Searching journal content for articles similar to Anders et al. 22 (10): 2008.

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  1. Method: Tree-based differential testing using inferential uncertainty for RNA-seq
    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    ...-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.RNA-seq has become the de facto technology for measuring the expression profiles of different genomic...
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  2. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...). To evaluate the feasibility of using 10x snRNA-seq data for detecting APA events, we first analyzed gene body coverage across different tissues and cell types. The results showed that 10x snRNA-seq reads were concentrated near the 3′-end regions of genes (Fig. 1A), enabling reliable detection of 3′ UTR...
  3. 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
    ..., -guided methods are more commonly used because they are usually more accurate (Shao and Kingsford 2017).Transcriptomic studies involve multiple samples. Constructing a consensus transcriptome from multiple samples is critical in an RNA-seq experiment for the subsequent quantification and differential...
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  4. Research: Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
    • John T. Chamberlin,
    • Younghee Lee,
    • Gabor T. Marth,
    • and Aaron R. Quinlan
    Genome Res. February 2024 34: 179-188; Published in Advance February 14, 2024, doi:10.1101/gr.278253.123
    ...longer genes results in increased statistical power to detect differential expression in these genes and vice versa. This phenomenon is similar to the fragmentation bias in conventional RNA-seq, in which longer transcripts yield more fragments that can be sequenced and, in turn, more stable expression...
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  5. Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
    • Yongkang Long,
    • Bin Zhang,
    • Shuye Tian,
    • Jia Jia Chan,
    • Juexiao Zhou,
    • Zhongxiao Li,
    • Yisheng Li,
    • Zheng An,
    • Xingyu Liao,
    • Yu Wang,
    • Shiwei Sun,
    • Ying Xu,
    • Yvonne Tay,
    • Wei Chen,
    • and Xin Gao
    Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
    ...rate (FPR) ranges from 30% to 50% (Shah et al. 2021). In addition, these computational methods mainly focus on APA within 3′ UTR. This might be due to the fact that drop of RNA-seq coverage across exon–intron boundaries impacts their detection of splicing-coupled APA, such as intronic polyadenylation...
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  6. Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    ...and indexed single-cell cDNA, which allows analysis to be combined with existing short-read RNA-seq data sets. In our investigation of BTK and SF3B1 genes in samples from patients with chronic lymphocytic leukemia (CLL), we detect SF3B1 isoforms and mutations with high sensitivity. Integration with short...
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  7. Method: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
    • Benjamin Kaminow,
    • Sara Ballouz,
    • Jesse Gillis,
    • and Alexander Dobin
    Genome Res. April 2022 32: 738-749; Published in Advance March 7, 2022, doi:10.1101/gr.275613.121
    ..., or other techniques. The human is no exception, and considering how best it should be summarized remains a crucial problem, which may have a use-dependent solution: What is essential for disease variant detection may not be necessary for RNA-seq alignment, and vice versa. The current reference has had...
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  8. Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
    • Steffen Erkelenz,
    • Stephan Theiss,
    • Wolfgang Kaisers,
    • Johannes Ptok,
    • Lara Walotka,
    • Lisa Müller,
    • Frank Hillebrand,
    • Anna-Lena Brillen,
    • Michael Sladek,
    • and Heiner Schaal
    Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
    ...site usage identifies noise candidatesIn our fibroblast data set, exon junction reads widely differed across several orders of magnitude due to differential gene expression and RNA-seq coverage. In order to adequately compare detected splice site usage across genes, we calculated the gene...
  9. Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
    • Anushka Gupta,
    • Farnaz Shamsi,
    • Nicolas Altemose,
    • Gabriel F. Dorlhiac,
    • Aaron M. Cypess,
    • Andrew P. White,
    • Nir Yosef,
    • Mary Elizabeth Patti,
    • Yu-Hua Tseng,
    • and Aaron Streets
    Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
    ...identifies the same preadipocyte populations as scRNA-seq and detects biologically relevant differential expressionTo evaluate the efficacy of snRNA-seq for recovering transcriptional heterogeneity, we sequenced the nuclear transcriptome of single preadipocytes from the white and brown lineages. Unsupervised...
  10. Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
    • Zhaozhao Zhao,
    • Qiushi Xu,
    • Ran Wei,
    • Weixu Wang,
    • Dong Ding,
    • Yu Yang,
    • Jun Yao,
    • Liye Zhang,
    • Yue-Qing Hu,
    • Gang Wei,
    • and Ting Ni
    Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
    ...(Supplemental Fig. S3). Although 3′-end sequencing strategies such as 3′-seq coupled with dedicated bioinformatic pipelines can identify IPA sites and detect changes in IPA site usage between different conditions, they are less extensively used in diverse biological processes than standard RNA-seq. In addition...
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