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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...DNA sequencing and forensics, the amount of DNA available is low and requires amplification (Butler 2006; Evrony et al. 2015). Although high-depth whole- sequencing (WGS) of PCR-amplified libraries could achieve large-scale, high-fidelity profiling of microsatellites, this is not feasible to scale...
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Method: Quantifying pathological progression from single-cell transcriptomic data with scPSS
- Samin Rahman Khan,
- M Saifur Rahman,
- M. Sohel Rahman,
- and Md Abul Hassan Samee
Genome Res. February 2026 36: 375-386; Published in Advance January 14, 2026, doi:10.1101/gr.280411.125
....scPSS identifies damaged cells and damage progression in mouse infarcted heart tissueWe validated scPSS using single-cell transcriptomic data from mouse hearts before and after myocardial infarction (MI) (Calcagno et al. 2022). The data set contains labeled cardiomyocytes (CMs) from three distinct regions...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...al. 2010) have found that CTCF regulates BCL6 expression by binding to specific intronic regions of BCL6 in a DNA methylation-sensitive manner, in which DNA methylation can prevent CTCF binding, leading to sustained BCL6 expression. Batlle-López et al. (2015) also claimed that CTCF binds...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...change in human and animal models have focused on DNA methylation. Multiple studies have characterized the DNA methylome response to both acute and chronic modes of resistance, high intensity, and endurance exercise in humans (Barrès et al. 2012; Nitert et al. 2012; Rowlands et al. 2014; Seaborne et al...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
...libraries were generated from 1–10 ng of total RNA from each replicate using the single-cell full-length mRNA kit (Vazyme N712) and TruePrep DNA library prep kit V2 (Vazyme TD502), according to the manufacturer's instructions. Quality control was performed using the fragment analyzer systems capillary...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...their cDNA, or in the case of ONT, the option of direct RNA sequencing. Early applications of these technologies have been constrained due to low throughput and high error rates. Recent advances in both long-read platforms have enabled high-throughput long-read transcriptome sequencing at high sequencing...
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Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
- Quanyou Cai,
- Lihui Lin,
- Xin Liu,
- and Jiekai Chen
Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
.... Corresponding authors: chen_jiekai@gibh.ac.cn, lin_lihui@gibh.ac.cnAbstractIntegration of single-cell and spatial transcriptomes represents a fundamental strategy to enhance spatial data quality. However, existing methods for mapping single-cell data to spatial coordinates struggle with large-scale data sets...
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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
...DNA samples. Leveraging somatic SNVs and fusions, LongSom found subclones with different predicted treatment outcomes. In summary, LongSom enables de novo variant detection without the need for normal samples, facilitating the study of cancer evolution, clonal heterogeneity, and treatment resistance...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
...Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics Vishvak Raghavan1,2,3, Yumin Zheng2, Yue Li1,3 and Jun Ding1,2,3 1School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada; 2Meakins...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
...Slide-seq (Rodriques et al. 2019), a spatial transcriptomics method, was used to profile kidney samples. There are in total 551,342 cells (DNA-barcoded beads) included in 19 Slide-seq data sets. Slide-seq generates short-read sequencing data that are equivalent to scRNA-seq data and were processed in the same way we...
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