Geoffrey Fudenberg

The paper shows how changes in sister chromatid folding over time encode mechanisms of cohesion maintenance, revealing how transient cofactor interactions regulate long-lived cohesin protection.

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

The paper develops a framework to correct cohesin positioning measurements in ChIP-seq by accounting for antibody background, revealing its impact on cohesin positioning estimates.

This paper identifies Ab-trapping as a staining artifact in antibody-based techniques, showing it results from high epitope abundance, high Ab affinity, and low diffusion rates, and suggests mitigation strategies.

The paper introduces CLASH, a method to quantify how genetic variation, methylation, and CTCF occupancy affect chromatin loop strength across individuals.

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

The paper develops a machine-learning model to predict how structural variants disrupt 3D chromatin structure in congenital heart disease and validates its predictions using induced pluripotent stem cells.

This study shows that cohesin loading at enhancers does not significantly contribute to genome folding or long-range transcriptional control, as inhibiting cohesin recruitment near enhancers reduces target promoter transcription.

The paper develops a minimal model of cohesin loop extrusion based on biochemical and biophysical data, showing how regulatory protein dynamics influence genome folding.

This paper introduces dLEM, a differentiable loop extrusion model that predicts genome folding mechanisms from contact maps and integrates with deep learning to infer extrusion parameters from genomic features.

The paper shows that the extrusion rate of cohesin is tunable by cofactor dosage and buffers chromosome structure against genetic disruption.

The paper develops a dynamic barrier model to explain genome folding features using biophysically measured CTCF and cohesin dynamics, showing that barrier bound times influence ChIP-seq, Hi-C, and chromosome morphology.

The paper uses AkitaV2 to analyze CTCF-binding site sequences and predict their role in genome folding, identifying key sequence determinants and grammatical rules for insulation strength and pattern formation.

This study shows that cohesin is not always necessary for enhancer function, as some enhancers can act independently through synergy or insulators.

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Bioframe provides a Python library for efficient genomic interval operations using pandas dataframes, extending the data science stack for computational genomics.

The paper identifies VNTR motifs linked to gene expression using a repeat-pangenome graph, showing motif variation explains more associations than VNTR length.

The paper investigates how meiotic chromatin organization influences recombination activity by analyzing 3D chromosomal structure and recombination rates at PRDM9 hotspots.

The paper investigates how CTCF binding polarity influences chromatin loop formation by showing that CTCF positions cohesin but does not control its binding dynamics.

This paper introduces a deep learning model that predicts 3D genome folding from DNA sequence and highlights the role of CTCF in genome structure.

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

The paper uses haplotype-resolved Hi-C to reveal structured homolog pairing and its global impact on gene activity in hybrid Drosophila cells.

This study investigates meiotic chromosome assembly in yeast, revealing cohesin-dependent Hi-C patterns and the role of convergent transcription in shaping chromosome organization.

The paper shows that chromatin features constrain structural variation in healthy humans and primates but not in developmental delay patients, suggesting enhancer hijacking in disease.

This paper investigates the mechanism of nuclear inversion in rod photoreceptors by combining Hi-C, microscopy, and polymer modeling, revealing that heterochromatin interactions drive phase separation and that lamina interactions maintain conventional nuclear organization.

This study shows that cohesin removal leads to loss of TADs and loops but preserves compartments, revealing two independent modes of chromosome organization.

This study investigates the roles of cohesin and condensin in mitotic chromosome organization in budding yeast using Hi-C and polymer modeling, revealing distinct functions for each complex.

This paper examines the differences between 3C and FISH in measuring chromosomal contacts and spatial distances, highlighting implications for integrating these methods.

The paper reviews polymer models and experimental evidence supporting loop extrusion as a mechanism for chromosome folding, focusing on CTCF and cohesin perturbations in interphase.