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Peer-Reviewed Publication
bioRxiv2026February 3, 2026Journal Article

HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.

Sion Kim1,2, Joseph T Jackson1, Henry B Zhang3, Minji Kim1,2
1Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
2Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
3AthenaHealth, Boston, MA 02135, USA.
PubMed PMC DOI PDF

Abstract

3D genome mapping technologies ChIA-PET, HiChIP, PLAC-seq, HiCAR, and ChIATAC yield pairwise contacts and a one-dimensional signal indicating protein binding or chromatin accessibility. However, a lack of computational tools to quantify the reproducibility of these enrichment-based 3C data prevents rigorous data quality assessment and interpretation. We developed HiChIA-Rep, an algorithm incorpora…

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