Searching journal content for articles similar to Ranallo-Benavidez et al. 31 (5): 910.

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  1. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    .... Despite its high accuracy, short-read sequencing struggles with the complete reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents an alternative that offers benefits including real-time sequencing and cost...
  2. Perspective: The impact of long-read sequencing on human population-scale genomics
    • Tobias Rausch,
    • Tobias Marschall,
    • and Jan O. Korbel
    Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
    ...Advances in long-read sequencing technology and computational tools have raised interest in the study of large human sample cohorts with long-reads to foster population-genetic studies and map complex phenotypes (Beyter et al. 2021; De Coster et al. 2021). Yet, there are current hurdles to scaling haplotype...
  3. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...University, Houston, Texas 77005, USA ↵4 These authors contributed equally to this work. Corresponding author: fritz.sedlazeck@bcm.eduAbstractOver the past decade, long-read sequencing has evolved into a pivotal technology for uncovering the hidden and complex regions of the . Significant cost efficiency...
  4. Method: Single-molecule long-read sequencing reveals the chromatin basis of gene expression
    • Yunhao Wang,
    • Anqi Wang,
    • Zujun Liu,
    • Andrew L. Thurman,
    • Linda S. Powers,
    • Meng Zou,
    • Yue Zhao,
    • Adam Hefel,
    • Yunyi Li,
    • Joseph Zabner,
    • and Kin Fai Au
    Genome Res. August 2019 29: 1329-1342; Published in Advance June 14, 2019, doi:10.1101/gr.251116.119
    ...widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility...
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  5. Method: MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome
    • John R. Tyson,
    • Nigel J. O'Neil,
    • Miten Jain,
    • Hugh E. Olsen,
    • Philip Hieter,
    • and Terrance P. Snutch
    Genome Res. February 2018 28: 266-274; Published in Advance December 22, 2017, doi:10.1101/gr.221184.117
    ...the contig.DiscussionAdvances in long-read sequencing have opened new avenues for analysis. The relatively short sequencing reads produced by NGS allow for effective and cost-efficient resequencing of less complex, nonrepetitive regions in well-characterized s. Long sequence reads can span repetitive regions...
    OPEN ACCESS ARTICLE
  6. Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
    • Sena A. Gocuk,
    • James Lancaster,
    • Shian Su,
    • Jasleen K. Jolly,
    • Thomas L. Edwards,
    • Doron G. Hickey,
    • Matthew E. Ritchie,
    • Marnie E. Blewitt,
    • Lauren N. Ayton,
    • and Quentin Gouil
    Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
    ...on long-read whole- sequencing to simultaneously identify variants and investigate the contribution of skew to X-linked diseases in females. We used the Oxford Nanopore Technologies PromethION 24 platform and its adaptive sampling capacity to enrich X Chromosome reads. We sequenced peripheral samples...
  7. Method: Polishing copy number variant calls on exome sequencing data via deep learning
    • Furkan Özden,
    • Can Alkan,
    • and A. Ercüment Çiçek
    Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
    ...set contains the WGS-based CNV calls of nine s selected from the 1000 Genomes Project samples, for which a consensus call set was obtained using 15 different WGS-based CNV callers with comparisons against high-quality SVs generated using long-read Pacific Biosciences (PacBio) data with a single...
  8. Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
    • Sergey Aganezov,
    • Sara Goodwin,
    • Rachel M. Sherman,
    • Fritz J. Sedlazeck,
    • Gayatri Arun,
    • Sonam Bhatia,
    • Isac Lee,
    • Melanie Kirsche,
    • Robert Wappel,
    • Melissa Kramer,
    • Karen Kostroff,
    • David L. Spector,
    • Winston Timp,
    • W. Richard McCombie,
    • and Michael C. Schatz
    Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
    ...sequenced this cell line using short-read paired-end Illumina and long-read PacBio sequencing (Nattestad et al. 2018); here, we additionally examine 10x Genomics Linked Reads and Oxford Nanopore sequencing for this sample (Fig. 1A; Methods).View larger version: In this window In a new window Figure 1...
  9. Method: Whole-genome bisulfite sequencing with improved accuracy and cost
    • Masako Suzuki,
    • Will Liao,
    • Frank Wos,
    • Andrew D. Johnston,
    • Justin DeGrazia,
    • Jennifer Ishii,
    • Toby Bloom,
    • Michael C. Zody,
    • Soren Germer,
    • and John M. Greally
    Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
    ...cell types.It has therefore become a major priority to try to harness the advances in technologies that are permitting whole- sequencing (WGS) to be performed increasingly cost-efficiently, so that similar cost savings can be applied to WGBS. The release of the Illumina HiSeq X reduced the cost of WGS...
  10. Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
    • Daniela Nachmanson,
    • Shenyi Lian,
    • Elizabeth K. Schmidt,
    • Michael J. Hipp,
    • Kathryn T. Baker,
    • Yuezheng Zhang,
    • Maria Tretiakova,
    • Kaitlyn Loubet-Senear,
    • Brendan F. Kohrn,
    • Jesse J. Salk,
    • Scott R. Kennedy,
    • and Rosa Ana Risques
    Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
    ...sequences of both strands of each DNA molecule (Fig. 1D; Kennedy et al. 2014). Due to the requirement of only one round of hybridization capture, the workflow of CRISPR-DS is almost one day shorter than standard-DS (Fig. 2; Supplemental Fig. S1), enabling a more cost-efficient and applicable method...
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