Searching journal content for articles similar to Barker et al. 32 (4): 750.

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  1. Method: Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
    • Seyed Ali Madani Tonekaboni,
    • Parisa Mazrooei,
    • Victor Kofia,
    • Benjamin Haibe-Kains,
    • and Mathieu Lupien
    Genome Res. October 2019 29: 1733-1743; Published in Advance September 18, 2019, doi:10.1101/gr.248658.119
    ...lines (Jaccard index <0.5) (Fig. 5A). Moreover, the pathway enrichment analysis based on genes within 10 kb of COREs or super-enhancers shows higher enrichment of phenotypic-specific pathways for COREs. For instance, enrichment for the B CELL RECEPTOR SIGNALING PATHWAY term is 2.6-fold more significant...
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  2. Method: A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model
    • Laetitia Davidovic,
    • Vincent Navratil,
    • Carmela M. Bonaccorso,
    • Maria Vincenza Catania,
    • Barbara Bardoni,
    • and Marc-Emmanuel Dumas
    Genome Res. December 2011 21: 2190-2202; Published in Advance September 7, 2011, doi:10.1101/gr.116764.110
    ...us to get new insight into FXS pathophysiology and to identify key FMRPmRNA targets involved in regulating its metabolic phenotype, as discussed in detail below. Comprehensive metabolic profiling of the brain of the mouse model of FXS: Identification of Fmr1-deficiency metabolic phenotypes specific...
  3. Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
    • Matthew D. Pollard,
    • Wynn K. Meyer,
    • and Emily E. Puckett
    Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
    ...and change in carnivory score. Many of these pathways take place in the kidneys. The results of our phenotype-specific enrichment analysis also support a diminished role for small molecule transportation in the kidneys of lineages with increasingly herbivorous diets. Of the five MGI phenotype gene sets...
  4. Method: A general calculus of fitness landscapes finds genes under selection in cancers
    • Teng-Kuei Hsu,
    • Jennifer Asmussen,
    • Amanda Koire,
    • Byung-Kwon Choi,
    • Mayur A. Gadhikar,
    • Eunna Huh,
    • Chih-Hsu Lin,
    • Daniel M. Konecki,
    • Young Won Kim,
    • Curtis R. Pickering,
    • Marek Kimmel,
    • Lawrence A. Donehower,
    • Mitchell J. Frederick,
    • Jeffrey N. Myers,
    • Panagiotis Katsonis,
    • and Olivier Lichtarge
    Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
    ...Research Network et al. 2013; Tomczak et al. 2015; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) yields a rich data set for discovering new cancer genes. Here, we used CI to prioritize the collective fitness impact of variants across all genes and all patients in a cohort in order...
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  5. Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
    • Annelien Verfaillie,
    • Dmitry Svetlichnyy,
    • Hana Imrichova,
    • Kristofer Davie,
    • Mark Fiers,
    • Zeynep Kalender Atak,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • and Stein Aerts
    Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
    ...factors. [Supplemental material is available for this article.] Enhancers are essential regulatory elements that are bound by transcription factors (TFs) to shape the gene expression network underlying a cellular phenotype. Understanding the enhancer code is crucial to achieve a functional regulatory...
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