Searching journal content for articles similar to Gibb and Padovan 4 (1): 56.

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  1. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
  2. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ...) Models are compared based on their ability to predict experimental ATAC-seq at 4-bp resolution from an input of 2048-bp long DNA sequences. (B) Models based on existing methods include CNN, LSTM, and dCNN-based architectures. Each model has a convolution-based stem to extract genomic features. (C) Models...
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  3. Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    • Inswasti Cahyani,
    • John Tyson,
    • Nadine Holmes,
    • Josh Quick,
    • Chris Moore,
    • Nick Loman,
    • and Matthew Loose
    Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
    ...; SPRI beads are mostly used for polymerase chain reaction (PCR) cleanup where the fragment length is much shorter (Rodrigue et al. 2010; Stortchevoi et al. 2020). In addition, the library is a complex of motor protein and DNA, and so alcohol-based precipitation and washes are not compatible. In our...
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  4. Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
    • Abigail L. Lind,
    • Nathan A. McDonald,
    • Elias R. Gerrick,
    • Ami S. Bhatt,
    • and Katherine S. Pollard
    Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
    ...-LSK110 kit LSK109 (Oxford Nanopore Technologies), sequenced on a full R10.4.1 flow cell, and basecalled with Dorado version 0.5.3 (https://github.com/nanoporetech/dorado).Short-read Illumina DNA and RNA libraries were prepared using the KAPA HyperPlus PCR-free and KAPA mRNA capture kits (Roche...
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  5. 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
    ...sets of 11 species using 14 feature encodings respectively, taking CNN as an example (Supplemental Fig. S6).As shown in Figure 4A, the 4mC data sets from EpiTEAmDNA were categorized into plant, animal, and microbial groups. Cross-prediction results showed that the diagonal species achieved the highest...
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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
    ...DNAm sequencing technologies, the scDNAm data often suffer from low coverage, high sparsity, and substantial technical noise (Kremer et al. 2024). These limitations arise from factors such as limited DNA input, bisulfite conversion inefficiencies, and sequencing dropouts, which together compromise the reliability...
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  7. 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
    ...were prepared with a starting amount of 300 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay kit, in a Qubit 2.0 Fluorometer (Life Technologies). All libraries from the two...
  8. 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
    ...analog bromodeoxyuridine (BrdU) to label replicating DNA. Next, GSC-like or CySC-like nuclei were extracted and sorted via flow cytometry into four S-phase fractions corresponding to early, early-mid, late-mid, and late S phase, based on their DNA content (Fig. 4A; Supplemental Fig. S5A–C). Brd...
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  9. Review: The structure, function, and evolution of plant centromeres
    • Matthew Naish and
    • Ian R. Henderson
    Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
    ...that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution...
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  10. Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    • Maria Grazia Mendoza-Ferri,
    • Gwendoline Lozachmeur,
    • Maximilien Duvina,
    • Laetitia Perret,
    • Didier Merciris,
    • Anne Gigout,
    • and Marco Antonio Mendoza-Parra
    Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
    ...(G) primer presenting a known adapter sequence at its 5′-extremity (Adpt1), followed by Klenow polymerase extension (Fig. 1E). Finally, DNA arrays are exposed again to alkaline conditions for releasing the elongated complementary DNA sequence and are collected in a tube for performing two rounds of PCR...
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