Searching journal content for articles similar to Andrie et al. 24 (12): 2000.

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  1. Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
    • Can Cenik,
    • Elif Sarinay Cenik,
    • Gun W. Byeon,
    • Fabian Grubert,
    • Sophie I. Candille,
    • Damek Spacek,
    • Bilal Alsallakh,
    • Hagen Tilgner,
    • Carlos L. Araya,
    • Hua Tang,
    • Emiliano Ricci,
    • and Michael P. Snyder
    Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
    ...-bound mRNA segments. The sequences of ribosome-protected mRNA fragments can then be used to deduce the number of ribosomes per message in conjunction with RNA-seq data. We integrated thesemeasurements with quantitative proteomics to reveal a comprehensive view of the variation in gene expression programs...
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  2. 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 Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis- and trans -acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority...
  3. Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
    • Xu Zhang,
    • Andrew J. Cal,
    • and Justin O. Borevitz
    Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
    ...abundance through nonsense-mediated decay. In Arabidopsis, eQTL mapping has been reported using recombinant inbred lines (RILs) (DeCook et al. 2006; Keurentjes et al. 2007; West et al. 2007). Linkage mapping in RILs can potentially map local regulatory variation segregating between parental lines...
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  4. LETTER: Nucleotide Frequency Variation Across Human Genes
    • Elizabeth Louie,
    • Jurg Ott,
    • and Jacek Majewski
    Genome Res. December 2003 13: 2594-2601; Published in Advance January 1, 2003, doi:10.1101/gr.1317703
    ...and identify motifs that are overrepresented within regulatory regions. By clustering and aligning such sequences, we recognize families of putative regulatory elements involved in exonic and intronic splicing control, and 3′ mRNA processing. Some of our motifs have been identified in prior theoretical...
  5. Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Daniel A. Skelly,
    • Marnie Johansson,
    • Jennifer Madeoy,
    • Jon Wakefield,
    • and Joshua M. Akey
    Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
    ...a longer persistence time of immature mRNAs or a higher percentage of intron retention in mature mRNA than for the RM allele. In addition to allele-specific alternative splicing, we found genes that appeared to demonstrate allele-specific variation in transcriptional start or stop sites. For example...
  6. Letter: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    • Jeremy R. Sanford,
    • Xin Wang,
    • Matthew Mort,
    • Natalia VanDuyn,
    • David N. Cooper,
    • Sean D. Mooney,
    • Howard J. Edenberg,
    • and Yunlong Liu
    Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108
    ...site selection (for review, see Lin and Fu 2007 ). In cultured cells, SFRS1 shuttles between the nucleus and the cytoplasm and also participates in post-splicing RNA processing reactions, including mRNA export, stability, nonsense-mediated decay, and translation ( Caceres et al. 1998 ; Huang and Steitz...
  7. Methods: Heritability of alternative splicing in the human genome
    • Tony Kwan,
    • David Benovoy,
    • Christel Dias,
    • Scott Gurd,
    • David Serre,
    • Harry Zuzan,
    • Tyson A. Clark,
    • Anthony Schweitzer,
    • Michelle K. Staples,
    • Hui Wang,
    • John E. Blume,
    • Thomas J. Hudson,
    • Rob Sladek,
    • and Jacek Majewski
    Genome Res. August 2007 17: 1210-1218; doi:10.1101/gr.6281007
    ..., and that such variation among individuals is heritable and genetically controlled. The human is estimated to contain ∼20,000–25,000 genes, and recent studies suggest that ∼50%–75% of multi-exon genes undergo alternative splicing (AS), generating multiple mRNA isoforms and greatly increasing human proteomic diversity...
  8. Research: Accumulation of RNA on chromatin disrupts heterochromatic silencing
    • Cornelia Brönner,
    • Luca Salvi,
    • Manuel Zocco,
    • Ilaria Ugolini,
    • and Mario Halic
    Genome Res. July 2017 27: 1174-1183; Published in Advance April 12, 2017, doi:10.1101/gr.216986.116
    ...complex involved in RNA surveillance, transcription elongation, RNA export, and DNA repair (Collart and Panasenko 2012; Miller and Reese 2012; Wahle and Winkler 2013; Inada and Makino 2014). The Ccr4-Not complex is the primary deadenylase and is essential for downstream decapping and mRNA decay by Xrn1...
  9. Perspective: Human genomic disease variants: A neutral evolutionary explanation
    • Joel T. Dudley,
    • Yuseob Kim,
    • Li Liu,
    • Glenn J. Markov,
    • Kristyn Gerold,
    • Rong Chen,
    • Atul J. Butte,
    • and Sudhir Kumar
    Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111
    ...variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have...
  10. Method: Prioritizing candidate disease genes by network-based boosting of genome-wide association data
    • Insuk Lee,
    • U. Martin Blom,
    • Peggy I. Wang,
    • Jung Eun Shim,
    • and Edward M. Marcotte
    Genome Res. July 2011 21: 1109-1121; Published in Advance May 2, 2011, doi:10.1101/gr.118992.110
    ...disease. Results HumanNet: an extended functional gene network for H. sapiens To test the ability of functional networks to improve gene association studies, we first constructed a -scale functional network for human genes. Diverse distinct lines of evidence, spanning human mRNA coexpression, protein...
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