Searching journal content for articles similar to Hilton and Gersbach 25 (10): 1442.

Displaying results 1-10 of 886
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  1. Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
    • Sophia N. Lee,
    • Erin C. Banda,
    • Lu Qiao,
    • Sarah L. Thompson,
    • Karan Singh,
    • Ryan A. Hagenson,
    • Teresa Davoli,
    • Stefan F. Pinter,
    • and Jason M. Sheltzer
    Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
    ...with dysregulated interferon signaling (Sullivan et al. 2016).Invdupdel(8p) antagonizes NDAs the revertant line can serve as an isogenic euploid control to the proband line, our chromosome engineering approach enables us to begin investigating how invdupdel(8p) alters neurodevelopment and causes other physiological...
  2. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
  3. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...prediction and emphasize the importance of explainable ML approaches, integration of prior information, and parameter optimization. The AIGP toolkit enables automated model optimization and interpretability, making ML-driven genomic selection more accessible and providing new tools to support genomic...
  4. Method: Minimizing reference bias with an imputed personalized reference
    • Kavya Vaddadi,
    • Mao-Jan Lin,
    • Sina Majidian,
    • Taher Mun,
    • and Ben Langmead
    Genome Res. April 2026 36: 740-753; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
    ...Genomes Project (1 KGP) (The 1000 Genomes Project Consortium et al. 2015) and Structural Variation Consortium (HGSVC) (Ebert et al. 2021; Logsdon et al. 2025). Because these panels are phased, they enable us to compute phased, diploid haplotypes, fully leveraging the genetic variation and linkage...
    OPEN ACCESS ARTICLE
  5. 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 genomic regions in the preprocessed scDNAm data set. Leveraging these inputs, scBOND enables bidirectional omic translation: predicting scRNA-seq data from scDNAm data through Ψr(Γm→r(Φm(Xm))) and predicting scDNAm data from scRNA-seq data through Ψm(Γr→m(Φr(Xr))). Detailed specifications of each...
    OPEN ACCESS ARTICLE
  6. Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
    • Yali Zhang,
    • Yayi Zhou,
    • Yangyang Chen,
    • Xueyu Wang,
    • Boyan Hu,
    • Shahid Siddique,
    • Romnick A. Latina,
    • Veronica I. Casey,
    • Dexin Bo,
    • Yucheng Liao,
    • Min Zhang,
    • Ming Sun,
    • Fengjuan Zhang,
    • and Dadong Dai
    Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
    ...Zhang6, Ming Sun2,3, Fengjuan Zhang1 and Dadong Dai2,3,4 1State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China; 2National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan...
    OPEN ACCESS ARTICLE
  7. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...in incomplete knockdown and can suffer from off-target effects, which complicate interpretation of transcriptional changes.Genome editing approaches, such as CRISPR–Cas9-mediated knockout (Nakamura et al. 2021), enable permanent removal of a TF. Knockouts are powerful for defining essential regulatory roles...
    OPEN ACCESS ARTICLE
  8. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...David R. Lougheed1,2, Tomi Pastinen3 and Guillaume Bourque1,2,4 1Canadian Centre for Computational Genomics, Montréal, Québec H3A 0G1, Canada; 2Department of Human Genetics, McGill University, Montréal, Québec H3A 0G1, Canada; 3Genomic Medicine Center, Children's Mercy Hospital and Research...
  9. 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
    ...Methods 7: 461–472. doi:10.1038/nmeth.1459 ↵Galeone V, Dabernig-Heinz J, Lohde M, Brandt C, Kohler C, Wagner GE, Hölzer M. 2025. Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications. BMC Genomics 26: 394. doi...
    OPEN ACCESS ARTICLE
  10. Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
    • Clotilde Garrido,
    • Cintia Gómez-Muñoz,
    • Etienne Kornobis,
    • Nicolas Agier,
    • Oana Ilioaia,
    • Gilles Fischer,
    • and Zhou Xu
    Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
    ...directly from ONT sequencing reads. It is highly versatile, as it can be applied to any S. cerevisiae sequencing data set without any particular telomere enrichment step, enabling the investigation of TL distribution diversity across numerous strains.TL distributions are highly diverse across S. cerevisiae...
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