Searching journal content for articles similar to Balwierz et al. 24 (5): 869.

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  1. Method: Integrated analysis of motif activity and gene expression changes of transcription factors
    • Jesper Grud Skat Madsen,
    • Alexander Rauch,
    • Elvira Laila Van Hauwaert,
    • Søren Fisker Schmidt,
    • Marc Winnefeld,
    • and Susanne Mandrup
    Genome Res. February 2018 28: 243-255; Published in Advance December 12, 2017, doi:10.1101/gr.227231.117
    ...the analysis toward transcription factors whose activity is regulated primarily by the expression level.Recently, a new method, ‘Motif Activity Response Analysis’ (MARA), for prediction of transcription factors involved in gene regulation has been developed. The core function of MARA is to model...
  2. Research: Enhancer RNA profiling predicts transcription factor activity
    • Joseph G. Azofeifa,
    • Mary A. Allen,
    • Josephina R. Hendrix,
    • Timothy Read,
    • Jonathan D. Rubin,
    • and Robin D. Dowell
    Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
    .... Nature 507: 455–461. ↵Azofeifa JG, Dowell RD. 2017. A generative model for the behavior of RNA polymerase. Bioinformatics 33: 227–234. ↵Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. 2014. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome...
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  3. Research: Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs
    • Jake Yeung,
    • Jérôme Mermet,
    • Céline Jouffe,
    • Julien Marquis,
    • Aline Charpagne,
    • Frédéric Gachon,
    • and Felix Naef
    Genome Res. February 2018 28: 182-191; Published in Advance December 18, 2017, doi:10.1101/gr.222430.117
    ..., Zavolan M, van Nimwegen E. 2014. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 24: 869–884. ↵Bass J, Lazar MA. 2016. Circadian time signatures of fitness and disease. Science 354: 994–999. ↵Bhargava A, Herzel H, Ananthasubramaniam B. 2015. Mining for novel...
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  4. Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
    • Yiming Kang,
    • Nikhil R. Patel,
    • Christian Shively,
    • Pamela Samantha Recio,
    • Xuhua Chen,
    • Bernd J. Wranik,
    • Griffin Kim,
    • R. Scott McIsaac,
    • Robi Mitra,
    • and Michael R. Brent
    Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
    ...-binding proteins known as transcription factors (TFs). Signaling cascades often change the activity levels of specific TFs—the extent to which they exert their regulatory potential on their target genes—via mechanisms that affect TFs’ abundance, localization, noncovalent interactions, or covalent modifications...
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