Searching journal content for articles similar to Boffelli et al. 14 (12): 2406.

Displaying results 1-10 of 107
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  1. 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
    ..., extrapolation to uncharacterized prokaryotes without methyltransferase annotation remains challenging.Looking forward, as genomic and epigenomic data sets continue to expand, covering increasingly diverse species and methylation systems, we anticipate that models like EnDeep4mC will gain further robustness...
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  2. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...the populations of the two nematodes, driving their incompatibilities, remain elusive.Here we performed a comparative pan analysis across populations of C. briggsae and C. nigoni to elucidate the genomic divergences underlying their speciation. We generated high-quality assemblies and annotations for seven C...
  3. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ...effectively. Moreover, ScPGE greatly reduces computational demands for modeling by using discrete cCREs instead of the entire genomic region flanking target genes, facilitating rapid training and deployment for new cell types. To quantify its computational demand, we systematically evaluated the model...
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  4. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...types (20 kbp) of pCht satellites across the subterminal caps of three African great apes. The highest proportion of shared pCht types among chimpanzees and gorillas are indicated (red line).Intraspecies sequence comparisons of the subterminal satellites show that some nonhomologous chromosomes are more...
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  5. Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
    • Byron J. Smith,
    • Chunyu Zhao,
    • Veronika Dubinkina,
    • Xiaofan Jin,
    • Liron Zahavi,
    • Saar Shoer,
    • Jacqueline Moltzau-Anderson,
    • Eran Segal,
    • and Katherine S. Pollard
    Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
    ...represents a major upgrade to the pan profiling pipeline intended to improve the completeness, curation, and interpretability of gene abundance estimates. We updated the pan database construction and gene annotation process, as well as the profiling algorithm, and describe these in the Methods section...
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  6. Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
    • Fu Xiang Quah,
    • Miguel Vasconcelos Almeida,
    • Moritz Blumer,
    • Chengwei Ulrika Yuan,
    • Bettina Fischer,
    • Kirsten See,
    • Ben Jackson,
    • Richard Zatha,
    • Bosco Rusuwa,
    • George F. Turner,
    • M. Emília Santos,
    • Hannes Svardal,
    • Martin Hemberg,
    • Richard Durbin,
    • and Eric Miska
    Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
    ...% in 910 African individuals) (Sherman et al. 2019). Direct comparisons of these values are not straightforward owing to variations in methodologies and lack of universal definitions of pangenomic terms (Sherman and Salzberg 2020), and it remains to be seen whether large genomic differences must...
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  7. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    ...-read sequencing reveals dynamic -wide SVs in three clinical isolates. (A) Genome-wide genomic landscape: Gene content and TE content in 5000 bp windows of the C. albicans reference . Distribution of SVs in SC5314, L26, and P75063. Colors indicate the SV type in comparison with the reference : green...
  8. Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    ...genomics and phylogeny-aware statistical methods, we quantify the association between the presence of seven widespread defense systems and the abundance of MGEs in the s of 196 bacterial and one archaeal species. We also calculate the differences in the rates of gene gain and loss between lineages...
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  9. Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
    • Shujun Ou,
    • Armin Scheben,
    • Tyler Collins,
    • Yinjie Qiu,
    • Arun S. Seetharam,
    • Claire C. Menard,
    • Nancy Manchanda,
    • Jonathan I. Gent,
    • Michael C. Schatz,
    • Sarah N. Anderson,
    • Matthew B. Hufford,
    • and Candice N. Hirsch
    Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
    ..., there have been a limited number of pan studies of TE variation within species owing to challenges in assembling and annotating genomic regions containing these highly repetitive elements (Ou et al. 2019). Instead, the vast majority of studies characterizing TE content have used resequencing data mapped...
  10. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...from annotation errors, because they are typically detected by comparative genomics approaches. These in turn rely on the automatic prediction of protein-coding open reading frames (ORFs) and sequence similarity searches between species, both potential sources of artifacts in the form of spurious ORFs...
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