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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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Method: Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples
- Lukas Bokelmann,
- Isabelle Glocke,
- and Matthias Meyer
Genome Res. October 2020 30: 1449-1457; Published in Advance September 22, 2020, doi:10.1101/gr.263863.120
...Seq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...are enriched in functions related to the regulation of immunity, such as interferon signaling and innate immune response (IRF2, IRF3, IRF5, IRF7, IRF9, IFI35, IFIT1, ISG20, IFNGR2, HLA-DQB1, CIITA, etc.), as well as proliferative (DNA repair, centrosome localization, etc.), housekeeping (ncRNA processing...
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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
...as sequencing artifacts, making true variants impossible to detect. There is a continued effort by multiple sequencing vendors to lower the single-molecule error rate to Q40 and beyond. Nevertheless, for uninformed SNV analysis in liquid biopsies, a Q70 or higher will be required to detect TFs > 1% in a cfDNA...
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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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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
...) attributed this bias to the use of cesium chloride DNA purification by Kim et al. (2014), which separates DNA based on density. Because the light AT-rich sequences form a band separated from the main DNA band (satellite bands) (see Kit 1961; Rae 1970; Gall and Atherton 1974; Altemose 2022) and because some...
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Method: Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
- Shijia Zhu,
- John Beaulaurier,
- Gintaras Deikus,
- Tao P. Wu,
- Maya Strahl,
- Ziyang Hao,
- Guanzheng Luo,
- James A. Gregory,
- Andrew Chess,
- Chuan He,
- Andrew Xiao,
- Robert Sebra,
- Eric E. Schadt,
- and Gang Fang
Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
...-Methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes; however, methods for high-resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...RNA 5-methylcytosine sites via pseudo nucleotide compositions. Mol Biosyst 12: 3307–3311. doi:10.1039/c6mb00471g ↵Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat...
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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
...quantities of DNA were available for our three sequencing platforms (Fig. 1A). Furthermore, several studies have shown organoids are superior to standard 2D cell culture for recapitulating the molecular characteristics, physiology, and treatment response of patient tissues (Clevers 2016), allowing us...
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Method: Density separation of petrous bone powders for optimized ancient DNA yields
- Daniel M. Fernandes,
- Kendra A. Sirak,
- Olivia Cheronet,
- Mario Novak,
- Florian Brück,
- Evelyn Zelger,
- Alejandro Llanos-Lizcano,
- Anna Wagner,
- Anna Zettl,
- Kirsten Mandl,
- Kellie Sara Duffet Carlson,
- Victoria Oberreiter,
- Kadir T. Özdoğan,
- Susanna Sawyer,
- Francesco La Pastina,
- Emanuela Borgia,
- Alfredo Coppa,
- Miroslav Dobeš,
- Petr Velemínský,
- David Reich,
- Lynne S. Bell,
- and Ron Pinhasi
Genome Res. April 2023 33: 622-631; Published in Advance April 18, 2023, doi:10.1101/gr.277714.123
.... Princeton University Press, Princeton, NJ. ↵Dabney J, Knapp M, Glocke I, Gansauge M-T, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga J-L, et al. 2013. Complete mitochondrial sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci 110: 15758...

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