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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
...FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data Can Luo1,3, Zimeng Jamie Zhou2,3, Yichen Henry Liu2 and Xin Maizie Zhou1,2 1Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA; 2...
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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
...to the refinement of isoform repertoires in model and nonmodel organisms (Byrne et al. 2019). Thus, single-molecule sequencing in combination with short-read RNA-seq and proteomic data appears as a powerful tool to disentangle the recent primate evolution of transcriptomes with isoform resolution, especially...
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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
...these standards to estimate base pair in genomic (TTAGGG)n tracts on single molecules based upon the measured fluorescent intensities. The initial results of the two colabeling strategies for the single-molecule telomere length assay are shown in Figure 3. In the first application, we tested the three...
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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
...hundreds of kilobase pairs. The method provides kilobase pair–scale genomic methylation patterns comparable to whole- bisulfite sequencing (WGBS) along genes and regulatory elements. These long single-molecule reads allow for methylation variation calling and analysis of large structural aberrations...
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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
..., Sundararajan K, Brown RR, Mishra R, Detweiler AM, Neff N, Miga KH, Straight AF, et al. 2022b. DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions wide. Nat Methods 19: 711–723. doi:10.1038/s41592-022-01475-6 ↵Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. 2020...
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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
...Comprehensive analysis of structural variants in breast cancer s using single-molecule sequencing Sergey Aganezov1, Sara Goodwin2, Rachel M. Sherman1, Fritz J. Sedlazeck3, Gayatri Arun2, Sonam Bhatia2, Isac Lee4, Melanie Kirsche1, Robert Wappel2, Melissa Kramer2, Karen Kostroff5, David L. Spector2...
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Method: Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
- John Beaulaurier,
- Elaine Luo,
- John M. Eppley,
- Paul Den Uyl,
- Xiaoguang Dai,
- Andrew Burger,
- Daniel J. Turner,
- Matthew Pendelton,
- Sissel Juul,
- Eoghan Harrington,
- and Edward F. DeLong
Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
...Assembly-free single-molecule sequencing recovers complete virus s from natural microbial communities John Beaulaurier1,5, Elaine Luo2,5, John M. Eppley2,5, Paul Den Uyl2, Xiaoguang Dai3, Andrew Burger2, Daniel J. Turner4, Matthew Pendelton3, Sissel Juul3, Eoghan Harrington3 and Edward F. DeLong2 1...
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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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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
...-generation sequencing [e.g., Illumina]), PCR amplification is not required for ONT sequencing, so each ONT read can reveal the genomic events at the single-molecule level; (3) ONT reads are ultralong (up to 2.3 Mb) (Payne et al. 2018) so that they can cover combinatorics of many nucleosomes and different chromatin...
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Method: Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
- Zhiyi Sun,
- Romualdas Vaisvila,
- Laura-Madison Hussong,
- Bo Yan,
- Chloé Baum,
- Lana Saleh,
- Mala Samaranayake,
- Shengxi Guan,
- Nan Dai,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Theodore B. Davis,
- Thomas C. Evans, Jr.,
- and Laurence M. Ettwiller
Genome Res. February 2021 31: 291-300; Published in Advance January 19, 2021, doi:10.1101/gr.265306.120
...the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long-range epigenetic analysis at single-molecule and single-nucleotide resolution.Long-read technologies have been a breakthrough in high-throughput sequencing for their abilities to phase...
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