4/4 Available as Python + R packages, scales to 100k+ regions. Code → github.com/DGStefano/T-...

#Bioinformatics #Epigenomics #Genomics

3/4 We tested it on macrophage activation, mouse liver development, and pediatric leukemia progression. Recovered known regulators, found new ones too, from just ATAC-seq or ChIP-seq.

2/4 The idea: CREs that share the same temporal accessibility patterns are likely co-regulated. T-ChroNet builds a network to detect those communities, then infers the upstream transcription factors and downstream pathways for each one.

T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset Abstract. Networks are widely applied to investigate relationships among individual components of complex biological systems. Recent application of biologi

1/4🧵 New paper out! We built T-ChroNet, a method to track how enhancers and regulatory elements change over time — and figure out who's driving them.
Read more → academic.oup.com/nargab/artic...