David Castillo

This study shows that 3D culture of breast cancer cells alters chromatin structure and gene expression, with LATS1 kinase playing a key role in CTCF displacement and hormonal response.

The paper introduces pTADbit, a machine learning method that improves 3D genome modeling using Hi-C data and microscopy distances, achieving higher accuracy and faster computation.

This paper introduces a method to reconstruct 3D chromatin organization from sparse 3C-based data, achieving reliable results with as little as 2-3% of the interaction matrix.

The paper introduces TADdyn, a tool that simulates chromatin structural rearrangements during cell reprogramming using time-course 3C data and molecular dynamics, revealing a hit-and-stick mechanism for transcriptional stabilization.

MuGVRE provides a cloud-based infrastructure for 3D/4D genomics analysis, supporting both high-computational and high-throughput applications.

The paper introduces a resolution-agnostic normalization method for Hi-C data that improves interaction and difference detection without requiring deeper sequencing.