Geoffrey Fudenberg

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus

  Nucleic Acids Research · 2026-06-08

• Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

  Molecular Cell · 2026-04-23 · 2 citations

• A PyTorch implementation of the AkitaV2 deep learning model for predicting contact matrices from DNA sequences.

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

• A PyTorch implementation of the AkitaV2 deep learning model for predicting contact matrices from DNA sequences.

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

• Antibody background in ChIP-seq skews estimates of cohesin positioning by CTCF barriers

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-27

• The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-22 · 3 citations

• The physical chemistry of interphase loop extrusion

  Cell Genomics · 2025-12-10 · 4 citations

• Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

  Science · 2025-11-27 · 16 citations

• Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruptionPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-15 · 15 citations

• Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

  Genome Research · 2025-07-08 · 6 citations

• Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomicsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-10 · 1 citations

• Relating DNA sequence, organization, and function

  Science · 2025-02-06

• Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

  PLoS Computational Biology · 2025-02-04 · 7 citations

• Recipes and ingredients for deep learning models of 3D genome folding

  Current Opinion in Genetics & Development · 2025-01-24 · 8 citations

• Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancyPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-12 · 4 citations

• Synergy between <i>cis</i> -regulatory elements can render cohesin dispensable for distal enhancer functionPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-04 · 28 citations

• The physical chemistry of interphase loop extrusionPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-24 · 6 citations

• Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2Preprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-04 · 1 citations