Bass
    • Vesteinn Thorsson
    • Jia Liu
    ResearchOpen Access
    Nature
    Volume: 513, P: 202-209