CUT&Tag

RPI-Zero: Zero-shot RNA-Protein Interaction Prediction

RPI-Zero predicts RNA-protein interactions without prior data by using a sequence-only model trained on a large benchmark of CLIP experiments.

FiberBrowser: a unified framework for single-molecule genomics

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

Myogenic and neural transcriptional circuitry determines PAX3::FOXO1 driven initiation of rhabdomyosarcoma

This study uses a PAX3::FOXO1 inducible model to show P3F initiates ARMS transformation but is not required for maintaining proliferation or transcriptional programs.

Deciphering Spatial Cellular Organization through RNA-Anchored Multi-Omics Deconvolution

SMODER deconvolves spatial multi-omics data by prioritizing RNA for cell-type identification and integrating other modalities, improving accuracy and spatial coherence.

KAS-CUT&Tag for direct mapping of transcription bubbles

N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.

Hyperosmotic stress induces rewiring of 3D chromatin interactions

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.