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  1. Method: P-value-based regulatory motif discovery using positional weight matrices
    • Holger Hartmann,
    • Eckhart W. Guthöhrlein,
    • Matthias Siebert,
    • Sebastian Luehr,
    • and Johannes Söding
    Genome Res. January 2013 23: 181-194; Published in Advance September 18, 2012, doi:10.1101/gr.139881.112
    ...sets for transcription factors from human, mouse, worm, and fly, as well as 10 target sets for microRNAs from human, and mouse from the metazoan target set compendium (Linhart et al. 2008). The plot is adapted from Linhart et al. (2008): The ‘‘Source’’ column indicates the experimental procedure...
  2. Method: Heterogeneity of transcription factor binding specificity models within and across cell lines
    • Mahfuza Sharmin,
    • Héctor Corrada Bravo,
    • and Sridhar Hannenhalli
    Genome Res. August 2016 26: 1110-1123; Published in Advance June 16, 2016, doi:10.1101/gr.199166.115
    ...type, many of which nevertheless transcend cell types. Notably, the putative targets of shared binding rules in different cell types, while distinct, exhibit significant functional coherence. [Supplemental material is available for this article.] Transcriptional regulation is mediated by the binding...
  3. Research: A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans
    • Chaim Linhart,
    • Yonit Halperin,
    • Amir Darom,
    • Shahar Kidron,
    • Limor Broday,
    • and Ron Shamir
    Genome Res. January 2012 22: 76-83; Published in Advance September 19, 2011, doi:10.1101/gr.115626.110
    ...and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Res 18: 1180–1189. Macdonald LD, Knox A, Hansen D. 2008. Proteasomal regulation of the proliferation vs. meiotic entry decision in the Caenorhabditis elegans germ line. Genetics 180: 905–920. Makeev VJ...
  4. Resource: A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
    • Christopher L. Plaisier,
    • Min Pan,
    • and Nitin S. Baliga
    Genome Res. November 2012 22: 2302-2314; Published in Advance June 28, 2012, doi:10.1101/gr.133991.111
    ...biomarkers. [Supplemental material is available for this article.] MicroRNAs (miRNAs) mediate degradation (Baek et al. 2008) or translational repression (Selbach et al. 2008) of gene transcripts associated with an array of biological processes including many of the hallmarks of cancer (Hanahan and Weinberg...
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  5. Resource: Extensive alternative polyadenylation during zebrafish development
    • Igor Ulitsky,
    • Alena Shkumatava,
    • Calvin H. Jan,
    • Alexander O. Subtelny,
    • David Koppstein,
    • George W. Bell,
    • Hazel Sive,
    • and David P. Bartel
    Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
    ..., such as targeting by microRNAs (miRNAs), has been hindered by incomplete 39UTR annotation. In version 66 of Ensembl zebrafish genes (Feb. 2012), only 64.4% of the transcriptmodels have any 39UTR annotation, and only 28.9% of the genes havemore than one annotated 39 end. By comparison, over 96% of the human genes...
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