ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed. The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.

{"references": ["Tan, Wuwei, and Yang Shen. \"Multimodal learning of noncoding variant effects using genome sequence and chromatin structure.\" bioRxiv (2022): 2022-12."]}