Chrom3D: a user-friendly whole-genome 3D computational modeling framework

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts. Genome Biology. 2017. 18:21. Abstract Current 3-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 framework that simulates positions of topologically-associated domains (TADs) relative to…
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Our review on the 4D nucleome in single cells

Sekelja M, Paulsen J, Collas P. 2016. 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation? Genome Biol. 2016, 17:54. PMID:27052789 Abstract: 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 in single…
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Our paper on lamin A-chromatin interactions during adipogenic induction

Rønningen T., Shah A, Oldenburg AR, Vekterud K, Delbarre E, Moskaug JØ, Collas P. 2015. Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B. Genome Res 25(12):1825-35. PMID: 26359231 Abstract Dynamic interactions of nuclear lamins with chromatin through lamin-associated domains (LADs) contribute to spatial arrangement of the genome. Here, we provide evidence…
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