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  • Genetic mechanisms of prima... Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia
    McNeer, Nicole A; Philip, John; Geiger, Heather ... Leukemia, 08/2019, Volume: 33, Issue: 8
    Journal Article
    Peer reviewed
    Open access

    Acute myeloid leukemias (AML) are characterized by mutations of tumor suppressor and oncogenes, involving distinct genes in adults and children. While certain mutations have been associated with the ...
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  • Human papillomavirus and th... Human papillomavirus and the landscape of secondary genetic alterations in oral cancers
    Gillison, Maura L; Akagi, Keiko; Xiao, Weihong ... Genome research, 01/2019, Volume: 29, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Human papillomavirus (HPV) is a necessary but insufficient cause of a subset of oral squamous cell carcinomas (OSCCs) that is increasing markedly in frequency. To identify contributory, secondary ...
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  • Comparative sequencing anal... Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions
    Brannon, A Rose; Vakiani, Efsevia; Sylvester, Brooke E ... Genome biology, 08/2014, Volume: 15, Issue: 8
    Journal Article
    Peer reviewed
    Open access

    Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of ...
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  • Somatic whole genome dynami... Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression
    Paulson, Thomas G; Galipeau, Patricia C; Oman, Kenji M ... Nature communications, 04/2022, Volume: 13, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to ...
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  • Genome-wide somatic variant... Genome-wide somatic variant calling using localized colored de Bruijn graphs
    Narzisi, Giuseppe; Corvelo, André; Arora, Kanika ... Communications biology, 01/2018, Volume: 1, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by ...
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  • Gustaf: Detecting and corre... Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone
    Trappe, Kathrin; Emde, Anne-Katrin; Ehrlich, Hans-Christian ... Bioinformatics, 2014-Dec-15, 2014-12-15, 20141215, Volume: 30, Issue: 24
    Journal Article
    Peer reviewed
    Open access

    The landscape of structural variation (SV) including complex duplication and translocation patterns is far from resolved. SV detection tools usually exhibit low agreement, are often geared toward ...
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  • Detection of a Recurrent DN... Detection of a Recurrent DNAJB1-PRKACA Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma
    Honeyman, Joshua N.; Simon, Elana P.; Robine, Nicolas ... Science, 02/2014, Volume: 343, Issue: 6174
    Journal Article
    Peer reviewed
    Open access

    Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare liver tumor affecting adolescents and young adults with no history of primary liver disease or cirrhosis. We identified a chimeric transcript ...
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  • RazerS--fast read mapping w... RazerS--fast read mapping with sensitivity control
    Weese, David; Emde, Anne-Katrin; Rausch, Tobias ... Genome Research 19, Issue: 9
    Journal Article
    Peer reviewed
    Open access

    Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly ...
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  • A novel and well-defined be... A novel and well-defined benchmarking method for second generation read mapping
    Holtgrewe, Manuel; Emde, Anne-Katrin; Weese, David ... BMC bioinformatics, 05/2011, Volume: 12, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar ...
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  • Diverse tumorigenic consequ... Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
    Symer, David E; Akagi, Keiko; Geiger, Heather M ... Genome research, 01/2022, Volume: 32, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes. The HPV oncoproteins E6 and E7 are necessary but insufficient for cancer formation, indicating ...
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