Chromatin-state discovery and genome annotation with ChromHMM

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CADD: predicting the deleteriousness of variants throughout the human genome (2018, methodology): “chromHMM (15): uses chromHMM 25 state model, ENCODE/Roadmap cell types only”
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal (2019, methodology): “The DCC will host and provide access to updated genome annotations generated by algorithms such as chromHMM (36) and Segway (37) The ENCODE DCC also supports users directly through the ENCODE help desk at encode-help@lists.stanford.edu. using the rich and diverse data submitted to the ENCODE portal.”
CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions (2024, methodology): “The ENCODE project and others initiated data portals with versioned and uniform data processing pipelines as well as explored imputation of molecular assays resulting from such data ( 3 ,82 ).”