Farré P, Heurteau A, Cuvier O, Emberly E. Dense neural networks for predicting chromatin conformation. BMC Bioinformatics. 2018;19:372 pubmed publisher
..Our analysis shows that the networks have learned physical insights that are informative and intuitive about this complex polymer problem. ..
Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, Hart C, et al. BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites. PLoS Biol. 2008;6:2896-910 pubmed publisher
..Our results reveal a novel role for BEAF chromatin dual-cores in regulating a distinct set of genes involved in chromosome organization/segregation and the cell cycle. ..
..PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin. ..