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Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
- Sara González,
- Alicia García,
- Enrique Vázquez,
- Rebeca Serrano,
- Mar Sánchez,
- Luis Quintales,
- and Francisco Antequera
Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
...Research 1533 www..org S1A). In this case, the impact was lower than in the 1_6 strain and affected preferentially the region encompassing these three nucleosomes, as revealed by the enhanced sensitivity to MNase of their linker regions (Fig. 1A, panel 1_3). To quantitatively measure the differences...
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ARTICLE: Genomic Analysis of Caenorhabditis elegans Reveals Ancient Families of Retroviral-like Elements
- Nathan J. Bowen and
- John F. McDonald
Genome Res. October 1, 1999 9: 924-935; doi:10.1101/gr.9.10.924
...: 335 – 340 . Genomic Analysis of Caenorhabditis elegans Reveals Ancient Families of Retroviral-like Elements Nathan J. Bowen and John F. McDonald 1 Department of Genetics, University of Georgia, Athens, Georgia 30602 USA View larger version: In this window In a new window Figure 1. Cer protein...
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ARTICLE: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
- Nathan J. Bowen,
- I. King Jordan,
- Jonathan A. Epstein,
- Valerie Wood,
- and Henry L. Levin
Genome Res. September 2003 13: 1984-1997; doi:10.1101/gr.1191603
...into the of the host. LTR retrotransposons are also genetically similar to endogenous retroviruses in that they are integrated in the germline of their host. Therefore, LTR retrotransposons serve as excellent model systems for understanding the evolutionary impact that they and endogenous retroviruses have on the host...
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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
...in wax biosynthesis and cuticle development, pointing to an epidermal identity (Supplemental Data Set S1). For example, genes encoding VERY-LONG-CHAIN ALDEHYDE DECARBONYLASE 3 (CER3) and CER8, required for cuticle biosynthesis (Lü et al. 2009), are strongly expressed in cells of this cluster (Fig. 1D...
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Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...for Amphimedon distal versus proximal cis-regulatory regions. Motifs are ordered according to their importance. Every dot in the model represents a peak used for the training of the XGB model. The SHAP values (x-axis) show the impact on the prediction. Color reflects the motif count in the peak. The name, class...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...of mice (Fraser et al. 2011). Here we apply a similar framework to study the impact of natural selection on translation using ribosome profiling in hybrids of closely related species of yeast. Unlike previous studies of translational divergence, which have either used codon usage as a proxy...
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ARTICLES: Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.
- T M Smith,
- M K Lee,
- C I Szabo,
- N Jerome,
- M McEuen,
- M Taylor,
- L Hood,
- and M C King
Genome Res. November 1996 6: 1029-1049; doi:10.1101/gr.6.11.1029
...elements. In Impact of short interspersed elements (SINEs) on the host (ed. RJ. Maraia), pp. 25–41. Landes Company, Austin, TX. Kelsey, J.L., ed. 1993 . Breast cancer. Epidemiol. Rev. 15 : 1 – 263 . Korenberg, J. and Rykowski. M. 1988 . Human organization: Alu , lines and the molecular structure...
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