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Showing 1–10 of 10 results
Advanced filters: Author: Guillaume J. Filion Clear advanced filters

  • Authors report a codon language representation and a model, CodonTransformer, open access and with a user-friendly interface. CodonTransformer generates species-specific DNA sequences with natural-like profiles and with minimum negative regulatory elements.

    • Adibvafa Fallahpour
    • Vincent Gureghian
    • Amir Pandi
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12

  • Both A/B compartments and TADs are thought to be absent from the inactive X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, the authors characterise gene reactivation, chromatin opening and chromosome topology during X-reactivation, observe A/B-like compartments on the inactive X that guide TAD formation independently of transcription during X-reactivation.

    • Moritz Bauer
    • Enrique Vidal
    • Bernhard Payer
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-21

  • HIV-1 usually targets active genes and integrates near the nuclear pore compartment. Here the authors show that recurrently targeted genes are proximal to super-enhancer genomic elements, which cluster in specific spatial compartments of the T cell nucleus, suggesting a role for nuclear organisation in viral infection.

    • Bojana Lucic
    • Heng-Chang Chen
    • Marina Lusic
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-12

  • How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.

    • Ruggero Cortini
    • Guillaume J. Filion
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-10

  • Barcoded HIV ensembles (B-HIVE) provides a new approach to map HIV integration sites and to determine how genomic context influences proviral transcription activity and response to latency-reversing agents.

    • Heng-Chang Chen
    • Javier P Martinez
    • Guillaume J Filion
    Research
    Nature Structural & Molecular Biology
    Volume: 24, P: 47-54

  • The authors analyze time-resolved changes in genome topology, gene expression, transcription-factor binding, and chromatin state during iPSC generation. They conclude that 3D genome reorganization generally precedes gene expression changes and that removal of locus-specific topological barriers explains why pluripotency genes are activated sequentially during reprogramming.

    • Ralph Stadhouders
    • Enrique Vidal
    • Thomas Graf
    Research
    Nature Genetics
    Volume: 50, P: 238-249

  • Arc-shaped scours, sandwaves and channels on the Hudson Bay seafloor suggest that the catastrophic drainage of lake Agassiz–Ojibway occurred as a subglacial flood beneath the Laurentide Ice Sheet, which covered northern North America.

    • Patrick Lajeunesse
    • Guillaume St-Onge
    Research
    Nature Geoscience
    Volume: 1, P: 184-188

  • Three-dimensional genome architecture has important roles in the regulation of gene expression and is therefore a key determinant of cell identity in normal development and in disease states.

    • Ralph Stadhouders
    • Guillaume J. Filion
    • Thomas Graf
    Reviews
    Nature
    Volume: 569, P: 345-354