Geometric diagrams of genomes: constructing a visual grammar for 3D genomics

Molins-Pitarch, Carla; Khao, Jonathan; Bonet, Santiago; Justicia, Yolanda; Altube, Clementina; Goodstadt, Mike N.; Ribot, Francesc; Lieberman Aiden, Erez; Neretti, Nicola; McGill, Gaël G.; Marti-Renom, Marc A.

doi:http://dx.doi.org/10.1186/s13059-025-03646-y

Geometric diagrams of genomes: constructing a visual grammar for 3D genomics

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Molins-Pitarch C, Khao J, Bonet S, Justicia Y, Altube C, Goodstadt M, et al. Geometric diagrams of genomes: constructing a visual grammar for 3D genomics. Genome Biol. 2025 Jun 26;26(1):181. DOI: 10.1186/s13059-025-03646-y

Abstract

Advances in the field of three-dimensional (3D) genomics have revealed an ever-expanding array of architectural features that were unknown only a few years ago. Just as ribbon diagrams integrate spatial and symbolic representation to communicate the shape of a protein, the representation of genomes in 3D space requires the development and use of new cartographic symbols and visual conventions. Here, we propose a conceptualized grammar that makes it easier to create visual 3D representations of genomes.