Searching journal content for articles similar to Chan et al. 14 (6): 1137.

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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
...with lower proportions of phasing-informative reads.FocalSV achieves superior performance in complex somatic SV detection in cancer dataTo extend the evaluation to include SV detection beyond deletions and insertions, we analyzed additional SV types involving complex DNA rearrangements...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...contributed equally to this work. Corresponding authors: mi.jain@northeastern.edu,kimberley.billingsley@nih.gov, cornelis.blauwendraat@nih.govAbstractDNA methylation most commonly occurs as 5-methylcytosine (5mC) in the human and has been associated with human diseases. Recent developments in single-molecule...
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Method: Long-read single-molecule maps of the functional methylome
- Hila Sharim,
- Assaf Grunwald,
- Tslil Gabrieli,
- Yael Michaeli,
- Sapir Margalit,
- Dmitry Torchinsky,
- Rani Arielly,
- Gil Nifker,
- Matyas Juhasz,
- Felix Gularek,
- Miguel Almalvez,
- Brandon Dufault,
- Sreetama Sen Chandra,
- Alexander Liu,
- Surajit Bhattacharya,
- Yi-Wen Chen,
- Eric Vilain,
- Kathryn R. Wagner,
- Jonathan Pevsner,
- Jeff Reifenberger,
- Ernest T. Lam,
- Alex R. Hastie,
- Han Cao,
- Hayk Barseghyan,
- Elmar Weinhold,
- and Yuval Ebenstein
Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
.../epigenetic fluorescent barcode for every DNA molecule. The detected molecular barcodes allow assigning the methylation profiles to their specific genomic locations, thus enabling the study of DNA methylation patterns over large genomic fragments at single-molecule resolution.Here we aim to harness the reduced...
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Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
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Method: High-throughput single-molecule telomere characterization
- Jennifer McCaffrey,
- Eleanor Young,
- Katy Lassahn,
- Justin Sibert,
- Steven Pastor,
- Harold Riethman,
- and Ming Xiao
Genome Res. November 2017 27: 1904-1915; Published in Advance October 12, 2017, doi:10.1101/gr.222422.117
.... An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in s that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif -wide. High-throughput imaging and analysis of large DNA single molecules from s labeled in this fashion...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...differ in distribution and function in bacteria, but all play pivotal roles in bacterial life processes. Long-read sequencing platforms, including PacBio single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technology (ONT) sequencing, have enabled the direct detection of DNA modifications...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...(NGI) in Stockholm (NGI-S) and Uppsala (NGI-U). After fragmenting to 350-bp inserts and library preparation, DNA samples underwent WGS on the Illumina HiSeq X platform using v2.5 chemistry (Ameur et al. 2017). The 1000 individuals included in the data set all passed QC. The original mappings were...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...Carthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10: giab008. doi:10.1093/gigascience/giab008 ↵Daron J, Slotkin RK. 2017. EpiTEome: simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biol 18: 91. doi:10.1186/s13059...
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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
...), the phased status of nucleosomes and chromatin accessibility at single DNA molecules remains incomplete (Kuleshov et al. 2014; Tilgner et al. 2018).The emerging single-molecule long-read sequencing technology (i.e., Oxford Nanopore Technologies, ONT) provides unique data features that are capable of filling...
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