Searching journal content for articles similar to Pontius et al. 17 (11): 1675.

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  1. 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
    ...Bio) and Oxford Nanopore Technologies (ONT), has markedly enhanced both the efficiency and accuracy of genomic studies (Sedlazeck et al. 2018). These technological advances have also propelled pan analyses. Initially developed for bacterial studies (Sherman and Salzberg 2020), the pan approach has now gained...
  2. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...for a CfxA2 beta-lactamase gene. We find clear recombination blocks for these AMR gene haplotypes, showcasing devider's ability to unveil evolutionary signals for heterogeneous mixtures.The presence of highly similar genomic sequences within a single organism or a group of organisms is common in biological...
  3. Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    • Ned Peel,
    • Samuel Martin,
    • Darren Heavens,
    • Douglas W. Yu,
    • Matthew D. Clark,
    • and Richard M. Leggett
    Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
    ...platform is currently the most well-known example of a real-time metagenomic analysis tool. Initially, ONT developed the EPI2ME Agent software, which featured several cloud-based analysis workflows including two popular metagenomic pipelines: What's In My Pot (WIMP) and Antimicrobial Resistance Mapping...
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  4. Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
    ...(Murphy et al. 2007; Davis et al. 2009; Montague et al. 2014; Li et al. 2016b; Buckley et al. 2020; Bredemeyer et al. 2021a, 2023). The motivation is to bring precision medicine to domestic cats in veterinary clinics and to advance conservation genomic initiatives in the 40+ other cat species...
  5. Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
    • Manuela Baquero Pérez,
    • Gertjan Laenen,
    • Isabelle Loïodice,
    • Mickaël Garnier,
    • Ugo Szachnowski,
    • Antonin Morillon,
    • Myriam Ruault,
    • and Angela Taddei
    Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
    ...U-seq; Methods) (Cucinotta et al. 2021) we define four classes of genes.View larger version: In this window In a new window Figure 3. Transcriptional output is scant, but homogeneous, in the quiescent population. (A) Representative Genome Browser views of genes classified according to binarized Rpb3-FLAG binding...
  6. Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
    • Anna Nordin,
    • Chaitali Chakraborty,
    • Mattias Jonasson,
    • Orgena Dano,
    • Gianluca Zambanini,
    • Pierfrancesco Pagella,
    • Silvia Remeseiro,
    • and Claudio Cantù
    Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
    ...by both CTCF and RAD21 (Fig. 2C). We decided to focus on these events and termed these 252 sites as CTCF Redistributions Under Wnt (Supplemental Table 1). When normalized and visualized via the Integrative Genome Viewer (IGV) (Robinson et al. 2023), nearby CTCF and RAD21 sites are comparable between cell...
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  7. Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    .... Although some of these data are publicly available, they are not analogous to the GIAB variant benchmarks.In animal genomics, method evaluation typically relies on indirect quality metrics owing to slight variations in context and software across studies. For example, we initially assessed the two variant...
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  8. Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
    • Ziyan Rao,
    • Min Zhang,
    • Shaodong Huang,
    • Chenyang Wu,
    • Yuheng Zhou,
    • Weijie Zhang,
    • Xia Lin,
    • and Dongyu Zhao
    Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
    ...aspects of cancer lncRNAs, including their expression patterns, genomic locations, and direct interactions with cancer driver PCGs, and developed a pipeline to identify candidate cancer driver lncRNAs. Finally, we validate the reliability of potential cancer driver lncRNAs through functional analysis...
  9. Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
    • Marlies E. Oomen,
    • A. Nicole Fox,
    • Inma Gonzalez,
    • Amandine Molliex,
    • Thaleia Papadopoulou,
    • Pablo Navarro,
    • and Job Dekker
    Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
    .... The average genomic size of mitotic loops is smaller in chicken (200–300 kb) compared to human (400–600 kb) and especially mouse (1–1.5 Mb). Interestingly, we find that this difference is correlated with the genomic length of q-arms in these species, a finding we confirm by microscopy measurements...
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  10. Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    • Shelley Reich,
    • Tobias Loschko,
    • Julie Jung,
    • Samantha Nestel,
    • Ralf J. Sommer,
    • and Michael S. Werner
    Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
    ...genes, which if expressed above a threshold, initiate downstream transcriptional changes observed at the end of the critical window (i.e., ≥60 h).View larger version: In this window In a new window Figure 2. A subset of the mouth-form GRN is environmentally responsive. (A–E) Volcano plots of genes...
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