Mendieta-Esteban, et al 2021 Dataset

Code and data (~2.6Gb) are available for modeling genomes based on sparse datasets.

"3D reconstruction of genomic regions from sparse interaction data".
by Mendieta-Esteban, Di Stefano, Castillo, Farabella and Marti-Renom. Submitted. (2021)

Farabella, et al 2020 Dataset

Code and data (~100Mb) are available for the reproducing one of the simulations.

"Three-dimensional genome organization via triplex forming RNAs".
by Farabella, Di Stefano Soler-Vila, Marti-Marimon and Marti-Renom. Submitted. (2020)

Di Stefano, et al 2020 Dataset

Videos (~700Mb) are available for the 21 dynamic simulations with TADdyn.
Download the code/data (~7.5Gb) to reproduce the SOX2 simulation and all figures in the manuscript:

"Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs".
by Di Stefano, Stadhouders, Farabella, Castillo, Serra, Graf, and Marti-Renom. Nature Communications. (2021)
doi: 10.1038/s41467-020-16396-1

Nir, Farabella, Perez-Estrada and Ebeling et al 2018 Dataset

Download a ZIP file (68Mb) that contains the OligoSTORM density maps and the IMGR models described in the article:

"Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling".
by Nir, Farabella, Pérez-Estrada, Ebeling, Beliveau, Sasaki, Lee, Nguyen, McCole, Chattoraj, Erceg, AlHaj-Abed, Martins,
Nguyen, Hannan, Russell, Durand, Rao, Kishi, Soler-Vila, Di Pierro, Onuchic, Callahan, Schreiner, Stuckey, Yin, Lieberman-Aiden,
Marti-Renom, and Wu. (2018) PLOS Genetics. 14(12):e1007872 10.1371/journal.pgen.1007872

For additional information refer to the README in the Zip file.

Serra et al 2015 Dataset

Browse the 50 modeled regions of the fly genome described in the article:

"Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors".
by François Serra, Davide Baù, et al (2017) PLOS Computational Biology 13(7) e1005665. 10.1371/journal.pcbi.1005665

Trussart et al 2015 Dataset

Download a ZIP file (67Mb) that contains all the data described in the article:

"Assessing the limits of restraint-based 3D modeling of genomes and genomic domains".
by Marie Trussart, Francois Serra, Davide Baù, Ivan Junier, Luis Serrano and Marc A. Marti-Renom. NAR. (2015) doi: 10.1093/nar/gkv221

For additional information refer to the article or the README in the Zip file.