Searching journal content for articles similar to Bulyk et al. 14 (2): 201.

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  1. Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
    • Jordan John,
    • Javaid Jabbar,
    • Nitika Badjatia,
    • Matthew J. Rossi,
    • William K.M. Lai,
    • and B. Franklin Pugh
    Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
    ...are enriched with YR nucleotides (IUPAC nomenclature), this determination was based on only 88 promoters (Hawley and McClure 1983). Genome-wide studies based on mapping RNA 5′ ends have found the YR motif to be enriched, with 79% of the +1 nucleotide being an R (Kim et al. 2012), whereas another study had R...
  2. Methods: Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
    • Jason Gertz,
    • Linda Riles,
    • Peter Turnbaugh,
    • Su-Wen Ho,
    • and Barak A. Cohen
    Genome Res. August 2005 15: 1145-1152; doi:10.1101/gr.3859605
    .... Sci. 45 : 18 –29. ↵ Sudarsanam, P., Pilpel, Y., and Church, G.M. 2002 . Genome-wide co-occurrence of promoter elements reveals a cis -regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 12 : 1723 –1731. ↵ Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R...
  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...sequence is functional, the reporter gene is expressed/induced and the cellular concentration of the gene product is measured (Smale 2010).TF binding predictionTFs bind DNA in a sequence-specific manner based on motifs, with each binding site having a consensus sequence that indicates prerequisites...
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  4. Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
    • Øystein Monsen,
    • Lars Grønvold,
    • Alex Datsomor,
    • Thomas Harvey,
    • James Kijas,
    • Alexander Suh,
    • Torgeir R. Hvidsten,
    • and Simen Rød Sandve
    Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
    ...) Correlation between TF tissue specificity and the proportion of wide TF motif matches located in TEs. Each point represents a TF motif. Tissue specificity is based on differential TF binding score from TOBIAS (Bentsen et al. 2020), which essentially summarizes the relative ATAC-seq footprint signal across all...
  5. Research: Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
    • Phuc-Loi Luu,
    • Hans R. Schöler,
    • and Marcos J. Araúzo-Bravo
    Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
    ...to recruit the ‘‘methylation/ unmethylation machinery’’ to specific loci. The TFs are highpotential recruiting candidates because of their DNA sequence recognition capability. To compare CpGMMs and TFBMs, we designed a technique based on detecting co-occurrences between the targets of the two types of motifs...
  6. ARTICLE: Extensive low-affinity transcriptional interactions in the yeast genome
    • Amos Tanay
    Genome Res. August 2006 16: 962-972; Published in Advance June 29, 2006, doi:10.1101/gr.5113606
    ...of the co-occurrence of GATA boxes and UISALL in DAL promoters and that Dal82 binding preferences may be modeled more accurately using the motif reported here. PREGO is therefore shown to be effective in controlling for co-occurrence artifacts that can bias the results of standard motif finders. Frequently...
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