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  • An open resource for accura... An open resource for accurately benchmarking small variant and reference calls
    Zook, Justin M; McDaniel, Jennifer; Olson, Nathan D ... Nature biotechnology, 05/2019, Volume: 37, Issue: 5
    Journal Article
    Peer reviewed
    Open access

    Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) ...
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  • A robust benchmark for dete... A robust benchmark for detection of germline large deletions and insertions
    Zook, Justin M; Hansen, Nancy F; Olson, Nathan D ... Nature biotechnology, 11/2020, Volume: 38, Issue: 11
    Journal Article
    Peer reviewed
    Open access

    New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to ...
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  • Curated variation benchmark... Curated variation benchmarks for challenging medically relevant autosomal genes
    Wagner, Justin; Olson, Nathan D; Harris, Lindsay ... Nature biotechnology, 05/2022, Volume: 40, Issue: 5
    Journal Article
    Peer reviewed
    Open access

    The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant ...
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  • Toward best practice in can... Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
    Xiao, Wenming; Ren, Luyao; Chen, Zhong ... Nature biotechnology, 09/2021, Volume: 39, Issue: 9
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    Peer reviewed
    Open access

    Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To ...
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  • Similarities and difference... Similarities and differences between variants called with human reference genome HG19 or HG38
    Pan, Bohu; Kusko, Rebecca; Xiao, Wenming ... BMC bioinformatics, 03/2019, Volume: 20, Issue: Suppl 2
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    Open access

    Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: ...
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  • Extensive sequencing of sev... Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Zook, Justin M; Catoe, David; McDaniel, Jennifer ... Scientific data, 06/2016, Volume: 3, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for ...
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  • Achieving robust somatic mu... Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample
    Sahraeian, Sayed Mohammad Ebrahim; Fang, Li Tai; Karagiannis, Konstantinos ... Genome Biology, 01/2022, Volume: 23, Issue: 1
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    Open access

    Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural ...
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  • Personalized genome assembl... Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples
    Xiao, Chunlin; Chen, Zhong; Chen, Wanqiu ... Genome Biology, 11/2022, Volume: 23, Issue: 1
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    Open access

    The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has ...
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  • A diploid assembly-based be... A diploid assembly-based benchmark for variants in the major histocompatibility complex
    Chin, Chen-Shan; Wagner, Justin; Zeng, Qiandong ... Nature communications, 09/2020, Volume: 11, Issue: 1
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    Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We ...
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  • Assessing reproducibility o... Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
    Pan, Bohu; Ren, Luyao; Onuchic, Vitor ... Genome Biology, 01/2022, Volume: 23, Issue: 1
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    Open access

    Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant ...
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