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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: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...↵3 These authors equally contributed to this work. Corresponding author: danxie@scu.edu.cnAbstractSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...://creativecommons.org/licenses/by-nc/4.0/.References ↵Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, et al. 2020. Comprehensive analysis of structural variants in breast cancer s using single-molecule sequencing. Genome Res 30: 1258–1273. doi:10.1101/gr.260497.119 ↵Aganezov S...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...by simulation with a custom script (aev_sim.py). Indel allele count benchmarking The Sequencing Quality Control Phase 2 (SEQC2) consortium established a reference somatic call set from the HCC1395 breast cancer cell line and the HCC1395BL cell line, which was derived from the normal B cell of the same donor...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...-dimensional RNA structures on local sequencing efficiency using an innovative unsupervised variational autoencoder-Gaussian mixture model (VAE-GMM). The VAE-GMM effectively captures intricate high-dimensional k-mer structural similarities by learning compact latent representations, which reduces dimensionality...
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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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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
..., 8200 Aarhus, Denmark; 4Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000 Aarhus, Denmark ↵5 These authors contributed equally to this work. Corresponding authors: thorkild.terkelsen@biomed.au.dk, uffejens@rm.dkAbstractStructural variations (SVs) play important roles in genetic...
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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
...revealed by single-molecule sequencingThe high conservation of the gene structures led us to analyze the evolution of transcript expression in primates. We focused on the set of orthologous transcript models in the five s, and quantified transcript expression levels using high-depth RNA-seq data from 15...
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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
...Bio) and Oxford Nanopore Technologies (ONT) are revolutionizing genomics: They are making chromosome-level assemblies routine, and full diploid, telomere-to-telomere (T2T) assemblies are becoming the standard for human assemblies. LRS employs single-molecule sequencing, avoiding many biases, errors...

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