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Geometric diagrams of genomes: constructing a visual grammar for 3D genomics Molins Pitarch, Carla Khao, Jonathan Bonet, Santiago Justicia, Yolanda Altube, Clementina Goodstadt, Mike Ribot Puntí, Francesc Aiden, Erez Lieberman Neretti, Nicola McGill, Gaël G. Martí Renom, Marc A. Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica Human genome Genomics Three-dimensional imaging Genòmica Genoma humà Imatgeria tridimensional Advances in the feld of three-dimensional (3D) genomics have revealed an everexpanding 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 devel- opment and use of new cartographic symbols and visual conventions. Here, we pro- pose a conceptualized grammar that makes it easier to create visual 3D representations of genomes. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Sklodowska-Curie grant agreement No 823327 to M.A.M-R. and F.R. M.A.M-R. also acknowledges support by the Spanish Ministerio de Ciencia e Innovación (PID2020-115696RB-I00 and PID2023-151484NB-I00). M.A.M-R., E.L.A., and N.N. acknowledge support by the National Human Genome Research Institute of the National Institutes of Health under Award Number RM1HG011016. The content is solely the responsibility of the authors and does not necessarily represent the ofcial views of the National Institutes of Health. Peer Reviewed Postprint (published version) 2025-06-26 Article https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03646-y http://creativecommons.org/licenses/by/4.0/ Open Access Attribution 4.0 International Springer