Djekidel, Mohamed NadhirChen, YangZhang, Michael Q.2019-05-032019-05-032018-02-121088-9051https://hdl.handle.net/10735.1/6457Includes supplementary materialPolymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio.enCC BY-NC 4.0 (Attribution-NonCommercial)©2018 The Authorshttp://creativecommons.org/licenses/by-nc/4.0/Human genomeBioconductor (Computer file)Gene expressionChromatinPoisson processesarticleDjekidel, Mohamed Nadhir, Yang Chen, and Michael Q. Zhang. 2018. "FIND: difFerential chromatin INteractions Detection using a spatial Poisson process." Genome Research 28(3): 412-422, doi:10.1101/gr.212241.116283