Domain annotation with graph-based regularization (GBR)

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. 2015. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression. Genome Research.

Libbrecht MW, Hoffman MM, Bilmes JA, Noble WS. 2015. Entropic graph-based posterior regularization. Proceedings of the International Conference on Machine Learning (IMCL) 2015. (Extended version) .

Domain annotations

View and download the domain annotations in the UCSC Genome Browser. Annotations are also available in bed format. Consistent domain boundary calls are available bed format. These data sets are also available from the ENCODE DCC. All coordinates are relative to hg19.

Source code

• Code for Segway with graph-based regularization
• Code for graph-based regularization in Matlab. Uses the UGM Matlab graphical models package, which is included this tarball. Requires Measure Propagation.

Support

If you have questions about the domain annotations or running Segway with GBR please write to the segway-users mailing list.