TY  - JOUR
A1  - Chen, Siyuan
A1  - Wang, Jiuming
A1  - Jung, Inkyung
A1  - Qiu, Zhaowen
A1  - Gao, Xin
A1  - Li, Yu
T1  - A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
Y1  - 2024/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1174 
EP  - 1184 
DO  - 10.1101/gr.279274.124 
VL  - 34 
IS  - 8 
UR  - http://genome.cshlp.org/content/34/8/1174.abstract 
N2  - Chromatin loop identification plays an important role in molecular biology and 3D genomics research, as it constitutes a fundamental process in transcription and gene regulation. Such precise chromatin structures can be identified across genome-wide interaction matrices via Hi-C data analysis, which is essential for unraveling the intricacies of transcriptional regulation. Given the increasing number of genome-wide contact maps, derived from both in situ Hi-C and single-cell Hi-C experiments, there is a pressing need for efficient and resilient algorithms capable of processing data from diverse experiments rapidly and adaptively. Here, we propose YOLOOP, a novel detection-based framework that is different from the conventional paradigm. YOLOOP stands out for its speed, surpassing the performance of previous state-of-the-art (SOTA) chromatin loop detection methods. It achieves a 30-fold acceleration compared with classification-based methods, up to 20-fold acceleration compared with the SOTA kernel-based framework, and a fivefold acceleration compared with statistical algorithms. Furthermore, the proposed framework is capable of generalizing across various cell types, multiresolution Hi-C maps, and diverse experimental protocols. Compared with the existing paradigms, YOLOOP shows up to a 10% increase in recall and a 15% increase in F1-score, particularly noteworthy in the GM12878 cell line. YOLOOP also offers fast adaptability with straightforward fine-tuning, making it readily applicable to extremely sparse single-cell Hi-C contact maps. It maintains its exceptional speed, completing genome-wide detection at a 10 kb resolution for a single-cell contact map within 1 min and for a 900-cell-superimposed contact map within 3 min, enabling fast analysis of large-scale single-cell data. 
ER  -