Searching journal content for articles similar to Silva Pereira et al. 28 (9): 1383.

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  1. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    ...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
  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
    ...and ultimately enable functional classification of regulatory variants identified by population studies.Most genetic associations with human diseases and traits lie within noncoding regulatory DNA (Maurano et al. 2012). Genome-scale methods to analyze the function of noncoding regulatory elements within...
  3. 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
    ...applied to data generated by state-of-the-art ONT sequencing, highlighting its potential as a rapid, cost-efficient screening tool that can usefully complement experimental profiling efforts.Cross-predictions between different speciesTo evaluate the cross-species generalization capability of EnDeep4mC, we...
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  4. Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
    • Daffodil M. Canson,
    • Michael T. Parsons,
    • Gemma Moir-Meyer,
    • Troy Dumenil,
    • Gemma Montalban,
    • Erica Lin,
    • Terri P. McVeigh,
    • Aimee L. Davidson,
    • Shaun M. Bouckaert,
    • Matt Trau,
    • Darren Korbie,
    • and Amanda B. Spurdle
    Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
    ...Splice exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 BRCA1 and 72 BRCA2 variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact...
  5. 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
    ...sites, in line with the differential intensity of CTCF binding at these sites and the presence of motifs of different quality (Owens et al. 2019). Similar to the ATAC-seq experiments described above, Hi-C is performed on a population of cells. Therefore, a possible explanation for the quantitative...
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  6. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ...the complex sources of variability inherent to this problem domain (e.g., the nonuniformity of read coverage and variant density within the and across different populations or read length and error profiles of different sequencing platforms).Learning-based approaches, on the other hand, can detect complex...
  7. Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
    • Antonio Nappi,
    • Liubov Shilova,
    • Theofanis Karaletsos,
    • Na Cai,
    • and Francesco Paolo Casale
    Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
    ...2019). For instance, COAST weights variants based on their predicted deleteriousness (McCaw et al. 2023), whereas DeepRVAT employs a data-driven approach to learn aggregation functions from multiple annotations using a neural network (Clarke et al. 2024). Despite these improvements, a unified framework...
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  8. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...spike-ins of equal length but varying GC-content, MFE, and tertiary structure. Although an RNA of length k can form 4k sequences (Supplemental Fig. S1A), we constrained the design to eight variable sites within a 50-nt core, flanked by 8-nt poly(A) tails at each end. This yielded 48 spike-in variants...
  9. Method: Modeling gene interactions in polygenic prediction via geometric deep learning
    • Han Li,
    • Jianyang Zeng,
    • Michael P. Snyder,
    • and Sai Zhang
    Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
    ....e., variants with minor allele frequency [MAF] < 0.05 in the population). This methodology empowers several aspects of precision medicine, including disease prevention, early intervention, and personalized treatment (Gibson 2019; Konuma and Okada 2021; Polygenic Risk Score Task Force of the International...
    OPEN ACCESS ARTICLE
  10. Method: Variations in antibody repertoires correlate with vaccine responses
    • Yana Safonova,
    • Sung Bong Shin,
    • Luke Kramer,
    • James Reecy,
    • Corey T. Watson,
    • Timothy P.L. Smith,
    • and Pavel A. Pevzner
    Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
    ...pharmaceutical potential in terms of targeting unusual antigens (Burke et al. 2020), their role in the native immune response remains unclear.The challenge of finding IgQTLsPrevious immunosequencing studies have succeeded in linking variants in the human IGH locus to disease and vaccination efficacy (Thomson et...
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