Publications
This manually curated list highlights research and software connected to genome architecture modeling.
Oliveira Junior A. B.; Mello M. F.; Oliveira R. J.; Dodero-Rojas E.; Brahmachari S.; Contessoto V. G.; Onuchic J. N.
Proceedings of the National Academy of Sciences
A full-inversion chromatin model for Hi-C-informed genome organization and chromatin dynamics.
Read publicationContessoto V. G.; Oliveira Junior A. B.; Brahmachari S.; Wolynes P. G.; Di Pierro M.; Onuchic J. N.
Proceedings of the National Academy of Sciences
Maximum entropy energy landscapes for chromosome organization across the cell cycle.
Read publicationDodero-Rojas E.; Mendieta A.; Fehlis Y.; Mayala N.; Contessoto V. G.; Onuchic J. N.
PLOS Computational Biology
Transformer-based prediction of chromatin structural annotations from epigenomic data.
Read publicationSandoval-Velasco M.; Dudchenko O.; Rodríguez J. A.; Pérez Estrada C.; Dehasque M.; Fontsere C.; Mak S. S. T.; Khan R.; Contessoto V. G.; Oliveira Junior A. B.; et al.
Cell
3D genome modeling contribution for ancient chromosome architecture.
Read publicationContessoto V. G.; Dudchenko O.; Aiden E. L.; Wolynes P. G.; Onuchic J. N.; Di Pierro M.
Nature Communications
Data-driven physical simulations of the Aedes aegypti genome.
Read publicationOliveira Junior A. B.; Contessoto V. G.; Mello M. F.; Onuchic J. N.
Journal of Molecular Biology
GPU-accelerated chromosome simulations built on OpenMM.
Read publicationContessoto V. G.; Cheng R. R.; Hajitaheri A.; Dodero-Rojas E.; Mello M. F.; Aiden E. L.; Wolynes P. G.; Di Pierro M.; Onuchic J. N.
Nucleic Acids Research
A web resource for 3D genome simulation, analysis, visualization, and sharing.
Read publicationHoencamp C.; Dudchenko O.; Elbatsh A. M. O.; Brahmachari S.; Raaijmakers J. A.; van Schaik T.; Sedeño Cacciatore A.; Contessoto V. G.; et al.
Science
Comparative 3D genomics across species with physical modeling of architecture type.
Read publication