Spatial reconstruction from contact networks: A unified approach for dynamics and genomics - Archive ouverte HAL Accéder directement au contenu
Communication Dans Un Congrès Année : 2024

Spatial reconstruction from contact networks: A unified approach for dynamics and genomics

Résumé

The physical proximity of genomic sites to each other, within the 3D structure of a chromosome, can be experimentally measured in living cells and represented in the form of a matrix, called a contact map. These maps are very similar to recurrence plots of dynamical systems. Consequently, the same methods can be used for reconstructing the underlying spatial structure, either the chromosome 3D spatial structure or the attractor in the phase space. These methods involve two steps: (1) de- riving a complete distance matrix of the structure using graph distances on a contact network associated with the contact map; (2) reconstructing the structure from this distance matrix, using well-established methods from distance geometry or multidimensional scaling. We here review the different options for implementing the first step, according to the binary, graded or weighted nature of the contact map. We illustrate on three benchmarks (Lorenz model, white noise and EEG data) a novel spectral criterion reflecting the spatial dimension relevant in the second step.
Fichier principal
Vignette du fichier
Lesne_proceedings_Tsukuba_revised2.pdf (850.23 Ko) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)

Dates et versions

hal-04636019 , version 1 (08-07-2024)

Identifiants

  • HAL Id : hal-04636019 , version 1

Citer

Annick Lesne, Julien Mozziconnacci, Sofiane Ramdani. Spatial reconstruction from contact networks: A unified approach for dynamics and genomics. 10th International Symposium on Recurrence Plots, Aug 2023, Tsukuba, Japan. ⟨hal-04636019⟩
18 Consultations
12 Téléchargements

Partager

Gmail Mastodon Facebook X LinkedIn More