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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...response kinetics across well-established treatments in the ciliate Tetrahymena thermophila. This extensive data set containing six conditions (HU, MMS, IR, HP, cisplatin, and UV) and seven time points (from 0 to 8 h) integrates over 250 paired transcriptome and proteome measurements. We observe...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...mechanistic and translational investigations. 92 93 Results 94 95 SomaGauss-SV demonstrates excellent performance in detecting somatic structural 96 variations 97 98 Current long-read sequencing algorithms for detecting SVs often exhibit reduced accuracy in 99 repetitive genomic regions. This limitation...
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Research: Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila
- Zhengyu Luo,
- Tengfei Hu,
- Hong Jiang,
- Ruoyu Wang,
- Qianlan Xu,
- Simo Zhang,
- Jun Cao,
- and Xiaoyuan Song
Genome Res. March 2020 30: 406-414; Published in Advance March 12, 2020, doi:10.1101/gr.241687.118
...for maintaining the TAD-like structure in single cells (Bintu et al. 2018). Thus, the mechanism of TADs formation and maintenance is still largely unknown.Tetrahymena thermophila, a ciliated protozoan, contains two nuclei in the same cell: the transcriptionally active polyploid macronucleus (MAC...
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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
...dosage for NMD-triggering mutations. The model predictions are validated by a pancancer bulk tumor analysis with somatic insertions/deletions (indels) from 9101 The Cancer Genome Atlas (TCGA) samples. A single-cell analysis in five cutaneous squamous cell carcinomas demonstrates the robustness...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...at Austin, Dell Pediatric Research Institute, Austin, Texas 78723, USA; 9Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; 10Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus...
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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
...). For example, Figure 2B shows a 1357 bp deletion (SOMATIC_SV_29) that can be clearly observed in all four cancer samples. Next, we used the UCSC Genome Browser (Kent et al. 2002) to annotate the somatic SVs for COLO829-T2T. Here, we observed similar results to the annotation of somatic SVs in GRCh38...
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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
....Cancer cells accumulate somatic genomic variations, such as single-nucleotide variants (SNVs), copy number alterations (CNAs), and gene fusions during their lifetime, leading to intratumor heterogeneity, i.e., the existence of cancer subpopulations with distinct genotypes and phenotypes. This is presumed...
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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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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...for detecting de novo somatic variants in single-cell RNA-seq data, addressing tumor heterogeneity. Jensen et al. (2025) integrate transcriptomics and long-read genomics to prioritize SVs, refining diagnostic workflows for undiagnosed cases. Beaulaurier et al. (2025) present a novel approach for de novo...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
..., and the mutation frequency varies among the subs. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale...

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