Searching journal content for articles similar to Tu et al. 22 (10): 2079.

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  1. Resource: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
    • Jian Ming Khor,
    • Jennifer Guerrero-Santoro,
    • William Douglas,
    • and Charles A. Ettensohn
    Genome Res. September 2021 31: 1680-1692; Published in Advance July 30, 2021, doi:10.1101/gr.275684.121
    ...widely used for the identification and analysis of CRMs in sea urchins (Cameron et al. 2004). One criterion was applied in selecting eRNAs; we required that the nearest gene have a known spatial pattern of expression based on prior WMISH analysis, so that any tissue-specific pattern of reporter...
  2. RESOURCE: Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters
    • Albert J. Poustka,
    • Detlef Groth,
    • Steffen Hennig,
    • Sabine Thamm,
    • Andrew Cameron,
    • Alfred Beck,
    • Richard Reinhardt,
    • Ralf Herwig,
    • Georgia Panopoulou,
    • and Hans Lehrach
    Genome Res. December 2003 13: 2736-2746; doi:10.1101/gr.1674103
    ..., and assembly of the of the sea urchin Strongylocentrotus purpuratus . Because sea urchins occupy an important phylogenetic position as one of the most basal deuterostomes, the study of the gene content of their or the composition of their transcriptome is essential to analyze the origin of deuterostomes...
  3. Method: General approach for in vivo recovery of cell type-specific effector gene sets
    • Julius C. Barsi,
    • Qiang Tu,
    • and Eric H. Davidson
    Genome Res. May 2014 24: 860-868; Published in Advance March 6, 2014, doi:10.1101/gr.167668.113
    ...and temporal map of C. elegans gene expression. Genome Res 21: 325–341. Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. 2012. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res 22: 2079–2087. Tu Q, Cameron RA, Davidson EH. 2014. Quantitative...
  4. Research: Transposable elements drive the evolution of metazoan zinc finger genes
    • Jonathan N. Wells,
    • Ni-Chen Chang,
    • John McCormick,
    • Caitlyn Coleman,
    • Nathalie Ramos,
    • Bozhou Jin,
    • and Cédric Feschotte
    Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
    ...(Imbeault et al. 2017). In both cases, we found good agreement between the simpler ORF counts and higher-quality estimates based on gene annotations (respectively, Spearman's rho = 0.91, P-value = 2.6 × 10−59; rho = 0.97, P-value = 1.7 × 10−5) (Supplemental Fig. 4B,C).Correlation between ZNFs...
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  5. Research: Cnidarian microRNAs frequently regulate targets by cleavage
    • Yehu Moran,
    • David Fredman,
    • Daniela Praher,
    • Xin Z. Li,
    • Liang Meng Wee,
    • Fabian Rentzsch,
    • Phillip D. Zamore,
    • Ulrich Technau,
    • and Hervé Seitz
    Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
    ...R-2030 shows a similar expression pattern to its host/target gene, and there is no support in the transcriptome for independent transcription of the intronic region, it is clear that the expression of the miRNA and the hosting target gene are tightly linked (Fig. 5A; unpubl.). Thus, miR-2030 is part...
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  6. PERSPECTIVE: Raising the estimate of functional human sequences
    • Michael Pheasant and
    • John S. Mattick
    Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
    ...included 83% of RefSeq annotated genes ( Waterston et al. 2002 ; Chiaromonte et al. 2003 ; Roskin et al. 2003 ). Subsequent studies seeking to identify the particular segments under selection report similar results, including the most recent finding that 5% of bases are confidently predicted as being under...
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