Searching journal content for articles similar to Gibbons and Roth 12 (10): 1574.

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  1. Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
    • Wei-Jen Chung,
    • Phaedra Agius,
    • Jakub O. Westholm,
    • Michael Chen,
    • Katsutomo Okamura,
    • Nicolas Robine,
    • Christina S. Leslie,
    • and Eric C. Lai
    Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
    ...16th) and NM_071540/C04E12.10_in10 (ranked 20th). Although not adjacent, these genes have been retained within a 70-kb genomic interval (Fig. 7B). Their 3p miRNAs are identical, but these introns have diverged such that their 5p ‘‘star’’ regions are distinct. Evidence for independent expression based...
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  2. Method: Quantitative prediction of enhancer–promoter interactions
    • Polina S. Belokopytova,
    • Miroslav A. Nuriddinov,
    • Evgeniy A. Mozheiko,
    • Daniil Fishman,
    • and Veniamin Fishman
    Genome Res. January 2020 30: 72-84; Published in Advance December 2, 2019, doi:10.1101/gr.249367.119
    ...-wide analysis of their relations to Hi-C loops. However, individual reports of genetically validated functional EP interactions support our general conclusion. For example, a recent study (Fulco et al. 2016) identified seven distal enhancers of the MYC gene, which form two clusters located 0.16 and 1...
  3. Methods: Identification of rare cancer driver mutations by network reconstruction
    • Ali Torkamani and
    • Nicholas J. Schork
    Genome Res. September 2009 19: 1570-1578; Published in Advance July 2, 2009, doi:10.1101/gr.092833.109
    ...L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, et al. 2008. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455: 1069–1075. Gibbons FD, Roth FP. 2002. Judging the quality of gene expression-based clustering methods using...
  4. Methods: A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
    • The Ludwig–FAPESP Transcript Finishing Initiative,
    • Mari Cleide Sogayar,
    • and Anamaria A. Camargo
    Genome Res. July 2004 14: 1413-1423; Published in Advance June 14, 2004, doi:10.1101/gr.2111304
    ...the generation of novel human transcript sequences on a -wide basis. By using the genomic sequence as a scaffold for EST mapping and clustering, we have used RT-PCR to bridge gaps between EST clusters that we judged as likely to be derived from the same genes. The resulting novel sequence confirms that the ESTs...
  5. LETTER: Relating Whole-Genome Expression Data with Protein-Protein Interactions
    • Ronald Jansen,
    • Dov Greenbaum,
    • and Mark Gerstein
    Genome Res. January 1, 2002 12: 37-46; doi:10.1101/gr.205602
    ....mbb.yale.edu/expression/interactions .) Analysis of gene expression data is currently one of the most exciting areas in genomics. Computationally, it involves clustering and grouping individual expression measurements and interrelating them to other sources of information, such as phenotypes, functional classifications, or cellular responses...
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