Searching journal content for articles similar to Marioni et al. 18 (9): 1509.

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  1. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
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  2. 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
    ..., the ratio of the logFC values with counting exons or exons and introns was strongly correlated with gene length (Pearson R = 0.69, P-value < 0.01) (Fig. 3E). Overall, our results show technical artifacts induced by gene length–associated detection bias in snRNA-seq upon inclusion of intronic reads. We...
  3. 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
    ...), making it a versatile tool in single-cell genomics.Traditionally, steady-state mRNA levels have been assessed using qPCR or RNA-seq, but these approaches capture both primary and secondary responses and are influenced by RNA stability. To address this limitation, a variety of nascent RNA profiling...
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  4. Method: Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
    • Chiaowen Joyce Hsiao,
    • PoYuan Tung,
    • John D. Blischak,
    • Jonathan E. Burnett,
    • Kenneth A. Barr,
    • Kushal K. Dey,
    • Matthew Stephens,
    • and Yoav Gilad
    Genome Res. April 2020 30: 611-621; Published in Advance April 20, 2020, doi:10.1101/gr.247759.118
    ..., even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq...
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  5. Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
    • Chuanyuan Wang and
    • Zhi-Ping Liu
    Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
    ...diverse biological contexts and data sets, we demonstrate the efficiency, robustness, and superiority of DigNet, particularly in terms of reproducing cell type gene regulatory specificity. Moreover, DigNet achieves single-cell-specific GRN inference from scRNA-seq data, identifying crucial regulatory...
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  6. Research: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
    • Jeremiah H. Li,
    • Chase A. Mazur,
    • Tomaz Berisa,
    • and Joseph K. Pickrell
    Genome Res. April 2021 31: 529-537; Published in Advance February 3, 2021, doi:10.1101/gr.266486.120
    ...proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using...
  7. Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
    • Christine R. Keenan,
    • Hannah D. Coughlan,
    • Nadia Iannarella,
    • Andres Tapia del Fierro,
    • Andrew Keniry,
    • Timothy M. Johanson,
    • Wing Fuk Chan,
    • Alexandra L. Garnham,
    • Lachlan W. Whitehead,
    • Marnie E. Blewitt,
    • Gordon K. Smyth,
    • and Rhys S. Allan
    Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
    ...of the three-dimensional (3D) nucleome through Lamin B1 ChIP-seq and in situ Hi-C.ResultsLoss of Suv39-dependent H3K9me3 results in paradoxical gene repressionTo investigate the molecular consequences of heterochromatin loss, we performed RNA-seq on Suv39DKO and littermate control CD4+ CD8+ double-positive (DP...
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  8. Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
    • Hideya Kawaji,
    • Marina Lizio,
    • Masayoshi Itoh,
    • Mutsumi Kanamori-Katayama,
    • Ai Kaiho,
    • Hiromi Nishiyori-Sueki,
    • Jay W. Shin,
    • Miki Kojima-Ishiyama,
    • Mitsuoki Kawano,
    • Mitsuyoshi Murata,
    • Noriko Ninomiya-Fukuda,
    • Sachi Ishikawa-Kato,
    • Sayaka Nagao-Sato,
    • Shohei Noma,
    • Yoshihide Hayashizaki,
    • Alistair R.R. Forrest,
    • Piero Carninci,
    • and The FANTOM Consortium
    Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
    ...in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies...
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  9. Resource: Differential expression in RNA-seq: A matter of depth
    • Sonia Tarazona,
    • Fernando García-Alcalde,
    • Joaquín Dopazo,
    • Alberto Ferrer,
    • and Ana Conesa
    Genome Res. December 2011 21: 2213-2223; Published in Advance September 8, 2011, doi:10.1101/gr.124321.111
    ...if compared to the other two data sets, which resulted in fewer significant genes declared at the highest SDs (Fig. 7) and an erratic behavior when considering other parameters analyzed. High technical reproducibility has been claimed for the RNA-seq technology (Marioni et al. 2008; Mortazavi et al. 2008...
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  10. Resource: Synthetic spike-in standards for RNA-seq experiments
    • Lichun Jiang,
    • Felix Schlesinger,
    • Carrie A. Davis,
    • Yu Zhang,
    • Renhua Li,
    • Marc Salit,
    • Thomas R. Gingeras,
    • and Brian Oliver
    Genome Res. September 2011 21: 1543-1551; Published in Advance August 4, 2011, doi:10.1101/gr.121095.111
    ...and sufficient read depth are important for quantifying transcript isoforms generated by alternative splicing, promoters, and termination sites. Discussion Here we characterized a complex pool of synthetic control RNAs for use in RNA-seq experiments. We assessed the precision (repeatability and reproducibility...
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