IceQream: Quantitative chromosome accessibility analysis using physical TF models.

ABSTRACT: Single-cell mapping of chromosomal accessibility patterns has recently led to improved predictive modelling of epigenomic activity from sequence. However, quantitative models explaining the epigenome using directly interpretable components are still lacking. Here we develop IceQream (IQ), a modelling strategy and inference algorithm for regressing accessibility from sequences using physical models of transcription factor (TF) binding. IQ uses spatial integration of sequences over a range of TF-DNA affinities and localization relative to the target locus. It infers TF effective concentrations as latent variables that activate or repress regulatory elements in a non-linear fashion. These are supplemented with synergistic and antagonistic pairwise interactions between TFs. Analysis of both hu

SUBMITTER: Bercovich A 

PROVIDER: S-EPMC12511641 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature