Evidence map›Paper›PMID 40571947›Full record

ArticleGenome biology2025

Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics.

Carla Molins-Pitarch, Jonathan Khao, Santiago Bonet, Yolanda Justicia, Clementina Altube, Mike Goodstadt, Francesc Ribot, Erez Lieberman Aiden, Nicola Neretti, Gaël G McGill and 1 more

Abstract read
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Carla Molins-PitarchImage Processing and Multimedia Technology Center, Universitat Politècnica de Catalunya-Barcelona Tech, 08222, Terrassa, Spain.
Jonathan KhaoDigizyme Inc, Brookline, MA, USA.
Santiago BonetElisava, Barcelona School of Design and Engineering (UVic-UCC), 08002, Barcelona, Spain.
Yolanda JusticiaElisava, Barcelona School of Design and Engineering (UVic-UCC), 08002, Barcelona, Spain.
Clementina AltubeElisava, Barcelona School of Design and Engineering (UVic-UCC), 08002, Barcelona, Spain.
Mike GoodstadtCentre Nacional d'Anàlisi Genòmica (CNAG), Baldiri I Reixac 4, 08028, Barcelona, Spain.
Francesc RibotElisava, Barcelona School of Design and Engineering (UVic-UCC), 08002, Barcelona, Spain.
Erez Lieberman AidenCenter for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Nicola NerettiDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
Gaël G McGillDigizyme Inc, Brookline, MA, USA.
Marc A Marti-RenomCentre Nacional d'Anàlisi Genòmica (CNAG), Baldiri I Reixac 4, 08028, Barcelona, Spain. martirenom@cnag.eu.

Funding

Center for Genome ImagingRM1HG011016 · NHGRI · HARVARD MEDICAL SCHOOL · PI WU, CHAO-TING · 2021 to 2025
$12.2M
Agencia Estatal de Investigación PID2020-115696RB-I00Agencia Estatal de Investigación,Spain PID2023-151484NB-I00European Commission 823327NHGRI NIH HHS RM1 HG011016NHGRI NIH HHS RM1HG011016
6 · The paper itself

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.

Indexed as

Computer GraphicsGenomeGenomicsImaging, Three-DimensionalHumans

Identifiers

PMID40571947
PMCPMC12203721

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.