Now showing items 1-4 of 4

  • Sekelja, Monika; Paulsen, Jonas; Collas, Philippe (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2016)
    Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensional genome ...
  • Paulsen, Jonas; Sekelja, Monika; Oldenburg, Anja R; Barateau, Alice; Briand, Nolwenn; Delbarre, Erwan; Shah, Akshay; Sørensen, Anita L; Vigouroux, Corinne; Buendia, Brigitte; Collas, Philippe (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling ...
  • Rossini, Roberto; Kumar, Vipin; Mathelier, Anthony; Rognes, Torbjørn; Paulsen, Jonas (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of ...
  • Liyakat Ali, Tharvesh M.; Brunet, Annaël; Collas, Philippe; Paulsen, Jonas (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    Background Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop ...