Searching journal content for articles similar to Robinson et al. 22 (12): 2489.

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  1. Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
    • Joanna Delimata-Raczek,
    • Natalia Koralewska,
    • Bart Krist,
    • Magdalena Rakoczy,
    • Marek Figlerowicz,
    • and Ireneusz Stolarek
    Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
    ...of differentiation efficiency. All cells in culture were maintained at 37°C in incubators with 5% CO2. RNA extraction and cDNA synthesis The RNA was extracted from the iCMs on day 4 and day 30. Cells were first washedwith PBS and dissociated from the plate either by 3 min incubation in 37°C with PBS with EDTA (4 day...
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  2. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (s...
  3. 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
    ...incrementally over 8 h. At each time point, samples were collected for processing for both RNA sequencing and quantitative mass spectrometry. (B) Venn diagram depicting the overlap between the identified transcripts and proteins. (C) Bar graph of enriched (full color) and detected (transparent color) DNA damage...
  4. 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
    ...of centromeric regions that limits 319 DNA accessibility and favors conserved repair mechanisms, reducing the occurrence 320 of large-scale SVs (Kashi and King 2006). Sequence annotation revealed that over 60% 321 of INS inserted in satellite/center, satellite, and simple repeat regions harbored 322 inserted...
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  5. Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
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  6. 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
    ...of one modality from another. However, existing methods for cross-modality translation between single-cell RNA sequencing (scRNA-seq) and single-cell DNA methylation (scDNAm) data face limitations, including unidirectionality, inadequate modeling of context-specific DNA methylation...
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  7. 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
    ...metabolism and autophagy which are known 20 to play a crucial role in megakaryocytic differentiation, impacting the development and maturation 21 of megakaryocytes. Further, integrative analysis demonstrates that IPA site usage is associated 22 with lower DNA methylation within introns, supporting...
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  8. Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
    • Philipp Rentzsch,
    • Aaron Kollotzek,
    • Kaushik Ram Ganapathy,
    • Pejman Mohammadi,
    • and Tuuli Lappalainen
    Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
    ...that this approach will simplify the identification of disease-causing molecular processes and enhance the discovery of therapeutic targets.Since the advent of cDNA microarrays (Schena et al. 1995), differential gene expression profiling has been used to examine the characteristic gene regulatory changes...
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  9. Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
    ...elements, and tandem repeats. More generally, the DNA sequences omitted from current reference s are likely a source of substantial epigenetic activity. Expanding the nonreference results to a larger number of human s and epis can expose population variation with potential new insights on trait variation...
  10. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...combinations, which provides experimental evidence for species-adaptive encoding strategies.DNA methylation is a form of DNA epigenetic modification, which modulates the genetic performance without changing the DNA sequence (Moore et al. 2013). Numerous studies have shown that DNA methylation can alter...
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