Searching journal content for articles similar to Taylor et al. 26 (11): 1600.

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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...in a final panel size of 22,314 regions for Panel 1 and 48,507 regions for Panel 2. The software then designed KAPA Target Enrichment Probes covering the inputted regions. These probes are 120 bp in length and, following hybridization with genomic DNA, can be captured through a bead-based capture method...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...%) and in Supplemental Figure S53, A–C, through Supplemental Figure S55, A–C (for an error rate of 20%). EquiRep is able to make better or similar predictions in all cases, indicating that its algorithm is the least affected by the presence of embedding k-mers within repeat units.Evaluation using human satellite DNA...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...ESCs (two-tailed Wilcoxon rank-sum test, P = 0.89) (Supplemental Fig. 9).Most dnSNVs are thought to arise from errors in DNA replication, with later-replicating regions of the exhibiting elevated mutation rates compared with early-replicating regions (Stamatoyannopoulos et al. 2009). Using published...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...and epigenomic data. We develop and apply a computational framework 74 called IPAseek for systematic identification and quantification of IPA events and use this approach 75 to characterize lineage-associated patterns of IPA site usage. We further examine the relationship 76 between DNA methylation and IPA...
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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
...:10.1177/106002808201600602 Fayyad N, Kobaisi F, Beal D, Mahfouf W, Ged C, Morice-Picard F, FayyadKazan M, Fayyad-Kazan H, Badran B, Rezvani HR, et al. 2020. Xeroderma pigmentosum C (XPC) mutations in primary fibroblasts impair base excision repair pathway and increase oxidative DNA damage. Front...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
...a positional bias in colibactin-induced mutations in bacteria (near the terminus).Our genetic screen uncovered that homologous recombination, an error-free repair pathway, plays a major role in mitigating colibactin-induced DNA damage. However, results from our mutation accumulation experiments revealed...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...network to dynamically assign input cells to specialized expert subnetworks. Given the complex interactions in DNA methylation and gene expression across different genomic regions, we further incorporate a self-attention mechanism and a feature recalibration module to effectively model long...
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Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
...of reads usable to study RNA translation. For low-input RNase footprinting conditions, the biotinylated oligonucleotide pulldown approach can decrease RNA amount and cause the PCR overamplification issue. However, the CRISPR-based depletion of unwanted fragments in the DNA library could be a promising...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...individuals, the Genomic DNA Isolation Kit from Norgen Biotek was used for DNA extraction, the NEBNext Ultra II DNA Kit for library preparation (DNA input 10 ng), and an Illumina HiSeq 2500 device for paired-end sequencing (2 × 101 cycles). Data were extracted using Illumina's bcl2fastq v2.20.0.422. Read...
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