Searching journal content for articles similar to Foulk et al. 25 (5): 725.

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  1. 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
    ...distribution to derive mean and standard deviation parameters (Fig. 3A, left). We then applied this parameterized model to the aggregated sequencing counts (Supplemental Fig. S6); discrepancies between the predicted and observed data revealed GC-content-related biases (Fig. 3A, right). We repeated this process...
  2. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...critical insights into transcription dynamics. Here, we combine transient transcriptome sequencing with transcription start site sequencing (TT-TSS-seq) to accurately map and quantify transcription initiation sites from nascent transcripts. Because transient metabolic labeling yields low-input RNA, we...
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  3. Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
    • Conghui Li,
    • Honghong Wang,
    • Zhinang Yin,
    • Pingping Fang,
    • Ruijing Xiao,
    • Ying Xiang,
    • Wen Wang,
    • Qiuzi Li,
    • Beili Huang,
    • Jian Huang,
    • and Kaiwei Liang
    Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
    ...understanding of G4 biology toward therapeutically targeting G4s in human diseases.G-quadruplexes (G4s) are four-stranded intramolecular structures that arise from the self-stacking of two or more guanine quartets (G-quartets), in which the four guanine molecules form a square planar arrangement in a cyclic...
  4. Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
    ...the many introns of a human gene are removed can substantially influence AS, while nascent RNA polyadenylation can affect RNA stability and decay. However, how splicing order and poly(A) tail length are regulated by genetic variation has never been explored. Here, we used direct RNA nanopore sequencing...
  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
  6. Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
    • Niccoló Tesi,
    • Alex Salazar,
    • Yaran Zhang,
    • Sven van der Lee,
    • Marc Hulsman,
    • Lydian Knoop,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Anne-Fleur Schneider,
    • Maartje Pennings,
    • Kristel Sleegers,
    • Erik-Jan Kamsteeg,
    • Marcel Reinders,
    • and Henne Holstege
    Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
    ...automatically adapts to sequencing error-rates and coverage levels per target region. TREAT integrates otter to enable end-to-end unified workflow for de novo motif characterization and downstream analysis, including TR visualization, outlier-based, and case-control comparisons (see Methods; Fig. 1A). Both...
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  7. 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
    ..., and four origin recognition complex (ORC) components are all enriched in GSC-like cells compared with CySC-like cells (Table 1).View this table: In this window In a new window Table 1. Composition and function of select DNA replication and chromatin regulation complexesTo control for potential biases...
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  8. 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
    ...-read technologies are unbiased and reveal a critical barrier to assembling sequences near repetitive regions. As large-scale sequencing projects move toward telomere-to-telomere assemblies in a wide range of organisms, recognizing and addressing these biases will be important to achieving truly complete...
  9. Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
    • Natnatee Dokmai,
    • Kaiyuan Zhu,
    • S. Cenk Sahinalp,
    • and Hyunghoon Cho
    Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
    ...the estimated phased haplotypes of the target sample through iterative sampling. We briefly outline the computation involved in each sampling iteration below.In each iteration, a small but targeted conditioned reference panel is constructed, which is a subset of haplotypes from the original reference panel...
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  10. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA enables the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6...
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