ArticleNature communications2025
IceQream: Quantitative chromosome accessibility analysis using physical TF models.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed.
- Neural stem cell epigenomes and fate bias are temporally coordinated during mouse cortical development.Genes & development · 2026Article
- IceQream: Quantitative chromosome accessibility analysis using physical TF models.Nature communications · 2025Article
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Authors and funding
7 authors.
Funding
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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 human and mouse data shows that IQ derives similar, and in some cases, better performance compared to state-of-the-art deep neural network models. IQ provides an essential mechanistic and explicable baseline for further developments toward understanding gene and genome regulation from sequence.
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