Open Access Publications from the University of California

## Efficient Algorithms for the Analysis of Hi-C Contact Maps

• Author(s): Roayaei Ardakany, Abbas
The research presented here is articulated around three main topics on the analysis of contact maps, namely (1) the detection of TADs, (2) how to compare two maps, and (3) how to detect chromatin loops. The detection of TADs has become a critical step in the analysis of Hi-C data, e.g., to identify enhancer-promoter associations. First, we present \textsc{East}, a novel TAD identification algorithm based on fast 2D convolution of Haar-like features, that is as accurate as the state-of-the-art method based on the directionality index, but 75-80$\times$ faster.