Marc A. Martı́-Renom

The paper investigates the role of CTCF and cohesin in X-inactivation escapee domains and finds that these domains are self-sustaining chromatin compartments independent of CTCF and cohesin.

The paper shows HIRA regulates early replication initiation zones independently of chromatin accessibility, histone marks, and 3D compartment organisation.

This study shows that STAG2 cohesin works with DREAM to maintain quiescence and prevent tumor formation in urothelial cells by regulating chromatin structure and cell cycle control.

This study shows that HIRA-dependent histone H3.3 deposition maintains 3D genome compartmentalisation in active chromatin, independent of histone PTMs.

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

This study shows BMAL1 represses transposable elements in pluripotent cells independently of CLOCK, leading to genome-wide changes and totipotency features when BMAL1 is deleted.

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.

The paper investigates how H1 depletion affects gene expression, H1 variant distribution, and genome 3D conformation in breast cancer cells.

The paper introduces LOOPbit, a method to detect chromatin loops from Hi-C data by classifying CTCF-CTCF interactions, achieving higher enhancer-promoter loop detection than existing tools.

The paper uses a multi-layered approach combining GWAS, spatial autocorrelation, and Hi-C to identify novel genetic variants associated with pancreatic cancer susceptibility.

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.

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.

TADpole identifies hierarchical chromatin domains in Hi-C data, revealing significant structural differences between wild-type and mutant mouse strains.

The paper maps transcriptionally active transposable elements in human adult tissues, identifying thousands of tissue-specific and phenotype-associated TEs.

The paper links diabetes-associated enhancers with their target genes using 3D chromatin architecture in human pancreatic islets, revealing genetic variants that impact insulin secretion heritability.

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 uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

The paper predicts the first eigenvector of the Hi-C matrix from whole genome bisulfite sequencing data, showing that methylation variability better predicts chromatin compartments than methylation levels.

This study investigates the distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization in non-transformed human cells, showing SA1 stabilizes TAD boundaries while SA2 facilitates enhancer-promoter interactions.

OneD improves Hi-C reproducibility for samples with abnormal karyotypes by addressing copy number variations, outperforming existing methods while maintaining performance on normal karyotypes.

The paper shows transcription factors drive genome topology changes before gene expression during cell reprogramming.

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

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.

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

The paper introduces TADbit, a computational framework for 3D chromatin modeling, and applies it to fly genomic domains to reveal structural differences linked to chromatin colors.

The paper examines how hormone-induced changes in gene regulation are coordinated by structural transitions of chromatin topological domains in breast cancer cells.