Jonathan Cairns

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

This study examines how 3D chromatin organization in mouse liver changes throughout the circadian cycle, revealing dynamic domain assignments and promoter-specific chromatin contacts.

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data

Chicdiff detects differential chromosomal interactions in Capture Hi-C data by improving normalization and statistical methods, identifying cell type-specific interactions in human Monocytes and CD4+ T cells.

DNA methylation oscillation defines classes of enhancers

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates

The paper introduces Proximity RNA-seq to study nuclear transcriptome organization, revealing bipartite compartments with distinct RNA density and transcription elongation rates.

Chromosome contacts in activated T cells identify autoimmune disease candidate genes

The paper identifies autoimmune disease candidate genes by integrating promoter capture Hi-C data with genetic associations in activated CD4+ T cells.

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

CHiCAGO detects DNA looping interactions in Capture Hi-C data by addressing statistical challenges with a background model and normalization algorithms, showing enrichment for regulatory features and disease SNPs.