Soffritto: a deep learning model for predicting high-resolution replication timing.

ABSTRACT:

Motivation

Replication timing (RT) refers to the order in which DNA loci are replicated during S phase. RT is cell-type specific and implicated in cellular processes including transcription, differentiation, and disease. RT is typically quantified genome-wide using two-fraction assays (e.g. Repli-Seq) which sort cells into early and late S phase fractions followed by DNA sequencing, yielding a ratio as the RT signal. While two-fraction RT data are widely available in multiple cell lines, it is limited in its ability to capture high-resolution RT features. To address this, high-resolution Repli-Seq, which quantifies RT across 16 fractions, was developed, but it is costly and technically challenging with very limited data generated to date.

Results

Here, we developed Soffritto

SUBMITTER: Bolzan D 

PROVIDER: S-EPMC12261407 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature