Searching journal content for articles similar to Kim et al. 21 (7): 1028.

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  1. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...are reduced by the consensus of multiple (≥3) repeats. NanoRCS offers a precise, multimodal nanopore sequencing-based strategy for cfDNA sequencing through the accurate identification of tumor-informed SNVs along with CNAs and fragmentation length patterns in cfDNA (Fig. 1D).View larger version...
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  2. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...leading to the clonal evolution of cancer cells (Qing et al. 2020; Chakravarty and Solit 2021). Somatic mutations in key genes and their regulatory sequences, especially oncogenes, tumor suppressors, and DNA repair genes, are frequently found in cancers and contribute to tumor progression and therapeutic...
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  3. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ...to determine the tissue of origin of individual long cfDNA molecules for the detection of HCC (AUC = 0.91). In addition, various deep learning algorithms have also been applied in nanopore sequencing for basecalling and detection of base modifications in a variety of biological contexts (Boža et al. 2017; Rang...
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  4. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...properties (Hall et al. 2002; Meijsing et al. 2009), meaning that the primary DNA sequence not only influences binding affinity but also coregulator recruitment and genomic interactions. Yet, which ERBS are functionally active—and what distinguishes active from inactive ones—remains poorly understood...
  5. Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
    • Alicia Petrany,
    • Ruoyu Chen,
    • Shaoqiang Zhang,
    • and Yong Chen
    Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
    ...University, Tianjin 300387, China Corresponding authors: chenyong@rowan.edu, zhangshaoqiang@tjnu.edu.cnAbstractHigh-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies...
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  6. Research: DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer
    • Yuya Kobayashi,
    • Devin M. Absher,
    • Zulfiqar G. Gulzar,
    • Sarah R. Young,
    • Jesse K. McKenney,
    • Donna M. Peehl,
    • James D. Brooks,
    • Richard M. Myers,
    • and Gavin Sherlock
    Genome Res. July 2011 21: 1017-1027; Published in Advance April 26, 2011, doi:10.1101/gr.119487.110
    ...DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer Yuya Kobayashi 1 , Devin M. Absher 2 , Zulfiqar G. Gulzar 3 , Sarah R. Young 3 , Jesse K. McKenney 4 , Donna M. Peehl 3...
  7. Method: Accurate and efficient detection of gene fusions from RNA sequencing data
    • Sebastian Uhrig,
    • Julia Ellermann,
    • Tatjana Walther,
    • Pauline Burkhardt,
    • Martina Fröhlich,
    • Barbara Hutter,
    • Umut H. Toprak,
    • Olaf Neumann,
    • Albrecht Stenzinger,
    • Claudia Scholl,
    • Stefan Fröhling,
    • and Benedikt Brors
    Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
    ..., the detection of integrated viral DNA into the host is impaired. A common and straightforward approach to detect viral integration is to align reads to concatenated s of the host and a collection of viruses. Viral integration can then be identified as reads aligning partially to both the host and a viral...
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  8. Research: C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
    • Bettina Meier,
    • Susanna L. Cooke,
    • Joerg Weiss,
    • Aymeric P. Bailly,
    • Ludmil B. Alexandrov,
    • John Marshall,
    • Keiran Raine,
    • Mark Maddison,
    • Elizabeth Anderson,
    • Michael R. Stratton,
    • Anton Gartner,
    • and Peter J. Campbell
    Genome Res. October 2014 24: 1624-1636; Published in Advance July 16, 2014, doi:10.1101/gr.175547.114
    ...C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency Bettina Meier 1 , 6 , Susanna L. Cooke 2 , 6 , Joerg Weiss 1 , Aymeric P. Bailly 1 , 3 , Ludmil B. Alexandrov...
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  9. Method: Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    • Aaron L. Statham,
    • Mark D. Robinson,
    • Jenny Z. Song,
    • Marcel W. Coolen,
    • Clare Stirzaker,
    • and Susan J. Clark
    Genome Res. June 2012 22: 1120-1127; Published in Advance March 30, 2012, doi:10.1101/gr.132076.111
    ...show that in normal cells, H3K27me3 marks many regions independent of DNA methylation and the underlying sequence. Discussion Here, we report a novel method, which combines bisulfite-conversion methodology with chromatin immunoprecipitation and deep sequencing, that allows a direct -wide interrogation...
  10. Method: Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
    • Arie B. Brinkman,
    • Hongcang Gu,
    • Stefanie J.J. Bartels,
    • Yingying Zhang,
    • Filomena Matarese,
    • Femke Simmer,
    • Hendrik Marks,
    • Christoph Bock,
    • Andreas Gnirke,
    • Alexander Meissner,
    • and Hendrik G. Stunnenberg
    Genome Res. June 2012 22: 1128-1138; Published in Advance March 30, 2012, doi:10.1101/gr.133728.111
    ...and the underlying DNA methylation. In our approach, termed ChIPBS-seq, ChIP capturing is followed by bisulfite conversion and deep sequencing to directly assess DNA methylation levels in captured chromatin fragments. While the use of whole- bisulfite shotgun sequencing is limited by the cost of the required...
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