Searching journal content for articles similar to Huddleston et al. 28 (1): 144.

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  1. Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
    • Can Luo,
    • Zimeng Jamie Zhou,
    • Yichen Henry Liu,
    • and Xin Maizie Zhou
    Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
    ...module identifies indel structural variants (SVs) by comparing the assembled contigs to the reference , followed by filtering and genotype (GT) correction in postprocessing steps. (B) Multiregion mode: the input data includes a high-quality reference and a BAM file containing aligned long reads. Focal...
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  2. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...of haplotypes. Reference-free approaches that tackle all or a subset of criteria 1–3 also exist (Baaijens et al. 2019; Luo et al. 2022), but the lack of reference adds additional algorithmic difficulties; we focus on the reference-based case. Long reads can connect more distant alleles across shared genomic...
  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
    ...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...
  4. 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
    ...sequencing for both germline and somatic cancer analysis. We provide an overview of the computational methodologies tailored to long-read data and highlight key discoveries and resources within cancer genomics that were previously inaccessible with prior technologies. We also address future opportunities...
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  5. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...that integrates into host genomic DNA and forms virus–virus and virus–host genomic structural rearrangements, which are unstable and lead to further intratumoral heterogeneity and clonal evolution; through long-read sequencing, unique breakpoints shared across structural variants were also observed in HPV...
  6. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    ...genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289–294. doi:10.1038/nature10413 ↵Keil N, Monzó C, McIntyre L, Conesa A. 2025. Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads. Genome Res (this issue) 35: 987–998. doi:10.1101/gr...
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  7. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...fails at multiple levels: read initiation (very few reads start within satellite regions), read elongation (satellite-containing reads are shorter on average), and basecalling (quality scores drop as sequencing enters a satellite sequence). These findings challenge the assumption that long-read...
  8. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...multiple LRS platforms, as well as a set of 30 trios sequenced using PacBio HiFi technology, we will evaluate our new software's effectiveness in capturing STR variation, including pathogenic expansions, and compare its genotyping and computational performance against other long-read STR genotyping tools...
  9. Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    • Nathan Hammond,
    • Linda Liao,
    • Pun Wai Tong,
    • Zena Ng,
    • Thuy-Mi P. Nguyen,
    • Chandler Ho,
    • Yao Yang,
    • and Stuart A. Scott
    Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
    ...Med Genomics 7: 20. doi:10.1186/1755-8794-7-20 ↵Logsdon GA, Vollger MR, Eichler EE. 2020. Long-read human sequencing and its applications. Nat Rev Genet 21: 597–614. doi:10.1038/s41576-020-0236-x ↵Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. 2019. Structural variant...
  10. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...). These assignments were based on 135,380 (replicate 1) and 134,585 (replicate 2) informative positions on the long-reads that overlapped known genetic variation between the strains (210,004 total SNPs).As an orthogonal approach to determine ASE, we used Illumina short-read sequencing. We found that RNA expression...
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