Searching journal content for articles similar to Shao et al. 23 (4): 665.

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  1. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...) gene, while the expansion of a GGGGCC repeat intronic of C9orf72 gene has been linked to increased risk of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (Pandolfo 2009; DeJesus-Hernandez et al. 2011). VNTR expansions have also been implicated in several diseases (De Roeck et al...
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  2. 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
    ...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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  3. Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
    • Netanya Keil,
    • Carolina Monzó,
    • Lauren McIntyre,
    • and Ana Conesa
    Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
    ...are informative of raw data quality. Multisample visualizations of QC metrics are presented by experimental design factors to identify outliers. We introduce new metrics for (1) the identification of potentially under-annotated genes and putative novel transcripts and for (2) quantifying variation in junction...
  4. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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  5. 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
    ...strengths and caveats.RNA interference (RNAi), typically in the form of short interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), has been widely used to reduce TF levels by promoting degradation of the corresponding mRNA. Although inexpensive and relatively easy to implement, RNAi often results...
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  6. Method: TransMeta simultaneously assembles multisample RNA-seq reads
    • Ting Yu,
    • Xiaoyu Zhao,
    • and Guojun Li
    Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
    ...performs the best on both real and simulated data sets at both the meta-assembly and individual sample levels.It is critical for an RNA-seq experiment to determine the set of expressed genes and transcripts for the subsequent quantification and differential expression and splicing analyses. However...
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  7. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...phenotype (Nevins and Potti 2007). One key application of signature scoring is cell annotation, as it offers a highly efficient and reliable method for classifying cells into types and states (Neftel et al. 2019). Notably, the quality of gene signatures plays a critical role in this process, as the accuracy...
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  8. 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
    ...gene receptor clusters found within this region (Giglio et al. 2001). Individuals affected by 8p syndrome present with a variety of clinical phenotypes, including agenesis of the corpus callosum, epilepsy, and other neurodevelopmental delays (Vibert et al. 2022).Over the past several decades...
  9. Method: Parallel analysis of replication timing, gene expression and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. March 19, 2026 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...to detect CNVs with this 263 sequencing depth makes this approach cost-effective and scalable for clonal tracking, 264 integrity screenings, and cancer alterations studies, with the addition of joint profiling of RT and gene 265 regulation. 266 For Repli-seq analysis in PARTAGE, we took advantage of our...
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  10. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    ...-specific elongation rates of more than 3000 genes. By combining short time point sampling after synchronized RNAPII release into the gene body and a new computational framework to track the distance traveled by RNAPII, we greatly increase the number of genes for which it is possible to obtain elongation rates. Our...
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